Erin W Dickie

what command are you using to export the variable to PATH - does the existing "PATH" come before or after the msm path? You want to `export PATH=/ wrote: >...

From what you describe - I think you need: for the freesurfer - it looks like the other option you where mentioning should have worked.. The freesurfer data should be...

From the error message - it looks like it is failing (in a not very user friendly way - sorry about that) when it failing to find a freesurfer license...

Weird - sounds like it is having trouble reading the input data. Do the content of $HOME/myinputpath pass the bids validator? https://bids-standard.github.io/bids-validator/ On Wed, Feb 3, 2021 at 12:02 PM...

It looks like your filesystem might not work well with symlinks. Try running everything with the ` --no-symlinks` flag. On Tue, Dec 6, 2022 at 10:37 AM andraderenew ***@***.***> wrote:...

how are your Freesurfer outputs organized - does the file /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls/s25634_T1MPRAGE_1mm_reconall/surf/lh.pial exist? On Tue, Dec 6, 2022 at 2:17 PM andraderenew ***@***.***> wrote: > I have another error. > >...

what happens when you try `mri_info /Users/neurolab/Desktop/Stephan/Oncology/Data/Recon/Sub0002_Ses1_Scan_01_ANAT1.gz/mri/brain.finalsurfs.mgz` ?

stack overflow says it might indicate a memory error - were you maybe running any other programs at the same time as ciftify? Can you replicate the error if you...

Also sorry to late respond to this. We've seen the "setNativeLocks failed:" message in other runs of ciftify - but it ciftify still finishes correctly - so it's more of...

You need to mount the freesurfer license into the docker as well ``` docker run -ti --rm -v /Users/neurolab/Desktop/Pipeline_test3/:/data:ro -v /Users/neurolab/Desktop/Pipeline_test4:/out -v /Users/neurolab/Desktop/license.txt:/fs_licence.txt tigrlab/fmriprep_ciftify:latest /data /out participant --participant_label 1 --fs-license...