Your --subjectDIR flag isn’t set correctly. Take a look at Examples/Scripts/FreeSurferPipelineBatch.sh for how FreeSurferPipeline.sh should be called. (Or modify the StudyFolder, Subjlist, and EnvironmentScript entries in Examples/Scripts/FreeSurferPipelineBatch.sh script and use that to actually run FreeSurferPipeline.sh).
The Examples/Scripts are the intended entry point for users. 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 3:32 PM To: "Harms, Michael" <mha...@wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] PostFreesurfer possible bug 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<mailto: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<mailto:mha...@wustl.edu> From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> Date: Wednesday, March 20, 2019 at 3:23 PM To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto: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"/"$FreeSurferFolder" #L140 Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> Date: Wednesday, March 20, 2019 at 2:42 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] PostFreesurfer possible bug Dear experts, in the PostFreeSurferPipeline script, the FreeSurferFolder is set to be "$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<mailto: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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