exceeds matrix dimensions when running denoise

[annapbarnes]

HI

When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs?

**Current indexing filetype: *rNEST*rsfMRI.nii

Index exceeds matrix dimensions.

Error in brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise>check_masks (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise (line 71) [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, denoise_infos.space_mask, nm_pos);

Error in brant_preprocess_jobman (line 164) end_prefix = brant_run_denoise(working_dir, run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, data_input.is4d, output_dirs, jobman.subj.out.nmpos);

Error in brant_preprocess>run_cb (line 343) brant_preprocess_jobman(jobman, gcf);

Error while evaluating UIControl Callback**

Anna

[YongLiuLab]

Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 3:06 AM To: YongLiuLab/brant brant@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

HI

When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs?

Anna

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/YongLiuLab/brant/issues/1 , or unsubscribe https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ . https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif

[annapbarnes]

Yes of course Error message, screenshot and log file attached

*Current indexing filetype: rNEST*rsfMRI.nii Index exceeds matrix dimensions.

Error in brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise>check_masks (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise (line 71) [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, denoise_infos.space_mask, nm_pos);

Error in brant_preprocess_jobman (line 164) end_prefix = brant_run_denoise(working_dir, run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, data_input.is4d, output_dirs, jobman.subj.out.nmpos);

Error in brant_preprocess>run_cb (line 343) brant_preprocess_jobman(jobman, gcf);

Error while evaluating UIControl Callback**

On 7 Aug 2020, at 01:34, Yong Liu notifications@github.com wrote:

Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 3:06 AM To: YongLiuLab/brant brant@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

HI

When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs?

Anna

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/YongLiuLab/brant/issues/1 , or unsubscribe https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ . https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif

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DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: rc1.nii ft_wm: rc2.nii ft_csf: rc3*.nii

mask_res_type: nearest neighbour ft_motion: rp*.txt

Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2

Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08

Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f

[YongLiuLab]

I think maybe you need to check

“rNESTrsfMRI.nii see how many time points, or how many nii files in the same directory

Then double-check the rp*.txt, how many time points.

I guess maybe you have so many nii files be read by the brant.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 4:27 PM To: YongLiuLab/brant brant@noreply.github.com Cc: Yong Liu yliu@nlpr.ia.ac.cn; Comment comment@noreply.github.com Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Yes of course Error message, screenshot and log file attached

*Current indexing filetype: rNEST*rsfMRI.nii Index exceeds matrix dimensions.

Error in brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise>check_masks (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise (line 71) [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, denoise_infos.space_mask, nm_pos);

Error in brant_preprocess_jobman (line 164) end_prefix = brant_run_denoise(working_dir, run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, data_input.is4d, output_dirs, jobman.subj.out.nmpos);

Error in brant_preprocess>run_cb (line 343) brant_preprocess_jobman(jobman, gcf);

Error while evaluating UIControl Callback**

On 7 Aug 2020, at 01:34, Yong Liu <notifications@github.com mailto:notifications@github.com > wrote:

Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 3:06 AM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Subscribed <subscribed@noreply.github.com mailto:subscribed@noreply.github.com > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

HI

When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs?

Anna

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DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: rc1.nii ft_wm: rc2.nii ft_csf: rc3*.nii

mask_res_type: nearest neighbour ft_motion: rp*.txt

Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2

Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08

Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/YongLiuLab/brant/issues/1#issuecomment-670398199 , or unsubscribe https://github.com/notifications/unsubscribe-auth/AEYVTUT7VNIRPAEOJ3UVM2TR7O3FJANCNFSM4PW4JKFQ . https://github.com/notifications/beacon/AEYVTUQHSVNXQFN5FG52SYLR7O3FJA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE72XN5Y.gif

[annapbarnes]

Hi Yong

I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file

thank you - your GUI is very nice and it is great that you have put all your tools together like this.

Anna

On 7 Aug 2020, at 10:01, Yong Liu notifications@github.com wrote:

I think maybe you need to check

“rNESTrsfMRI.nii see how many time points, or how many nii files in the same directory

Then double-check the rp*.txt, how many time points.

I guess maybe you have so many nii files be read by the brant.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 4:27 PM To: YongLiuLab/brant brant@noreply.github.com Cc: Yong Liu yliu@nlpr.ia.ac.cn; Comment comment@noreply.github.com Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Yes of course Error message, screenshot and log file attached

*Current indexing filetype: rNEST*rsfMRI.nii Index exceeds matrix dimensions.

Error in brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise>check_masks (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise (line 71) [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, denoise_infos.space_mask, nm_pos);

Error in brant_preprocess_jobman (line 164) end_prefix = brant_run_denoise(working_dir, run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, data_input.is4d, output_dirs, jobman.subj.out.nmpos);

Error in brant_preprocess>run_cb (line 343) brant_preprocess_jobman(jobman, gcf);

Error while evaluating UIControl Callback**

On 7 Aug 2020, at 01:34, Yong Liu <notifications@github.com mailto:notifications@github.com > wrote:

Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 3:06 AM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Subscribed <subscribed@noreply.github.com mailto:subscribed@noreply.github.com > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

HI

When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs?

Anna

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/YongLiuLab/brant/issues/1 , or unsubscribe https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ . https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif

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DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: rc1.nii ft_wm: rc2.nii ft_csf: rc3*.nii

mask_res_type: nearest neighbour ft_motion: rp*.txt

Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2

Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08

Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/YongLiuLab/brant/issues/1#issuecomment-670398199 , or unsubscribe https://github.com/notifications/unsubscribe-auth/AEYVTUT7VNIRPAEOJ3UVM2TR7O3FJANCNFSM4PW4JKFQ . https://github.com/notifications/beacon/AEYVTUQHSVNXQFN5FG52SYLR7O3FJA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE72XN5Y.gif

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[YongLiuLab]

Yes, pls double-check it to make sure you have No of “rNESTrsfMRI.nii” = size (‘rp*.txt’,1) in the same directory.

Any further question, please let me know.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 5:27 PM To: YongLiuLab/brant brant@noreply.github.com Cc: Yong Liu yliu@nlpr.ia.ac.cn; Comment comment@noreply.github.com Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Hi Yong

I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file

thank you - your GUI is very nice and it is great that you have put all your tools together like this.

Anna

On 7 Aug 2020, at 10:01, Yong Liu <notifications@github.com mailto:notifications@github.com > wrote:

I think maybe you need to check

“rNESTrsfMRI.nii see how many time points, or how many nii files in the same directory

Then double-check the rp*.txt, how many time points.

I guess maybe you have so many nii files be read by the brant.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 4:27 PM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Yong Liu <yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn >; Comment <comment@noreply.github.com mailto:comment@noreply.github.com > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Yes of course Error message, screenshot and log file attached

*Current indexing filetype: rNEST*rsfMRI.nii Index exceeds matrix dimensions.

