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ecr05 / MSM_HOCR

Multimodal Surface Matching with Higher order Clique Reduction: Mac OS and Linux binaries
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--regoption: Option doesn't exist! #17

Closed sameera2004 closed 4 years ago

sameera2004 commented 4 years ago

Hi,

I am using HCP pipeline 4.2 to process our fMRI data. I am getting above error (--regoption: Option doesn't exist!) when I am trying to use "MSMSulc" for the surface registration. I didn't see any issue when I am using " FS" option. I followed all the steps in "MSM_HOCR/compilation instructions" to compile. Below, please find the PostFreeSurfer - error file.

reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt)

WARNING: input sphere is either unusually irregular or not centered, inspect the input

Part of FSL (ID: 6.0.3:b862cdd5) msm configuration parameters

Usage:

Optional arguments (You may optionally specify one or more of): --opt optimisation method. Choice of: AFFINE,DISCRETE (default) --simval code for determining which similarty measure is used to assess cost during registration: options are 1) SSD; 2) pearsons correlation (default); 3) NMI;) --it number of iterations at each resolution (default -–it=3,3,3) --sigma_in smoothing parameter for input image (default --sigma_in=2,2,2) --sigma_ref Sigma parameter - smoothing parameter for reference image (set equal to sigma_in by default) --lambda Lambda parameter - controls contribution of regulariser --datagrid DATA grid resolution (default --datagrid=5,5,5). If parameter = 0 then the native mesh is used. --CPgrid Control point grid resolution (default --CPgrid=2,3,4) --SGgrid Sampling grid resolution (default = 2 levels higher than the control point grid) --anatgrid Anatomical grid resolution (default = 2 levels higher than the control point grid) --aKNN Number of neighbours for estimation of kNN graph and alpha entropy measure (default --aKNN=5,5,5) --cutthr Upper and lower thresholds for defining cut vertices (default --cutthr=0,0) --mInt Method used for mesh interpolations, options: TPS or BARY (default) --dInt Method used for data interpolations, options: GAUSSIAN or ADAP_BARY (default) --regexp Regulariser exponent 'rexp' (default 2.0) --weight weight regulariser cost using areal distortion weighting --anorm norm regulariser cost using mean angle (for HCP compatibility) --rescaleL rescale label grid rather than using barycentres --log log transform and normalise the data --IN Normalize intensity ranges using histogram matching --INc Normalize intensity ranges using histogram matching excluding cut --VN Variance normalize data --scale Scale intensity ranges of a features in multivariate data to be equal to that of the first (useful for multimodal contrasts) --excl Ignore the cut when resampling the data --stepsize gradient stepping for affine optimisation (default 0.01) --gradsampling Determines the finite distance spacing for the affine gradient calculation (default 0.5) --numthreads number of threads for tbb (default 1)

