External Email - Use Caution
This seems a better question for the HCP-Users (hcp-users@humanconnectome.orgmailto: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@nmr.mgh.harvard.edu on behalf of Mark Wagshul mark.wagshul@einsteinmed.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, March 2, 2023 at 9:15 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@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@einsteinmed.edumailto:mark.wagshul@einsteinmed.edu
[einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