Error in brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise>check_masks (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise (line 71) [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, denoise_infos.space_mask, nm_pos);

Error in brant_preprocess_jobman (line 164) end_prefix = brant_run_denoise(working_dir, run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, data_input.is4d, output_dirs, jobman.subj.out.nmpos);

Error in brant_preprocess>run_cb (line 343) brant_preprocess_jobman(jobman, gcf);

Error while evaluating UIControl Callback**

On 7 Aug 2020, at 01:34, Yong Liu <notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com mailto:notifications@github.com > wrote:

Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 3:06 AM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Subscribed <subscribed@noreply.github.com mailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com mailto:subscribed@noreply.github.com > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

HI

When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs?

Anna

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/YongLiuLab/brant/issues/1 , or unsubscribe https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ . https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif

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DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: rc1.nii ft_wm: rc2.nii ft_csf: rc3*.nii

mask_res_type: nearest neighbour ft_motion: rp*.txt

Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2

Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08

Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/YongLiuLab/brant/issues/1#issuecomment-670398199 , or unsubscribe https://github.com/notifications/unsubscribe-auth/AEYVTUT7VNIRPAEOJ3UVM2TR7O3FJANCNFSM4PW4JKFQ . https://github.com/notifications/beacon/AEYVTUQHSVNXQFN5FG52SYLR7O3FJA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE72XN5Y.gif

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[annapbarnes]

Hi Yong

Definitely have 260 rows in the rp.txt file and 260 volumes in the 4D .nii file.

Attached is the log file, text file and a link to my data, in individual space

https://drive.google.com/file/d/1a-WaU8w04eKMXgS3ocUNsFH1kdBSxyrI/view?usp=sharing https://drive.google.com/file/d/1a-WaU8w04eKMXgS3ocUNsFH1kdBSxyrI/view?usp=sharing

thanks Anna

On 9 Aug 2020, at 08:57, Yong Liu notifications@github.com wrote:

Yes, pls double-check it to make sure you have No of “rNESTrsfMRI.nii” = size (‘rp*.txt’,1) in the same directory.

Any further question, please let me know.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 5:27 PM To: YongLiuLab/brant brant@noreply.github.com Cc: Yong Liu yliu@nlpr.ia.ac.cn; Comment comment@noreply.github.com Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Hi Yong

I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file

thank you - your GUI is very nice and it is great that you have put all your tools together like this.

Anna

On 7 Aug 2020, at 10:01, Yong Liu <notifications@github.com mailto:notifications@github.com > wrote:

I think maybe you need to check

“rNESTrsfMRI.nii see how many time points, or how many nii files in the same directory

Then double-check the rp*.txt, how many time points.

I guess maybe you have so many nii files be read by the brant.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 4:27 PM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Yong Liu <yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn >; Comment <comment@noreply.github.com mailto:comment@noreply.github.com > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Yes of course Error message, screenshot and log file attached

*Current indexing filetype: rNEST*rsfMRI.nii Index exceeds matrix dimensions.

Error in brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise>check_masks (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise (line 71) [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, denoise_infos.space_mask, nm_pos);

Error in brant_preprocess_jobman (line 164) end_prefix = brant_run_denoise(working_dir, run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, data_input.is4d, output_dirs, jobman.subj.out.nmpos);

Error in brant_preprocess>run_cb (line 343) brant_preprocess_jobman(jobman, gcf);

Error while evaluating UIControl Callback**

On 7 Aug 2020, at 01:34, Yong Liu <notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com mailto:notifications@github.com > wrote:

Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 3:06 AM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Subscribed <subscribed@noreply.github.com mailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com mailto:subscribed@noreply.github.com > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

HI

When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs?

Anna

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DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: rc1.nii ft_wm: rc2.nii ft_csf: rc3*.nii

mask_res_type: nearest neighbour ft_motion: rp*.txt

Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2

Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08

Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f

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DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: c1.nii ft_wm: c2.nii ft_csf: c3*.nii

mask_res_type: nearest neighbour ft_motion: rp*.txt

Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2

Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08

Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f

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-3.7349342e-03 -1.2249137e-01 6.1054324e-03 6.4465330e-02 1.0361227e-02 -7.0414103e-04 -4.1862403e-03 -1.2257925e-01 -3.7396623e-02 1.3451627e-01 1.0552847e-02 -6.4483757e-04 -4.2028068e-03 -1.2044991e-01 1.6280418e-02 7.9556347e-02 1.0525331e-02 -8.6953567e-04 -4.3368924e-03 -1.0926393e-01 -4.2976488e-02 7.8891866e-02 1.0522318e-02 -2.5211097e-04 -4.0977243e-03 -1.0556261e-01 8.3328859e-02 5.4410014e-02 9.2856133e-03 1.2271228e-04 -3.6150113e-03 -9.0141175e-02 -2.9519579e-02 6.1168057e-02 9.6000809e-03 3.0863778e-04 -3.2425938e-03 -8.0014958e-02 1.3701368e-01 6.8627196e-02 9.2280831e-03 4.0498730e-04 -2.7671696e-03 -6.3981071e-02 -2.4222860e-02 8.8179662e-02 1.0211860e-02 8.6134309e-04 -2.8180324e-03 -5.3803840e-02 8.3894567e-02 7.8868506e-02 9.5418829e-03 7.7348932e-04 -2.9366260e-03 -5.4238224e-02 -4.6791539e-02 9.3106381e-02 9.6780495e-03 1.0365282e-03 -3.0383204e-03 -4.9914585e-02 6.0297941e-02 7.9496752e-02 8.9079809e-03 9.2077914e-04 -3.0099493e-03 -4.7571762e-02 -3.8005786e-02 7.6928120e-02 9.4364698e-03 1.1515302e-03 -2.9595845e-03 -5.4455166e-02 1.0663712e-01 9.4289374e-02 8.5740746e-03 8.6697003e-04 -2.6712009e-03 -4.4159663e-02 -5.8517992e-02 5.2161981e-02 9.6982143e-03 1.3034092e-03 -2.9408374e-03 -5.0228471e-02 9.6189276e-03 8.4923582e-02 9.5867329e-03 1.2808920e-03 -2.9947519e-03 -5.0904516e-02 4.1347728e-02 4.9313518e-02 9.5175203e-03 1.3388032e-03 -3.0245171e-03 -5.2464572e-02 -3.0730934e-02 6.0065728e-02 9.5709181e-03 1.4187692e-03 -3.0530555e-03 -5.8464347e-02 5.1842244e-02 7.1734230e-02 9.4784346e-03 1.3682015e-03 -3.0485601e-03 -5.6486504e-02 -2.8626180e-02 5.0363106e-02 9.7707961e-03 1.6052963e-03 -3.2066207e-03 -6.1247194e-02 6.8411954e-02 5.8221844e-02 9.5307512e-03 1.4964219e-03 -2.8924018e-03 -5.2873755e-02 -3.6496147e-02 4.5312874e-02 9.8420366e-03 1.7971649e-03 -3.1184988e-03 -6.2337307e-02 2.8697504e-02 7.8454545e-02 9.9303149e-03 1.6330756e-03 -3.1732515e-03 -5.7434567e-02 2.2036561e-02 5.8094715e-02 1.0063592e-02 1.6610840e-03 -3.4093484e-03 -6.4280858e-02 -4.2757220e-02 9.0698666e-02 1.0723815e-02 1.3597731e-03 -3.7012746e-03 -8.7126539e-02 5.1528145e-02 1.0899859e-01 1.0389357e-02 4.2088635e-04 -3.9484273e-03 -8.6187946e-02 -4.3524158e-02 1.1564132e-01 1.0721588e-02 3.2674072e-04 -3.7553934e-03 -9.0142353e-02 7.8062597e-02 9.2760387e-02 9.9912936e-03 2.8159115e-04 -3.6236680e-03 -8.5454483e-02 -3.5384405e-02 9.5200060e-02 1.0388927e-02 7.8104216e-04 -3.8440345e-03 -8.4641559e-02 8.0601688e-02 9.1999785e-02 1.0389279e-02 5.4705601e-04 -3.6435536e-03 -8.1845872e-02 -1.7014589e-02 1.1595864e-01 1.0864381e-02 8.4354168e-04 -3.7177410e-03 -7.2619905e-02 4.3486199e-02 1.0312556e-01 1.0835300e-02 8.7042791e-04 -3.7413756e-03

