Hi Matt, this is most likely a very silly question, but where can I find the logs? Best, Darko
On Mon, Jan 22, 2018 at 6:06 PM, Glasser, Matthew <[email protected]> wrote: > I would look into the logs for the FreeSurfer pipeline. Perhaps it did > not complete correctly. > > Peace, > > Matt. > > From: <[email protected]> on behalf of Darko Komnenić > <[email protected]> > Date: Monday, January 22, 2018 at 10:59 AM > To: "[email protected]" <[email protected]> > 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 > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
