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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