[annapbarnes]

Hello Did you manage to get take a look at the data set I sent you?

Any clues as to what I am doing wrong?

Very best wishes Anna

Anna Barnes, PhD, CSci, FIPEM IPEM Representative NHS-England National Imaging Optimisation Delivery Board Honorary Associate Professor
Centre for Medical Imaging, University College London 43-45 Foley St, London, W1W 7TS

On 9 Aug 2020, at 08:57, Yong Liu notifications@github.com wrote:

Yes, pls double-check it to make sure you have No of “rNESTrsfMRI.nii” = size (‘rp*.txt’,1) in the same directory.

Any further question, please let me know.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 5:27 PM To: YongLiuLab/brant brant@noreply.github.com Cc: Yong Liu yliu@nlpr.ia.ac.cn; Comment comment@noreply.github.com Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Hi Yong

I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file

thank you - your GUI is very nice and it is great that you have put all your tools together like this.

Anna

On 7 Aug 2020, at 10:01, Yong Liu <notifications@github.com mailto:notifications@github.com > wrote:

I think maybe you need to check

“rNESTrsfMRI.nii see how many time points, or how many nii files in the same directory

Then double-check the rp*.txt, how many time points.

I guess maybe you have so many nii files be read by the brant.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 4:27 PM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Yong Liu <yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn >; Comment <comment@noreply.github.com mailto:comment@noreply.github.com > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Yes of course Error message, screenshot and log file attached

*Current indexing filetype: rNEST*rsfMRI.nii Index exceeds matrix dimensions.

Error in brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise>check_masks (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise (line 71) [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, denoise_infos.space_mask, nm_pos);

Error in brant_preprocess_jobman (line 164) end_prefix = brant_run_denoise(working_dir, run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, data_input.is4d, output_dirs, jobman.subj.out.nmpos);

Error in brant_preprocess>run_cb (line 343) brant_preprocess_jobman(jobman, gcf);

Error while evaluating UIControl Callback**

On 7 Aug 2020, at 01:34, Yong Liu <notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com mailto:notifications@github.com > wrote:

Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 3:06 AM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Subscribed <subscribed@noreply.github.com mailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com mailto:subscribed@noreply.github.com > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

HI

When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs?

Anna

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DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: rc1.nii ft_wm: rc2.nii ft_csf: rc3*.nii

mask_res_type: nearest neighbour ft_motion: rp*.txt

Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2

Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08

Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f

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[YongLiuLab]

Hi, Anna,

Could you please send me a link of your data so that I can try to proprecess it.

Very best

Yours

Yong

From: noreply@github.com [mailto:noreply@github.com] On Behalf Of annapbarnes Sent: Friday, August 14, 2020 3:13 PM To: YongLiuLab/brant brant@noreply.github.com Cc: Yong Liu yliu@nlpr.ia.ac.cn; Comment comment@noreply.github.com Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Hello Did you manage to get take a look at the data set I sent you?

Any clues as to what I am doing wrong?

Very best wishes Anna

Anna Barnes, PhD, CSci, FIPEM IPEM Representative NHS-England National Imaging Optimisation Delivery Board Honorary Associate Professor Centre for Medical Imaging, University College London 43-45 Foley St, London, W1W 7TS

On 9 Aug 2020, at 08:57, Yong Liu <notifications@github.com mailto:notifications@github.com > wrote:

Yes, pls double-check it to make sure you have No of “rNESTrsfMRI.nii” = size (‘rp*.txt’,1) in the same directory.

Any further question, please let me know.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 5:27 PM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Yong Liu <yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn >; Comment <comment@noreply.github.com mailto:comment@noreply.github.com > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Hi Yong

I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file

thank you - your GUI is very nice and it is great that you have put all your tools together like this.

Anna

On 7 Aug 2020, at 10:01, Yong Liu <notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com mailto:notifications@github.com > wrote:

I think maybe you need to check

“rNESTrsfMRI.nii see how many time points, or how many nii files in the same directory

Then double-check the rp*.txt, how many time points.

I guess maybe you have so many nii files be read by the brant.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 4:27 PM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Yong Liu <yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn%20%3cmailto:yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn >; Comment <comment@noreply.github.com mailto:comment@noreply.github.com%20%3cmailto:comment@noreply.github.com mailto:comment@noreply.github.com > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Yes of course Error message, screenshot and log file attached

*Current indexing filetype: rNEST*rsfMRI.nii Index exceeds matrix dimensions.

Error in brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise>check_masks (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise (line 71) [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, denoise_infos.space_mask, nm_pos);

Error in brant_preprocess_jobman (line 164) end_prefix = brant_run_denoise(working_dir, run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, data_input.is4d, output_dirs, jobman.subj.out.nmpos);

Error in brant_preprocess>run_cb (line 343) brant_preprocess_jobman(jobman, gcf);

Error while evaluating UIControl Callback**

On 7 Aug 2020, at 01:34, Yong Liu <notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com%20%3cmailto:notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com mailto:notifications@github.com > wrote:

Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 3:06 AM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Subscribed <subscribed@noreply.github.com mailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com mailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com mailto:subscribed@noreply.github.com > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

HI

When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs?

Anna

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/YongLiuLab/brant/issues/1 , or unsubscribe https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ . https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif

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DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: rc1.nii ft_wm: rc2.nii ft_csf: rc3*.nii

mask_res_type: nearest neighbour ft_motion: rp*.txt

Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2

Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08

Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f

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[annapbarnes]

Please let me know if there is a problem with the link

Hi Yong

Definitely have 260 rows in the rp.txt file and 260 volumes in the 4D .nii file.

