Segmentation fault

[jguerrerogon]

Hi there,

Thank you for these great set of tools. I've been getting this 'Segmentation fault' at the final stage of the processing:

Writing final data... Segmentation fault (core dumped)

not really any other information in the output log. I can see that "structural_0.nii" is saved in the location I'm specifying for the final output nifti image. I've checked that there are no issues with disk space. Any idea what could be the reason?

Thanks!

[eurotomania]

Hello,

This can be due to many reasons as there are not any more information output.

You eliminated disk space. IT is not write permission either as structural_0 is written.

Is it immediately after "Writing final data..." or is it after "transforming volumes" ?

IF it is after transforming volumes, generally this is an insufficient RAM problem. The latest version of the software significantly reduces RAM usage at this stage (which is the largest in the entire pipeline) so might want to do another git pull.

Also do you have gradient nonlinearity input? Can you copy paste your entire command (without any iid of course)?

Thanks.

On Sun, Feb 18, 2024 at 1:34 PM jguerrerogon @.***> wrote:

Hi there,

Thank you for these great set of tools. I've been getting this 'Segmentation fault' at the final stage of the processing:

Writing final data... Segmentation fault (core dumped)

not really any other information in the output log. I can see that "structural_0.nii" is saved in the location I'm specifying for the final output nifti image. I've checked that there are no issues with disk space. Any idea what could be the reason?

Thanks!

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[jguerrerogon]

Thanks much, Okan. After doing some more tinkering, I found that it may be related to the data itself. I tried it with a scan collected with a different diffusion sequence, and it successfully made it all the way through. But have not quite figured out what about the data may be the cause, as I've processed these same data with a different pipeline, which runs topup and eddy.

The fault does happen right after "Writing final data". It does successfully make it through the "Transforming Volume" stage. I'm not running gradient nonlinearity correction at this point.

Here is my inputs and command:

preprocessed_data_dir=/scratch/processed-data rawdwidir=${preprocessed_data_dir}/rawdata/sub-${sub}/ses-001/dwi

up-data

pepolar0=${rawdwidir}/sub-${sub}_ses-001_desc-pepolar-0 pepolar0_bval=${pepolar0}_dwi.bval pepolar0_bvec=${pepolar0}_dwi.bvec pepolar0_json=${pepolar0}_dwi.json pepolar0_dwi=${pepolar0}_dwi.nii.gz

down-data

pepolar1=${rawdwidir}/sub-${sub}_ses-001_desc-pepolar-1 pepolar1_bval=${pepolar1}_dwi.bval pepolar1_bvec=${pepolar1}_dwi.bvec pepolar1_json=${pepolar1}_dwi.json pepolar1_dwi=${pepolar1}_dwi.nii.gz

output

tortoise_preprocessed=${preprocessed_data_dir}/derivatives/tortoise-preproc out_dwi=${tortoise_preprocessed}/sub-${sub}/ses-001/dwi/sub-${sub}_ses-001_desc-preproc_dwi.nii

TORTOISEProcess \ --up_data $pepolar0_dwi \ --up_json $pepolar0_json \ --down_data $pepolar1_dwi \ --ub $pepolar0_bval \ --uv $pepolar0_bvec \ --db $pepolar1_bval \ --dv $pepolar1_bvec \ -o $out_dwi \ --epi DRBUDDI

[eurotomania]

One quick question before I get to it tomorrow.

Are you giving nii.gz as input?

TORTOISE does memory mapping so it does not support nii.gz actually. All images should be pure NIFTI.

I will add a warning about this tomorrow.

On Wed, Feb 21, 2024 at 9:40 PM jguerrerogon @.***> wrote:

Thanks much, Okan. After doing some more tinkering, I found that it may be related to the data itself. I tried it with a scan collected with a different diffusion sequence, and it successfully made it all the way through. But have not quite figured out what about the data may be the cause, as I've processed these same data with a difference pipeline, which runs topup and eddy.

The fault does happen right after "Writing final data". It does successfully make it through the "Transforming Volume" stage. I'm not running gradient nonlinearity correction at this point.

Here is my inputs and command:

preprocessed_data_dir=/scratch/processed-data rawdwidir=${preprocessed_data_dir}/rawdata/sub-${sub}/ses-001/dwi up-data

pepolar0=${rawdwidir}/sub-${sub}_ses-001_desc-pepolar-0 pepolar0_bval=${pepolar0}_dwi.bval pepolar0_bvec=${pepolar0}_dwi.bvec pepolar0_json=${pepolar0}_dwi.json pepolar0_dwi=${pepolar0}_dwi.nii.gz down-data

pepolar1=${rawdwidir}/sub-${sub}_ses-001_desc-pepolar-1 pepolar1_bval=${pepolar1}_dwi.bval pepolar1_bvec=${pepolar1}_dwi.bvec pepolar1_json=${pepolar1}_dwi.json pepolar1_dwi=${pepolar1}_dwi.nii.gz output

tortoise_preprocessed=${preprocessed_data_dir}/derivatives/tortoise-preproc

out_dwi=${tortoise_preprocessed}/sub-${sub}/ses-001/dwi/sub-${sub}_ses-001_desc-preproc_dwi.nii

TORTOISEProcess --up_data $pepolar0_dwi --up_json $pepolar0_json --down_data $pepolar1_dwi --ub $pepolar0_bval --uv $pepolar0_bvec --db $pepolar1_bval --dv $pepolar1_bvec -o $out_dwi --epi DRBUDDI

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[jguerrerogon]

I was providing the zipped niftis (nii.gz). I tried it this morning with unzipped (nii) inputs, but still got the same result.

