External Email - Use Caution
This seems a better question for the HCP-Users (hcp-users(a)humanconnectome.org<mailto:hcp-users@humanconnectome.org>) list than the FreeSurfer list, given that you are using the HCP Pipelines and MSM is an FSL rather than a FreeSurfer tool. When you repost on the HCP-Users list, you should probably note how you are calling the PostFreeSurfer pipeline.
Matt.
From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Mark Wagshul <mark.wagshul(a)einsteinmed.edu>
Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>
Date: Thursday, March 2, 2023 at 9:15 AM
To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu>
Subject: [Freesurfer] MSM error
External Email - Use Caution
Dear Freesurfer experts,
Hi. I am running “msm” within a singularity package of the HCP pipeline (“PostFreesurfer”), and running into a strange error. Note – I have processed 15 subjects successfully without running into this error, it’s only occurring for one subject.
Here is the msm call it’s failing on:
/public/apps/fsl/6.0.5_cpu/bin/msm --conf=/gs/gsfs0/users/mrrc-all/PROJECTS/P65-ALL/SCRIPTS/HCP//MSMConfig/MSMSulcStrainFinalconf --inmesh=BIDS_HCP/hcp_output//sub-A000/MNINonLinear/Native/sub-A000.L.sphere.rot.native.surf.gii --refmesh=BIDS_HCP/hcp_output//sub-A000/MNINonLinear/sub-A013.L.sphere.164k_fs_LR.surf.gii --indata=BIDS_HCP/hcp_output//sub-A000/MNINonLinear/Native/sub-A000.L.sulc.native.shape.gii --refdata=BIDS_HCP/hcp_output//sub-A000/MNINonLinear/sub-A000.L.refsulc.164k_fs_LR.shape.gii --out=BIDS_HCP/hcp_output//sub-A000/MNINonLinear/Native/MSMSulc/L. –verbose
And the error it reports is:
terminate called after throwing an instance of 'std::runtime_error'
what(): Cannot create directory BIDS_HCP/hcp_output//sub-A000/MNINonLinear/Native/MSMSulc/L.logdir++++++++++++++++++++
Write permissions in that folder are fine, so I’m not sure what this is coming from. I’m also puzzled that it is trying to create a directory with so many “+” signs, there are no currect L.logdir folders in there.
Thank you in advance for any thoughts on how to debug this.
Mark
____________________
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461
Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wagshul(a)einsteinmed.edu<mailto:mark.wagshul@einsteinmed.edu>
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