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.edu

 

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.