i am using version 4. this is my call - /root/hcppilelines/HCPpipelines-master/FreeSurfer/FreeSurferPipeline.sh --subject=102 --subjectDIR=/root/hcppilelines/piano_hcp/working_directory/102 --t1=/root/hcppilelines/piano_hcp/working_directory/102/T1w/T1w_acpc_dc_restore.nii.gz --t1brain=/root/hcppilelines/piano_hcp/working_directory/102/T1w/T1w_acpc_dc_restore_brain.nii.gz --t2=/root/hcppilelines/piano_hcp/working_directory/102/T1w/T2w_acpc_dc_restore.nii.gz
On Wed, 20 Mar 2019 at 22:26, Harms, Michael <mha...@wustl.edu> wrote: > > > No idea. Are you using a modified/customized version of the > HCPpipelines? Which exact version are you using? > > > > What is your exact call to FreeSurferPipeline.sh? > > > > Cheers, > > -MH > > > > -- > > Michael Harms, Ph.D. > > ----------------------------------------------------------- > > Associate Professor of Psychiatry > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave. Tel: 314-747-6173 > > St. Louis, MO 63110 Email: mha...@wustl.edu > > > > *From: *Shachar Gal <gal.shac...@gmail.com> > *Date: *Wednesday, March 20, 2019 at 3:23 PM > *To: *"Harms, Michael" <mha...@wustl.edu> > *Cc: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > *Subject: *Re: [HCP-Users] PostFreesurfer possible bug > > > > well, for some reason, when i run the piplines it gets created under the > subject directory > > this is the ls for my subject directory > > drwxr-x--- 3 shachar Users 4096 Mar 19 16:24 unprocessed > > drwxr-xr-x 6 root root 4096 Mar 20 10:47 T2w > > drwxrwxr-x 10 root root 4096 Mar 20 11:46 102 > > lrwxrwxrwx 1 root root 40 Mar 20 18:48 fsaverage -> > /usr/local/freesurfer/subjects/fsaverage > > drwxr-xr-x 8 root root 4096 Mar 20 21:28 T1w > > drwxr-xr-x 8 root root 4096 Mar 20 21:28 MNINonLinear > > > > and this is the ls for my T1w folder > > > > -rw-r----- 1 root root 9483849 Mar 20 10:25 T1w1_gdc.nii.gz > > -rw-r----- 1 root root 9483849 Mar 20 10:25 T1w.nii.gz > > -rw-r--r-- 1 root root 8576542 Mar 20 10:26 T1w_acpc.nii.gz > > drwxr-xr-x 2 root root 4096 Mar 20 10:26 ACPCAlignment > > -rw-r--r-- 1 root root 150860 Mar 20 10:35 T1w_acpc_brain_mask.nii.gz > > -rw-r--r-- 1 root root 3944745 Mar 20 10:35 T1w_acpc_brain.nii.gz > > drwxr-xr-x 2 root root 4096 Mar 20 10:35 BrainExtraction_FNIRTbased > > -rw-r--r-- 1 root root 3949152 Mar 20 10:58 T1w_acpc_dc_brain.nii.gz > > -rw-r--r-- 1 root root 31765336 Mar 20 11:09 BiasField_acpc_dc.nii.gz > > drwxr-xr-x 2 root root 4096 Mar 20 11:09 > BiasFieldCorrection_sqrtT1wXT1w > > -rw-r--r-- 1 root root 10344806 Mar 20 11:10 T1w_acpc_dc.nii.gz > > -rw-r--r-- 1 root root 27636096 Mar 20 11:10 T1w_acpc_dc_restore.nii.gz > > -rw-r--r-- 1 root root 7850049 Mar 20 11:10 > T1w_acpc_dc_restore_brain.nii.gz > > drwxr-xr-x 2 root root 4096 Mar 20 11:11 xfms > > -rw-r--r-- 1 root root 12258808 Mar 20 11:11 T2w_acpc_dc.nii.gz > > -rw-r--r-- 1 root root 28123873 Mar 20 11:11 T2w_acpc_dc_restore.nii.gz > > -rw-r--r-- 1 root root 8000278 Mar 20 11:11 > T2w_acpc_dc_restore_brain.nii.gz > > drwxr-xr-x 2 root root 4096 Mar 20 21:28 Native > > drwxr-xr-x 2 root root 4096 Mar 20 21:28 fsaverage_LR32k > > > > any idea why would that be? > > > > > > On Wed, 20 Mar 2019 at 21:49, Harms, Michael <mha...@wustl.edu> wrote: > > > > Hi, > > The FreeSurferFolder is located at $StudyFolder/$Subject/T1w/$Subject, > which is what PostFreeSurferPipeline.sh is setting up via the following > combination of lines: > > > > FreeSurferFolder="$Subject" #L101 > > T1wFolder="$StudyFolder"/"$Subject"/"$T1wFolder" #L137 > > FreeSurferFolder="$T1wFolder"/"$FreeSurferFolder" #L140 > > > > Cheers, > > -MH > > > > -- > > Michael Harms, Ph.D. > > ----------------------------------------------------------- > > Associate Professor of Psychiatry > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave. Tel: 314-747-6173 > > St. Louis, MO 63110 Email: mha...@wustl.edu > > > > *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Shachar Gal < > gal.shac...@gmail.com> > *Date: *Wednesday, March 20, 2019 at 2:42 PM > *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > *Subject: *[HCP-Users] PostFreesurfer possible bug > > > > Dear experts, > > > > in the PostFreeSurferPipeline script, the FreeSurferFolder is set to be > "$T1wFolder"/"$FreeSurferFolder" > > even though, the free surfer folder isnt actually under the T1w folder... > its right inside the subject's directory > (WorkingDirectory/SubjectNumber/SubjectNumber) > > > > is this a bug, or am i missing something? > > > > thanks, > > Shachar Gal > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. 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