Attached is the log file, text file and a link to my data, in individual space

https://drive.google.com/file/d/1a-WaU8w04eKMXgS3ocUNsFH1kdBSxyrI/view?usp=sharing https://drive.google.com/file/d/1a-WaU8w04eKMXgS3ocUNsFH1kdBSxyrI/view?usp=sharing

thanks Anna

On 9 Aug 2020, at 08:57, Yong Liu <notifications@github.com mailto:notifications@github.com> wrote:

Yes, pls double-check it to make sure you have No of “rNESTrsfMRI.nii” = size (‘rp*.txt’,1) in the same directory.

Any further question, please let me know.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 5:27 PM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com> Cc: Yong Liu <yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn>; Comment <comment@noreply.github.com mailto:comment@noreply.github.com> Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Hi Yong

I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file

thank you - your GUI is very nice and it is great that you have put all your tools together like this.

Anna

On 7 Aug 2020, at 10:01, Yong Liu <notifications@github.com mailto:notifications@github.com <mailto:notifications@github.com mailto:notifications@github.com> > wrote:

I think maybe you need to check

“rNESTrsfMRI.nii see how many time points, or how many nii files in the same directory

Then double-check the rp*.txt, how many time points.

I guess maybe you have so many nii files be read by the brant.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com <mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com> [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 4:27 PM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com <mailto:brant@noreply.github.com mailto:brant@noreply.github.com> > Cc: Yong Liu <yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn <mailto:yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn> >; Comment <comment@noreply.github.com mailto:comment@noreply.github.com <mailto:comment@noreply.github.com mailto:comment@noreply.github.com> > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Yes of course Error message, screenshot and log file attached

*Current indexing filetype: rNEST*rsfMRI.nii Index exceeds matrix dimensions.

Error in brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise>check_masks (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise (line 71) [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, denoise_infos.space_mask, nm_pos);

Error in brant_preprocess_jobman (line 164) end_prefix = brant_run_denoise(working_dir, run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, data_input.is4d, output_dirs, jobman.subj.out.nmpos);

Error in brant_preprocess>run_cb (line 343) brant_preprocess_jobman(jobman, gcf);

Error while evaluating UIControl Callback**

On 7 Aug 2020, at 01:34, Yong Liu <notifications@github.com mailto:notifications@github.com<mailto:notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com mailto:notifications@github.com> <mailto:notifications@github.com mailto:notifications@github.com> > wrote:

Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com <mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com> <mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com> [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 3:06 AM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com <mailto:brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com mailto:brant@noreply.github.com> <mailto:brant@noreply.github.com mailto:brant@noreply.github.com> > Cc: Subscribed <subscribed@noreply.github.com mailto:subscribed@noreply.github.com<mailto:subscribed@noreply.github.com mailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com mailto:subscribed@noreply.github.com> <mailto:subscribed@noreply.github.com mailto:subscribed@noreply.github.com> > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

HI

When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs?

Anna

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DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: rc1.nii ft_wm: rc2.nii ft_csf: rc3*.nii

mask_res_type: nearest neighbour ft_motion: rp*.txt

Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2

Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08

Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f

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DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: c1.nii ft_wm: c2.nii ft_csf: c3*.nii

mask_res_type: nearest neighbour ft_motion: rp*.txt

Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2

Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08

Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f

0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 3.3307993e-03 7.6357832e-02 1.7837401e-02 -5.7212151e-05 -9.1547221e-05 3.1301502e-04 1.1045703e-02 -4.8566539e-02 5.5413523e-02 5.4641878e-04 2.4185371e-04 3.8254776e-05 4.0980593e-03 8.7049996e-02 1.0105286e-01 -2.7974734e-04 1.3759804e-04 2.3560535e-04 1.0759222e-02 -7.6154145e-02 6.1559750e-02 7.8099839e-04 3.2107491e-04 1.1398264e-04 3.9933509e-03 5.6641275e-02 1.1100836e-01 4.3179485e-04 3.2500407e-04 4.1196128e-04 1.1026180e-02 -5.4313580e-02 6.8301063e-02 1.7886331e-03 6.9689813e-04 2.3084203e-04 8.9221013e-03 4.5564678e-02 1.1214351e-01 1.5546312e-03 7.9475567e-04 4.8282913e-04 1.5056796e-02 -4.5147521e-02 8.6086866e-02 2.3726663e-03 1.1437559e-03 -3.3900531e-05 1.7188667e-02 2.1131851e-02 1.1550300e-01 2.2338689e-03 9.8264240e-04 6.2381435e-05 2.2465154e-02 -2.5434334e-02 1.0038872e-01 2.5997593e-03 1.1526634e-03 -2.9864705e-04 9.7490396e-03 -4.6641506e-03 1.4527627e-01 3.0556698e-03 1.2238104e-03 -4.0370007e-04 7.8653866e-03 -2.1064100e-02 1.2118487e-01 3.7208829e-03 1.2003351e-03 -7.4868483e-04 -7.7287144e-03 -1.6836813e-02 1.7318403e-01 4.4283537e-03 1.0726939e-03 -8.7248629e-04 -5.5430210e-03 -2.0111557e-02 1.2890937e-01 4.7847941e-03 1.2371482e-03 -1.0714683e-03 -1.1339527e-02 -1.8964360e-02 1.7428462e-01 5.4393139e-03 1.0591503e-03 -9.8615887e-04 -2.6929375e-02 2.5206516e-02 1.3869669e-01 6.2797810e-03 8.2195584e-04 -1.3694136e-03 -3.1366533e-02 -6.1678209e-02 1.6449045e-01 6.8154553e-03 7.5190683e-04 -1.3976787e-03 -4.0988305e-02 4.1421174e-02 1.8523076e-01 6.9988193e-03 3.5699118e-04 -2.2649226e-03 -2.8302532e-02 -6.5902861e-02 1.8321736e-01 7.5793965e-03 7.5615702e-04 -2.2202790e-03 -2.8199333e-02 4.2508314e-02 1.9324546e-01 7.6818582e-03 5.6232829e-04 -2.3493687e-03 -3.2942276e-02 -4.8040281e-02 1.8642514e-01 8.5270880e-03 6.3702637e-04 -2.3857711e-03 -3.7148015e-02 3.9752043e-02 1.8314337e-01 8.2180140e-03 5.8241101e-04 -2.6705009e-03 -3.7537532e-02 -8.0195439e-02 1.8836682e-01 9.0567512e-03 6.1697043e-04 -3.0209171e-03 -3.8962181e-02 2.6122167e-02 2.2539417e-01 8.6105191e-03 2.3121241e-04 -2.9671686e-03 -3.0554065e-02 -7.2414516e-02 1.9240405e-01 8.4766305e-03 6.0274744e-04 -2.9664471e-03 -4.2993491e-02 1.0363025e-01 1.9842944e-01 6.7077934e-03 6.1936340e-04 -3.1758653e-03 -2.1844603e-02 -5.5344894e-02 6.6461994e-02 6.0481902e-03 1.8518538e-03 -3.1587764e-03 -1.5157686e-02 -1.8006780e-02 1.7968741e-01 5.2669579e-03 2.2761067e-03 -2.9569090e-03 -3.4272251e-04 7.0267298e-02 2.0506759e-01 4.4282450e-03 2.0026958e-03 -2.5940440e-03 2.4046402e-02 -1.2104664e-01 1.5103650e-01 5.3626576e-03 2.5107116e-03 -2.5545483e-03 1.4594468e-02 3.4485156e-02 1.8637083e-01 4.7570255e-03 2.4716655e-03 -2.4033700e-03 2.0956713e-02 -1.0430358e-01 1.5147814e-01 5.4203114e-03 2.4118177e-03 -2.7113747e-03 1.5419786e-02 1.2156667e-02 1.8896368e-01 5.0947799e-03 2.2765526e-03 -2.5651504e-03 2.2882354e-02 -6.4684440e-02 1.5745287e-01 5.9321072e-03 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-3.4093484e-03 -6.4280858e-02 -4.2757220e-02 9.0698666e-02 1.0723815e-02 1.3597731e-03 -3.7012746e-03 -8.7126539e-02 5.1528145e-02 1.0899859e-01 1.0389357e-02 4.2088635e-04 -3.9484273e-03 -8.6187946e-02 -4.3524158e-02 1.1564132e-01 1.0721588e-02 3.2674072e-04 -3.7553934e-03 -9.0142353e-02 7.8062597e-02 9.2760387e-02 9.9912936e-03 2.8159115e-04 -3.6236680e-03 -8.5454483e-02 -3.5384405e-02 9.5200060e-02 1.0388927e-02 7.8104216e-04 -3.8440345e-03 -8.4641559e-02 8.0601688e-02 9.1999785e-02 1.0389279e-02 5.4705601e-04 -3.6435536e-03 -8.1845872e-02 -1.7014589e-02 1.1595864e-01 1.0864381e-02 8.4354168e-04 -3.7177410e-03 -7.2619905e-02 4.3486199e-02 1.0312556e-01 1.0835300e-02 8.7042791e-04 -3.7413756e-03

