I would look into the logs for the FreeSurfer pipeline. Perhaps it did not complete correctly.
Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Darko Komnenić <komnen...@gmail.com<mailto:komnen...@gmail.com>> Date: Monday, January 22, 2018 at 10:59 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] An error in Post-FreeSurfer Pipeline Dear HCP experts, I am trying to compare the cortical myelin content between patients and healthy controls. I ran the pre-FreeSurfer and FreeSurfer pipelines, and they finished without reporting an error. When I tried to run the Post-FreeSurfer pipeline, I received the following error note after each individual participant in the subject list (the only thing changing are the file paths): START: FS2CaretConvertRegisterNonlinear FreeSurfer2CaretConvertAndRegisterNonLinear.sh: RegName: FS Cannot open volume /home/lisak/Desktop/NMDA_HCP/controls/VIMS_HC_070/T1w/wmparc_1mm for reading! set -- --path=/home/lisak/Desktop/NMDA_HCP/controls --subject=VIMS_HC_070 --surfatlasdir=/home/lisak/Desktop/Pipelines/global/templates/standard_mesh_atlases --grayordinatesdir=/home/lisak/Desktop/Pipelines/global/templates/91282_Greyordinates --grayordinatesres=2 --hiresmesh=164 --lowresmesh=32 --subcortgraylabels=/home/lisak/Desktop/Pipelines/global/config/FreeSurferSubcorticalLabelTableLut.txt --freesurferlabels=/home/lisak/Desktop/Pipelines/global/config/FreeSurferAllLut.txt --refmyelinmaps=/home/lisak/Desktop/Pipelines/global/templates/standard_mesh_atlases/Conte69.MyelinMap_BC.164k_fs_LR.dscalar.nii --regname=FS --printcom= . /home/lisak/Desktop/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh So in this particular example, VIMS_HC_070 is a subject codename, and s/he is in the "controls" subfolder. When I navigate to ~/controls/VIMS_HC_070/T1w folder, there is nothing (neither file or folder) called wmparc_1mm in there. So it seems like one of the previous pipelines (maybe the FreeSurfer one) finished in a faulty way? Some maybe relevant background information: I was able to run all the pipelines without issue last summer, but in the meantime a colleague updated python on the computer by downloading the version 3.6, which made FSL scripts not work (since they require python 2). In an attempt to fix it, he uninstalled the entire python3 from the computer, which basically incapacitated the entire system. We have since restored it more or less to its previous functioning, but I cannot be 100% sure that there aren't maybe some residual glitches still left. After running the PreFS pipeline, there were 17 items in the T1w subfolder in each participant's folder, and after the FS pipeline, the number went up to 20. I'm not sure if this is enough to let you know whether something was missing after each step. I'm looking forward to any help or suggestions you can provide! Thanks in advance, Darko _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
