Dear FreeSurfer experts,

 

I hope this email finds you all well.

I am trying to run TRACULA (FreeSurfer version 7.2.0) on our university cluster computing system and am getting stuck on the bedpostx command. The staff at our computing cluster think that it might be an issue with a slurm script created along with the -bedp command (“it is an issue with the slurm command formed inside (with srun command)”), but are not sure and were unable to help beyond that as they are not experienced in FreeSurfer.

I am hoping a FreeSurfer expert here might be able to help me figure out how to fix this error.

 

I run these commands without errors:

recon-all -i /fs0/users/harrioem/DWI_practice/rawdata/RC3001_v1/T1.nii -s RC3001_v1 -sd /fs0/users/harrioem/DWI_practice/subjects -all

segmentThalamicNuclei.sh RC3001_v1

trac-all -prep -c /fs0/users/harrioem/DWI_practice/subjects/RC3001_v1/dmrirc.file

 

When I try to run:

trac-all -bedp -c /fs0/users/harrioem/DWI_practice/subjects/RC3001_v1/dmrirc.file

 

I get this error:

(base) [harrioem@cutting subjects]$ trac-all -bedp -c /fs0/users/harrioem/DWI_practice/subjects/RC3001_v1/dmrirc.file

INFO: SUBJECTS_DIR is /fs0/users/harrioem/DWI_practice/subjects

INFO: Diffusion root is /fs0/users/harrioem/DWI_practice/subjects

Actual FREESURFER_HOME /cvmfs/oasis.opensciencegrid.org/accre/mirror/common/easybuild/software/FreeSurfer/7.2.0

ln -sf ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz /fs0/users/harrioem/DWI_practice/subjects/RC3001_v1/dmri/nodif_brain_mask.nii.gz

WARN: Running bedbostx locally - this might take a while

WARN: It is recommended to run this step on a cluster

bedpostx_mgh -n 2 -model 1 /fs0/users/harrioem/DWI_practice/subjects/RC3001_v1/dmri

subjectdir is /fs0/users/harrioem/DWI_practice/subjects/RC3001_v1/dmri

Making bedpostx directory structure

Queuing preprocessing stages

srun: error: Invalid --mail-type specification

Queuing parallel processing stage

 

----- Bedpostx Monitor -----

srun: error: invalid partition specified: normal

srun: error: Unable to allocate resources: Invalid partition name specified

Queuing post processing stage

srun: error: invalid partition specified: normal

srun: error: Unable to allocate resources: Invalid partition name specified

 

 

I have attached the dmrirc.file and the trac-all log hoping they might help. The dmrirc.file only contains 3 tracts for ease of testing but will eventually (once everything works!) contain them all.

 

 

Any assistance anyone might be able to provide would be so greatly appreciated.

 

Thank you so very much!

Emily Harriott

PhD student, Vanderbilt University