[annapbarnes]

Hi Yong

Did you manage to download the data ok? I expect I was just doing something a bit silly.

Much thanks Anna

On 14 Aug 2020, at 08:17, Yong Liu notifications@github.com wrote:

Hi, Anna,

Could you please send me a link of your data so that I can try to proprecess it.

Very best

Yours

Yong

From: noreply@github.com [mailto:noreply@github.com] On Behalf Of annapbarnes Sent: Friday, August 14, 2020 3:13 PM To: YongLiuLab/brant brant@noreply.github.com Cc: Yong Liu yliu@nlpr.ia.ac.cn; Comment comment@noreply.github.com Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Hello Did you manage to get take a look at the data set I sent you?

Any clues as to what I am doing wrong?

Very best wishes Anna

Anna Barnes, PhD, CSci, FIPEM IPEM Representative NHS-England National Imaging Optimisation Delivery Board Honorary Associate Professor Centre for Medical Imaging, University College London 43-45 Foley St, London, W1W 7TS

On 9 Aug 2020, at 08:57, Yong Liu <notifications@github.com mailto:notifications@github.com > wrote:

Yes, pls double-check it to make sure you have No of “rNESTrsfMRI.nii” = size (‘rp*.txt’,1) in the same directory.

Any further question, please let me know.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 5:27 PM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Yong Liu <yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn >; Comment <comment@noreply.github.com mailto:comment@noreply.github.com > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Hi Yong

I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file

thank you - your GUI is very nice and it is great that you have put all your tools together like this.

Anna

On 7 Aug 2020, at 10:01, Yong Liu <notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com mailto:notifications@github.com > wrote:

I think maybe you need to check

“rNESTrsfMRI.nii see how many time points, or how many nii files in the same directory

Then double-check the rp*.txt, how many time points.

I guess maybe you have so many nii files be read by the brant.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 4:27 PM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Yong Liu <yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn%20%3cmailto:yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn >; Comment <comment@noreply.github.com mailto:comment@noreply.github.com%20%3cmailto:comment@noreply.github.com mailto:comment@noreply.github.com > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Yes of course Error message, screenshot and log file attached

*Current indexing filetype: rNEST*rsfMRI.nii Index exceeds matrix dimensions.

Error in brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise>check_masks (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise (line 71) [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, denoise_infos.space_mask, nm_pos);

Error in brant_preprocess_jobman (line 164) end_prefix = brant_run_denoise(working_dir, run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, data_input.is4d, output_dirs, jobman.subj.out.nmpos);

Error in brant_preprocess>run_cb (line 343) brant_preprocess_jobman(jobman, gcf);

Error while evaluating UIControl Callback**

On 7 Aug 2020, at 01:34, Yong Liu <notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com%20%3cmailto:notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com mailto:notifications@github.com > wrote:

Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 3:06 AM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Subscribed <subscribed@noreply.github.com mailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com mailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com mailto:subscribed@noreply.github.com > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

HI

When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs?

Anna

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DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: rc1.nii ft_wm: rc2.nii ft_csf: rc3*.nii

mask_res_type: nearest neighbour ft_motion: rp*.txt

Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2

Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08

Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f

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[YongLiuLab]

Hi Anna

I do not get any link or attached about the data, could you please zip that file and then send me a link so that I can download it

Very best

Yours

Yong

From: noreply@github.com [mailto:noreply@github.com] On Behalf Of annapbarnes Sent: Monday, August 17, 2020 4:54 PM To: YongLiuLab/brant brant@noreply.github.com Cc: Yong Liu yliu@nlpr.ia.ac.cn; Comment comment@noreply.github.com Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Hi Yong

Did you manage to download the data ok? I expect I was just doing something a bit silly.

Much thanks Anna

On 14 Aug 2020, at 08:17, Yong Liu <notifications@github.com mailto:notifications@github.com > wrote:

Hi, Anna,

Could you please send me a link of your data so that I can try to proprecess it.

Very best

Yours

Yong

From: noreply@github.com mailto:noreply@github.com [mailto:noreply@github.com] On Behalf Of annapbarnes Sent: Friday, August 14, 2020 3:13 PM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Yong Liu <yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn >; Comment <comment@noreply.github.com mailto:comment@noreply.github.com > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Hello Did you manage to get take a look at the data set I sent you?

Any clues as to what I am doing wrong?

Very best wishes Anna

Anna Barnes, PhD, CSci, FIPEM IPEM Representative NHS-England National Imaging Optimisation Delivery Board Honorary Associate Professor Centre for Medical Imaging, University College London 43-45 Foley St, London, W1W 7TS

On 9 Aug 2020, at 08:57, Yong Liu <notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com mailto:notifications@github.com > wrote:

Yes, pls double-check it to make sure you have No of “rNESTrsfMRI.nii” = size (‘rp*.txt’,1) in the same directory.

Any further question, please let me know.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 5:27 PM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Yong Liu <yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn%20%3cmailto:yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn >; Comment <comment@noreply.github.com mailto:comment@noreply.github.com%20%3cmailto:comment@noreply.github.com mailto:comment@noreply.github.com > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Hi Yong

I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file

thank you - your GUI is very nice and it is great that you have put all your tools together like this.