[eurotomania]

Would it be possible to share this data for me to diagnose things? Anonymized of course.

On Mon, Feb 26, 2024 at 2:39 PM jguerrerogon @.***> wrote:

I was providing the zipped niftis (nii.gz). I tried it this morning with unzipped (nii) inputs, but still got the same result.

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[jguerrerogon]

Hi Okan, sorry for my delayed response. I am able to provide example data. To comply with our institutional policies, I can place it in a Box folder and share the link with you. Would that work?

[eurotomania]

Sure.

If you can send the log_main.txt file in the logs folder, it would help too. Please make sure the data is anonymized as well.

Thanks.

On Wed, Mar 6, 2024 at 11:41 AM jguerrerogon @.***> wrote:

Hi Okan, sorry for my delayed response. I am able to provide example data. To comply with our institutional policies, I can place it in a Box folder and share the link with you. Would that work?

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[jguerrerogon]

Yes, will do. Is this an email address I can use? : [Clickable Email icon] @.> @*.**@*.***>

---

From: M. Okan Irfanoglu @.> Sent: Wednesday, March 6, 2024 11:32 AM To: eurotomania/TORTOISEV4 @.> Cc: Jose Guerrero Gonzalez @.>; Author @.> Subject: Re: [eurotomania/TORTOISEV4] Segmentation fault (Issue #13)

Sure.

If you can send the log_main.txt file in the logs folder, it would help too. Please make sure the data is anonymized as well.

Thanks.

On Wed, Mar 6, 2024 at 11:41 AM jguerrerogon @.***> wrote:

Hi Okan, sorry for my delayed response. I am able to provide example data. To comply with our institutional policies, I can place it in a Box folder and share the link with you. Would that work?

— Reply to this email directly, view it on GitHub https://github.com/eurotomania/TORTOISEV4/issues/13#issuecomment-1981307494https://urldefense.com/v3/__https://github.com/eurotomania/TORTOISEV4/issues/13*issuecomment-1981307494*3E__;IyU!!Mak6IKo!OPqcxXoGnER5OMmt_-gvEU3KnQFZEaF6T_umUrZB4oUqUy50Deeaee41PJiSLc4UivZgcrfm_3_EsFN7ygkt8cqrsdJ-$, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEFQZWAIQLGXDLRM7WKWCTDYW5BNPAVCNFSM6AAAAABDOLK2WKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBRGMYDONBZGQhttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AEFQZWAIQLGXDLRM7WKWCTDYW5BNPAVCNFSM6AAAAABDOLK2WKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBRGMYDONBZGQ*3E__;JQ!!Mak6IKo!OPqcxXoGnER5OMmt_-gvEU3KnQFZEaF6T_umUrZB4oUqUy50Deeaee41PJiSLc4UivZgcrfm_3_EsFN7ygkt8ZR0p911$ . You are receiving this because you commented.Message ID: @.***>

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[eurotomania]

You can use my official email for this:

@.***

On Wed, Mar 6, 2024 at 1:08 PM jguerrerogon @.***> wrote:

Yes, will do. Is this an email address I can use? : [Clickable Email icon] @.> @*.**@*.***>

---

From: M. Okan Irfanoglu @.> Sent: Wednesday, March 6, 2024 11:32 AM To: eurotomania/TORTOISEV4 @.> Cc: Jose Guerrero Gonzalez @.>; Author @.> Subject: Re: [eurotomania/TORTOISEV4] Segmentation fault (Issue #13)

Sure.

If you can send the log_main.txt file in the logs folder, it would help too. Please make sure the data is anonymized as well.

Thanks.

On Wed, Mar 6, 2024 at 11:41 AM jguerrerogon @.***> wrote:

Hi Okan, sorry for my delayed response. I am able to provide example data. To comply with our institutional policies, I can place it in a Box folder and share the link with you. Would that work?

— Reply to this email directly, view it on GitHub < https://github.com/eurotomania/TORTOISEV4/issues/13#issuecomment-1981307494 < https://urldefense.com/v3/__https://github.com/eurotomania/TORTOISEV4/issues/13*issuecomment-1981307494*3E__;IyU!!Mak6IKo!OPqcxXoGnER5OMmt_-gvEU3KnQFZEaF6T_umUrZB4oUqUy50Deeaee41PJiSLc4UivZgcrfm_3_EsFN7ygkt8cqrsdJ-$>,

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