--regoption: Option doesn't exist! @
Thu Jul 16 16:24:36 EDT 2020:FreeSurfer2CaretConvertAndRegisterNonlinear.sh: While running '/mnt/tools/HCP-4.2-Prerequisites/HCPpipelines-4.2.0/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh /mnt/hcp01/scR21_HCP4_2_MSMSulc 50016 /mnt/hcp01/scR21_HCP4_2_MSMSulc/50016/T1w /mnt/hcp01/scR21_HCP4_2_MSMSulc/50016/MNINonLinear Native /mnt/hcp01/scR21_HCP4_2_MSMSulc/50016/T1w/50016 T1w_acpc_dc_restore_1mm T1w_acpc_dc_restore T2w_acpc_dc_restore /mnt/jxvs01/tools/HCP-4.2-Prerequisites/HCPpipelines-4.2.0/global/templates/standard_mesh_atlases 164 32 /mnt/hcp01/scR21_HCP4_2_MSMSulc/50016/MNINonLinear/xfms/acpc_dc2standard /mnt/hcp01/scR21_HCP4_2_MSMSulc/50016/MNINonLinear/xfms/standard2acpc_dc T1w_restore T2w_restore brainmask_fs /mnt/tools/HCP-4.2-Prerequisites/HCPpipelines-4.2.0/global/config/FreeSurferAllLut.txt /mnt/tools/HCP-4.2-Prerequisites/HCPpipelines-4.2.0/global/templates/91282_Greyordinates 2 /mnt/tools/HCP-4.2-Prerequisites/HCPpipelines-4.2.0/global/config/FreeSurferSubcorticalLabelTableLut.txt MSMSulc 1': Thu Jul 16 16:24:36 EDT 2020:FreeSurfer2CaretConvertAndRegisterNonlinear.sh: ERROR: '/mnt/tools/HCP-4.2-Prerequisites/MSM_HOCR-3.0FSL/src/MSM/msm' command failed with return code: 1 Thu Jul 16 16:24:36 EDT 2020:PostFreeSurferPipeline.sh: While running '/mnt/tools/HCP-4.2-Prerequisites/HCPpipelines-4.2.0/PostFreeSurfer/PostFreeSurferPipeline.sh --path=/mnt/hcp01/scR21_HCP4_2_MSMSulc --subject=50016 --surfatlasdir=/mnt/HCP-4.2-Prerequisites/HCPpipelines-4.2.0/global/templates/standard_mesh_atlases --grayordinatesdir=/mnt/HCP-4.2-Prerequisites/HCPpipelines-4.2.0/global/templates/91282_Greyordinates --grayordinatesres=2 --hiresmesh=164 --lowresmesh=32 --subcortgraylabels=/mnt/tools/HCP-4.2-Prerequisites/HCPpipelines-4.2.0/global/config/FreeSurferSubcorticalLabelTableLut.txt --freesurferlabels=/mnt/tools/HCP-4.2-Prerequisites/HCPpipelines-4.2.0/global/config/FreeSurferAllLut.txt --refmyelinmaps=/mnt/tools/HCP-4.2-Prerequisites/HCPpipelines-4.2.0/global/templates/standard_mesh_atlases/Conte69.MyelinMap_BC.164k_fs_LR.dscalar.nii --regname=MSMSulc --printcom=': Thu Jul 16 16:24:36 EDT 2020:PostFreeSurferPipeline.sh: ERROR: '/mnt/tools/HCP-4.2-Prerequisites/HCPpipelines-4.2.0/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh' command failed with return code: 1

Can anyone seen this issue before?

Thank you Best Regards Sameera

ecr05 commented 4 years ago

This is because you are probably using the FSL version instead of this version. Perhaps there is a clash of paths on your computer?

sameera2004 commented 4 years ago

thanks @ecr05, the issue was source code (tar.gz) is incomplete. Matt Glasser told me to use release before. Later I saw the open issue regarding that (https://github.com/ecr05/MSM_HOCR/issues/13). Then, I cloned the git repo and complied. I was able to use "MSMSulc" to do the surface registration for all our data.

ecr05 commented 4 years ago

OK, I'm still not following this. I've copied all the source code to a zip file for the release but I'm concerned this is something else. The code should not include the newmesh library as this is no longer compatible with FSLv6 so the code available by cloning the master should be sufficient?

sameera2004 commented 4 years ago

Hi @ecr05, No zip file is not complete the time I was downloading (12 days ago). Did you upload it again recently ?

ecr05 commented 4 years ago

Today. Which zip file are you talking about?

sameera2004 commented 4 years ago

Source code(tar.gz)

ecr05 commented 4 years ago

I don't know what you mean. Where are you downloading it from?

I've uploaded a copy of the source code to the recent release. Beyond that I don't know how to help. The clone from the master will work when compiled with FSLv6.

Dr Emma C. Robinson

Apologies if you get emails outside normal work hours - I am at home with small children. I don't expect a reply at these times.

Lecturer In Medical Image Analysis

School of Biomedical Engineering and Imaging Sciences

Kings College London

Office: 5th floor, Becket House, 1 Lambeth Palace Road, London SE1 7EU, UK Mail: 4th Floor, Lambeth Wing, St Thomas' Hospital, London SE1 7EH Tel. +44 (0)20 784 89557

From: Sameera Abeykoon notifications@github.com Sent: Wednesday, July 29, 2020 8:17 PM To: ecr05/MSM_HOCR MSM_HOCR@noreply.github.com Cc: Robinson, Emma emma.robinson@kcl.ac.uk; Mention mention@noreply.github.com Subject: Re: [ecr05/MSM_HOCR] --regoption: Option doesn't exist! (#17)

Source code(tar.gz)

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sameera2004 commented 4 years ago

Hi @ecr05, This is same issue regarding to open issue you had . (https://github.com/ecr05/MSM_HOCR/issues/13).

If you uploaded zip file again, then it should be fine. I was able to solve my issue and processed my dataset using "MSMSulc". I thought this will help. Thank you so much.