Anna

On 7 Aug 2020, at 10:01, Yong Liu <notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com%20%3cmailto:notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com mailto:notifications@github.com > wrote:

I think maybe you need to check

“rNESTrsfMRI.nii see how many time points, or how many nii files in the same directory

Then double-check the rp*.txt, how many time points.

I guess maybe you have so many nii files be read by the brant.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 4:27 PM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Yong Liu <yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn%20%3cmailto:yliu@nlpr.ia.ac.cn%20%3cmailto:yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn%20%3cmailto:yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn >; Comment <comment@noreply.github.com mailto:comment@noreply.github.com%20%3cmailto:comment@noreply.github.com%20%3cmailto:comment@noreply.github.com mailto:comment@noreply.github.com%20%3cmailto:comment@noreply.github.com mailto:comment@noreply.github.com > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Yes of course Error message, screenshot and log file attached

*Current indexing filetype: rNEST*rsfMRI.nii Index exceeds matrix dimensions.

Error in brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise>check_masks (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise (line 71) [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, denoise_infos.space_mask, nm_pos);

Error in brant_preprocess_jobman (line 164) end_prefix = brant_run_denoise(working_dir, run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, data_input.is4d, output_dirs, jobman.subj.out.nmpos);

Error in brant_preprocess>run_cb (line 343) brant_preprocess_jobman(jobman, gcf);

Error while evaluating UIControl Callback**

On 7 Aug 2020, at 01:34, Yong Liu <notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com%20%3cmailto:notifications@github.com%20%3cmailto:notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com%20%3cmailto:notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com mailto:notifications@github.com > wrote:

Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 3:06 AM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Subscribed <subscribed@noreply.github.com mailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com mailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com mailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com mailto:subscribed@noreply.github.com > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

HI

When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs?

Anna

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DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: rc1.nii ft_wm: rc2.nii ft_csf: rc3*.nii

mask_res_type: nearest neighbour ft_motion: rp*.txt

Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2

Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08

Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f

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[annapbarnes]

please could you click on this link and let me know if you can see the data

https://drive.google.com/drive/folders/1KjhssjmW4dAPXKmP7E4XwgDIjV2BGPxw?usp=sharing

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-2.9879251e-03 -7.9941628e-02 3.2732075e-02 3.3987140e-02 6.3616945e-03 4.0777707e-04 -3.0245762e-03 -8.3233029e-02 6.4332048e-02 7.4612872e-02 6.4452796e-03 5.2114388e-04 -2.8935561e-03 -7.4122642e-02 4.3239847e-02 8.8096464e-03 6.7195046e-03 5.3051536e-04 -3.0053744e-03 -7.5486042e-02 4.7070891e-02 5.5418369e-02 6.5085905e-03 5.4926825e-04 -2.8139000e-03 -7.4554932e-02 -7.0266907e-03 9.1069107e-03 6.6023261e-03 5.6706231e-04 -3.0462626e-03 -8.0131240e-02 5.9421009e-02 6.1793702e-02 6.2981939e-03 7.2183740e-04 -2.8063153e-03 -6.3447570e-02 -1.8805709e-02 3.6973098e-02 7.3772190e-03 7.9356878e-04 -3.0303958e-03 -6.7329726e-02 7.8832674e-02 6.8159483e-02 7.2125696e-03 7.8969936e-04 -3.0037756e-03 -5.9694406e-02 -3.2780723e-02 5.8207108e-02 7.7974252e-03 9.5679836e-04 -3.0040257e-03 -7.0697416e-02 1.3339224e-01 7.8246765e-02 6.3411946e-03 7.0458220e-04 -3.1241581e-03 -5.9705913e-02 -7.3255394e-02 3.1242918e-02 7.0479611e-03 9.8351323e-04 -3.0273826e-03 -6.5755037e-02 1.4587266e-02 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-3.7349342e-03 -1.2249137e-01 6.1054324e-03 6.4465330e-02 1.0361227e-02 -7.0414103e-04 -4.1862403e-03 -1.2257925e-01 -3.7396623e-02 1.3451627e-01 1.0552847e-02 -6.4483757e-04 -4.2028068e-03 -1.2044991e-01 1.6280418e-02 7.9556347e-02 1.0525331e-02 -8.6953567e-04 -4.3368924e-03 -1.0926393e-01 -4.2976488e-02 7.8891866e-02 1.0522318e-02 -2.5211097e-04 -4.0977243e-03 -1.0556261e-01 8.3328859e-02 5.4410014e-02 9.2856133e-03 1.2271228e-04 -3.6150113e-03 -9.0141175e-02 -2.9519579e-02 6.1168057e-02 9.6000809e-03 3.0863778e-04 -3.2425938e-03 -8.0014958e-02 1.3701368e-01 6.8627196e-02 9.2280831e-03 4.0498730e-04 -2.7671696e-03 -6.3981071e-02 -2.4222860e-02 8.8179662e-02 1.0211860e-02 8.6134309e-04 -2.8180324e-03 -5.3803840e-02 8.3894567e-02 7.8868506e-02 9.5418829e-03 7.7348932e-04 -2.9366260e-03 -5.4238224e-02 -4.6791539e-02 9.3106381e-02 9.6780495e-03 1.0365282e-03 -3.0383204e-03 -4.9914585e-02 6.0297941e-02 7.9496752e-02 8.9079809e-03 9.2077914e-04 -3.0099493e-03 -4.7571762e-02 -3.8005786e-02 7.6928120e-02 9.4364698e-03 1.1515302e-03 -2.9595845e-03 -5.4455166e-02 1.0663712e-01 9.4289374e-02 8.5740746e-03 8.6697003e-04 -2.6712009e-03 -4.4159663e-02 -5.8517992e-02 5.2161981e-02 9.6982143e-03 1.3034092e-03 -2.9408374e-03 -5.0228471e-02 9.6189276e-03 8.4923582e-02 9.5867329e-03 1.2808920e-03 -2.9947519e-03 -5.0904516e-02 4.1347728e-02 4.9313518e-02 9.5175203e-03 1.3388032e-03 -3.0245171e-03 -5.2464572e-02 -3.0730934e-02 6.0065728e-02 9.5709181e-03 1.4187692e-03 -3.0530555e-03 -5.8464347e-02 5.1842244e-02 7.1734230e-02 9.4784346e-03 1.3682015e-03 -3.0485601e-03 -5.6486504e-02 -2.8626180e-02 5.0363106e-02 9.7707961e-03 1.6052963e-03 -3.2066207e-03 -6.1247194e-02 6.8411954e-02 5.8221844e-02 9.5307512e-03 1.4964219e-03 -2.8924018e-03 -5.2873755e-02 -3.6496147e-02 4.5312874e-02 9.8420366e-03 1.7971649e-03 -3.1184988e-03 -6.2337307e-02 2.8697504e-02 7.8454545e-02 9.9303149e-03 1.6330756e-03 -3.1732515e-03 -5.7434567e-02 2.2036561e-02 5.8094715e-02 1.0063592e-02 1.6610840e-03 -3.4093484e-03 -6.4280858e-02 -4.2757220e-02 9.0698666e-02 1.0723815e-02 1.3597731e-03 -3.7012746e-03 -8.7126539e-02 5.1528145e-02 1.0899859e-01 1.0389357e-02 4.2088635e-04 -3.9484273e-03 -8.6187946e-02 -4.3524158e-02 1.1564132e-01 1.0721588e-02 3.2674072e-04 -3.7553934e-03 -9.0142353e-02 7.8062597e-02 9.2760387e-02 9.9912936e-03 2.8159115e-04 -3.6236680e-03 -8.5454483e-02 -3.5384405e-02 9.5200060e-02 1.0388927e-02 7.8104216e-04 -3.8440345e-03 -8.4641559e-02 8.0601688e-02 9.1999785e-02 1.0389279e-02 5.4705601e-04 -3.6435536e-03 -8.1845872e-02 -1.7014589e-02 1.1595864e-01 1.0864381e-02 8.4354168e-04 -3.7177410e-03 -7.2619905e-02 4.3486199e-02 1.0312556e-01 1.0835300e-02 8.7042791e-04 -3.7413756e-03

DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: c1.nii ft_wm: c2.nii ft_csf: c3*.nii

mask_res_type: nearest neighbour ft_motion: rp*.txt

Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2

Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08

Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f

[annapbarnes]

Hi Yong

Hope this worked. I think it went wrong because I invited you directly from the account which has a different email address from my own as was called inmpod@gmail.commailto:inmpod@gmail.com and probably went to you junk mail

Very sorry Anna

On 17 Aug 2020, at 12:16, BARNES, Anna (UNIVERSITY COLLEGE LONDON HOSPITALS NHS FOUNDATION TRUST) anna.barnes1@nhs.net<mailto:anna.barnes1@nhs.net> wrote:

please could you click on this link and let me know if you can see the data

https://drive.google.com/drive/folders/1KjhssjmW4dAPXKmP7E4XwgDIjV2BGPxw?usp=sharing

On 17 Aug 2020, at 11:36, Yong Liu > wrote: Hi Anna I do not get any link or attached about the data, could you please zip that file and then send me a link so that I can download it Very best Yours Yong From: noreply@github.com [mailto:noreply@github.com] On Behalf Of annapbarnes Sent: Monday, August 17, 2020 4:54 PM To: YongLiuLab/brant > Cc: Yong Liu >; Comment > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Hi Yong Did you manage to download the data ok? I expect I was just doing something a bit silly. Much thanks Anna > On 14 Aug 2020, at 08:17, Yong Liu > wrote: > > > Hi, Anna, > > > > Could you please send me a link of your data so that I can try to proprecess it. > > > > > > > > Very best > > Yours > > Yong > > > > From: noreply@github.com [mailto:noreply@github.com] On Behalf Of annapbarnes > Sent: Friday, August 14, 2020 3:13 PM > To: YongLiuLab/brant > > Cc: Yong Liu >; Comment > > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > Hello > Did you manage to get take a look at the data set I sent you? > > Any clues as to what I am doing wrong? > > Very best wishes > Anna > > Anna Barnes, PhD, CSci, FIPEM > IPEM Representative NHS-England National Imaging Optimisation Delivery Board > Honorary Associate Professor > Centre for Medical Imaging, > University College London > 43-45 Foley St, London, W1W 7TS > > > > On 9 Aug 2020, at 08:57, Yong Liu > > wrote: > > > > > > Yes, pls double-check it to make sure you have No of “*rNEST*rsfMRI.nii” = size (‘rp*.txt’,1) in the same directory. > > > > > > > > Any further question, please let me know. > > > > > > > > > > > > Very best > > > > Yours > > > > Yong > > > > > > > > From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes > > Sent: Friday, August 07, 2020 5:27 PM > > To: YongLiuLab/brant > > > > Cc: Yong Liu > >; Comment > > > > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > > > > > > > Hi Yong > > > > I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file > > > > thank you - your GUI is very nice and it is great that you have put all your tools together like this. > > > > Anna > > > > > On 7 Aug 2020, at 10:01, Yong Liu %20%3cmailto:notifications@github.com> > > wrote: > > > > > > > > > I think maybe you need to check > > > > > > > > > > > > “*rNEST*rsfMRI.nii see how many time points, or how many nii files in the same directory > > > > > > > > > > > > Then double-check the rp*.txt, how many time points. > > > > > > > > > > > > I guess maybe you have so many nii files be read by the brant. > > > > > > > > > > > > > > > > > > Very best > > > > > > Yours > > > > > > Yong > > > > > > > > > > > > From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes > > > Sent: Friday, August 07, 2020 4:27 PM > > > To: YongLiuLab/brant %20%3cmailto:brant@noreply.github.com> > > > > > Cc: Yong Liu %20%3cmailto:yliu@nlpr.ia.ac.cn> > >; Comment %20%3cmailto:comment@noreply.github.com> > > > > > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > > > > > > > > > > > > > Yes of course > > > Error message, screenshot and log file attached > > > > > > **Current indexing filetype: *rNEST*rsfMRI.nii > > > Index exceeds matrix dimensions. > > > > > > Error in > > > brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] > > > (line 413) > > > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > > > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > > > > > Error in brant_run_denoise>check_masks (line 413) > > > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > > > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > > > > > Error in brant_run_denoise (line 71) > > > [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, > > > denoise_infos.space_mask, nm_pos); > > > > > > Error in brant_preprocess_jobman (line 164) > > > end_prefix = brant_run_denoise(working_dir, > > > run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, > > > data_input.is4d, output_dirs, jobman.subj.out.nmpos); > > > > > > Error in brant_preprocess>run_cb (line 343) > > > brant_preprocess_jobman(jobman, gcf); > > > > > > Error while evaluating UIControl Callback** > > > > > > > > > > On 7 Aug 2020, at 01:34, Yong Liu %20%3cmailto:notifications@github.com%20%3cmailto:notifications@github.com> %20%3cmailto:notifications@github.com> > > wrote: > > > > > > > > > > > > Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Very best > > > > > > > > Yours > > > > > > > > Yong > > > > > > > > > > > > > > > > From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes > > > > Sent: Friday, August 07, 2020 3:06 AM > > > > To: YongLiuLab/brant %20%3cmailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com> %20%3cmailto:brant@noreply.github.com> > > > > > > Cc: Subscribed %20%3cmailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com> %20%3cmailto:subscribed@noreply.github.com> > > > > > > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > > > > > > > > > > > HI > > > > > > > > When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs? > > > > > > > > Anna > > > > > > > > — > > > > You are receiving this because you are subscribed to this thread. > > > > Reply to this email directly, view it on GitHub , or unsubscribe . > > > > > > > > — > > > > You are receiving this because you authored the thread. > > > > Reply to this email directly, view it on GitHub , or unsubscribe . > > > > > > > > > > > > > DENOISE > > > Space & Masks > > > running in individual space. > > > selected masks' wildcards are > > > ft_gs: rc1*.nii > > > ft_wm: rc2*.nii > > > ft_csf: rc3*.nii > > > > > > mask_res_type: nearest neighbour > > > ft_motion: rp*.txt > > > > > > Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2 > > > > > > Filter options: > > > TR(s): 2.0 > > > lower cutoff: 0.01 > > > upper cutoff: 0.08 > > > > > > Process options > > > Order: Regression first, then filter > > > save option: all selected options will have output files > > > gzip option: output files will be saved as input format > > > GSR option: regression and selected following process will be done with and without GSR > > > regression output prefix: d > > > filter output prefix: f > > > > > > > > > > > > — > > > You are receiving this because you commented. > > > Reply to this email directly, view it on GitHub , or unsubscribe . > > > > > > — > > > You are receiving this because you authored the thread. > > > Reply to this email directly, view it on GitHub , or unsubscribe . > > > > > > > > > > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub , or unsubscribe . > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub , or unsubscribe . > > > > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub , or unsubscribe . > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub , or unsubscribe . > — You are receiving this because you commented. 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[YongLiuLab]

