External Email - Use Caution
Hi Anastasia Thanks so much for the reply. My trac-path worked until last step-it says dmric path done but it exited without creating a merged_avg_16_syn_bbr and I also dont see pathoverall stat etc for individual tracts The error I get is: fslmaths /gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dpath/acomm_avg16_syn_bbr/path.pd.nii.gz -thr /gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dpath/acomm_avg16_syn_bbr/tmp.nii.gz Error: no output filename specified! I am not sure if I am supposed to specify a output file name in the configuration file ( in addition to output directory)
Also, I have used a similar configuration file for other subjects -their pre-processing is done without errors but they miss nodif_brain_mask.nii so I can't run bedpostx
Any suggestion on what I can try for both these issue is really appreciated Oshadi ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia AYENDIKI@mgh.harvard.edu Sent: Thursday, July 21, 2022 4:30 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error in path construction
Could be that you reached a memory limit? If the same analysis runs fine on your computer, then it's probably a cloud issue, not a TRACULA issue. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Shanika Jayakody shanika.jayakody@einsteinmed.edu Sent: Thursday, July 21, 2022 3:58 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula error in path construction
External Email - Use Caution
Dear Anastasia I am running tracula on FreeSurfer 7.2. It worked fine on a linux computer now I am changing to a Cloud workstation. Attached is my Configuration file. For this person the pipeline worked without errors until path reconstruction but exists saying the following I have checked my bvecs and bvals in the subjects directory and also in dmri Any suggestion for me to try would be great-thanks so much! I tried to attach the trac-all log file but then the email is too big to be posted. Oshadi
Loading DWIs from /gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri/data.nii.gz Loading mask from /gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri.bedpostX Killed Linux sjayakody 4.18.0-348.el8.x86_64 #1 SMP Mon Oct 4 12:17:22 EDT 2021 x86_64 x86_64 x86_64 GNU/Linux