Hi Yong

Did the data come through yet? I sent it via UCL dropbox and also a link to the data on my Google drive?

Best wishes Anna

From: Yong Liu yliu@nlpr.ia.ac.cn Date: Monday, 17 August 2020 at 11:35 To: 'YongLiuLab/brant' reply@reply.github.com Cc: "anna.p.barnes@ucl.ac.uk" anna.p.barnes@ucl.ac.uk Subject: RE: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Resent from: anna.p.barnes@ucl.ac.uk Resent date: Monday, 17 August 2020 at 11:35

Hi Anna

I do not get any link or attached about the data, could you please zip that file and then send me a link so that I can download it

Very best Yours Yong

From: noreply@github.com [mailto:noreply@github.com] On Behalf Of annapbarnes Sent: Monday, August 17, 2020 4:54 PM To: YongLiuLab/brant brant@noreply.github.com Cc: Yong Liu yliu@nlpr.ia.ac.cn; Comment comment@noreply.github.com Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Hi Yong

Did you manage to download the data ok? I expect I was just doing something a bit silly.

Much thanks Anna

On 14 Aug 2020, at 08:17, Yong Liu notifications@github.com<mailto:notifications@github.com> wrote:

Hi, Anna,

Could you please send me a link of your data so that I can try to proprecess it.

Very best

Yours

Yong

From: noreply@github.commailto:noreply@github.com [mailto:noreply@github.com] On Behalf Of annapbarnes Sent: Friday, August 14, 2020 3:13 PM To: YongLiuLab/brant brant@noreply.github.com<mailto:brant@noreply.github.com> Cc: Yong Liu yliu@nlpr.ia.ac.cn<mailto:yliu@nlpr.ia.ac.cn>; Comment comment@noreply.github.com<mailto:comment@noreply.github.com> Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Hello Did you manage to get take a look at the data set I sent you?

Any clues as to what I am doing wrong?

Very best wishes Anna

Anna Barnes, PhD, CSci, FIPEM IPEM Representative NHS-England National Imaging Optimisation Delivery Board Honorary Associate Professor Centre for Medical Imaging, University College London 43-45 Foley St, London, W1W 7TS

On 9 Aug 2020, at 08:57, Yong Liu <notifications@github.com mailto:notifications@github.com<mailto:notifications@github.com%20%3cmailto:notifications@github.com> > wrote:

Yes, pls double-check it to make sure you have No of “rNESTrsfMRI.nii” = size (‘rp*.txt’,1) in the same directory.

Any further question, please let me know.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.commailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 5:27 PM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com<mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com> > Cc: Yong Liu <yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn<mailto:yliu@nlpr.ia.ac.cn%20%3cmailto:yliu@nlpr.ia.ac.cn> >; Comment <comment@noreply.github.com mailto:comment@noreply.github.com<mailto:comment@noreply.github.com%20%3cmailto:comment@noreply.github.com> > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Hi Yong

I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file

thank you - your GUI is very nice and it is great that you have put all your tools together like this.

Anna

On 7 Aug 2020, at 10:01, Yong Liu <notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com<mailto:notifications@github.com%20%3cmailto:notifications@github.com%20%3cmailto:notifications@github.com> mailto:notifications@github.com > wrote:

I think maybe you need to check

“rNESTrsfMRI.nii see how many time points, or how many nii files in the same directory

Then double-check the rp*.txt, how many time points.

I guess maybe you have so many nii files be read by the brant.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.commailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 4:27 PM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com<mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com> mailto:brant@noreply.github.com > Cc: Yong Liu <yliu@nlpr.ia.ac.cn mailto:yliu@nlpr.ia.ac.cn%20%3cmailto:yliu@nlpr.ia.ac.cn<mailto:yliu@nlpr.ia.ac.cn%20%3cmailto:yliu@nlpr.ia.ac.cn%20%3cmailto:yliu@nlpr.ia.ac.cn> mailto:yliu@nlpr.ia.ac.cn >; Comment <comment@noreply.github.com mailto:comment@noreply.github.com%20%3cmailto:comment@noreply.github.com<mailto:comment@noreply.github.com%20%3cmailto:comment@noreply.github.com%20%3cmailto:comment@noreply.github.com> mailto:comment@noreply.github.com > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

Yes of course Error message, screenshot and log file attached

*Current indexing filetype: rNEST*rsfMRI.nii Index exceeds matrix dimensions.

Error in brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise>check_masks (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise (line 71) [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, denoise_infos.space_mask, nm_pos);

Error in brant_preprocess_jobman (line 164) end_prefix = brant_run_denoise(working_dir, run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, data_input.is4d, output_dirs, jobman.subj.out.nmpos);

Error in brant_preprocess>run_cb (line 343) brant_preprocess_jobman(jobman, gcf);

Error while evaluating UIControl Callback**

On 7 Aug 2020, at 01:34, Yong Liu <notifications@github.com mailto:notifications@github.com%20%3cmailto:notifications@github.com%20%3cmailto:notifications@github.com<mailto:notifications@github.com%20%3cmailto:notifications@github.com%20%3cmailto:notifications@github.com%20%3cmailto:notifications@github.com> mailto:notifications@github.com%20%3cmailto:notifications@github.com mailto:notifications@github.com > wrote:

Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections.

Very best

Yours

Yong

From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.commailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 3:06 AM To: YongLiuLab/brant <brant@noreply.github.com mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com<mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com> mailto:brant@noreply.github.com%20%3cmailto:brant@noreply.github.com mailto:brant@noreply.github.com > Cc: Subscribed <subscribed@noreply.github.com mailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com<mailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com> mailto:subscribed@noreply.github.com%20%3cmailto:subscribed@noreply.github.com mailto:subscribed@noreply.github.com > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1)

HI

When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs?

Anna

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DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: rc1.nii ft_wm: rc2.nii ft_csf: rc3*.nii

mask_res_type: nearest neighbour ft_motion: rp*.txt

Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2

Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08

Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f

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