Hi Matt, could you please tell me which editor with shell syntax highlighting you are using? I don't see any option to change the view/display mode of the text in the one I have installed on my computer. Thanks, Darko
On 1/26/18, Glasser, Matthew <[email protected]> wrote: > Here is the relevant part of the log: > > START: FreeSurferHighResWhite > Unmatched ". > > You don’t ever get a message that this script finishes. If I paste the > current version of the script from GitHub into a editor with shell syntax > highlighting there are no unopposed quotes, so you must have done something > to your version of the script. > > Peace, > > Matt. > > From: Darko Komnenić <[email protected]<mailto:[email protected]>> > Date: Friday, January 26, 2018 at 11:58 AM > To: Matt Glasser <[email protected]<mailto:[email protected]>> > Cc: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > Subject: Re: [HCP-Users] An error in Post-FreeSurfer Pipeline > > If I interpreted the error message correctly, the unmatched quote error > appears after recon-all, and right after the pipeline tries to perform > FreeSurferHiresWhite.sh > This is what that part of script looks like in my case: > #Highres white stuff and Fine Tune T2w to T1w Reg > log_Msg "High resolution white matter and fine tune T2w to T1w > registration" > "$PipelineScripts"/FreeSurferHiresWhite.sh "$SubjectID" "$SubjectDIR" > "$T1wImage" "$T2wImage" > > There doesn't seem to me to be a quote problem, but I'm not sure? Also, the > FreeSurferHiresWhite.sh script was never edited, and I've had the pipelines > run successfully before, so I doubt that the problem is there. > Any ideas on where I should keep looking (i.e. which particular script or > section)? Thanks! > > On Fri, Jan 26, 2018 at 6:34 PM, Darko Komnenić > <[email protected]<mailto:[email protected]>> wrote: > I did the usual changes of subject list and folder paths, as well as the > number of cores in the FreeSurfer script (not the FreeSurferPipelineBatch, > but the one that's found in the Pipelines/FreeSurfer folder), I will go over > them now, thanks! > > On Fri, Jan 26, 2018 at 6:24 PM, Glasser, Matthew > <[email protected]<mailto:[email protected]>> wrote: > Did you accidentally change on of the pipeline scripts? If you look at the > end of that log file it complaining about an unmatched quote. > > Peace, > > Matt. > > From: > <[email protected]<mailto:[email protected]>> > on behalf of Darko Komnenić > <[email protected]<mailto:[email protected]>> > Date: Friday, January 26, 2018 at 10:58 AM > > Cc: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > Subject: Re: [HCP-Users] An error in Post-FreeSurfer Pipeline > > Dear HCP experts, I reran the PreFS and FS pipeline, with an added argument > for generating error and output logs. Once again, wmparc_1mm is not inside > the T1w subfolder within individual partcipants' folders. I am now sending > the log attached. If someone could take a look and tell me what went wrong, > I'd be very grateful! > Best, > Darko > > On Mon, Jan 22, 2018 at 8:25 PM, Harms, Michael > <[email protected]<mailto:[email protected]>> wrote: > > If you want to separate stderr and stdout at the terminal you can also do > (in an ‘sh/bash’ shell): > > ./FreeSurferPipelineBatch.sh 2> stderr.txt 1> stdout.txt > > cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid > Ave<https://maps.google.com/?q=660+South+Euclid+Ave&entry=gmail&source=g>. > Tel: 314-747-6173<tel:(314)%20747-6173> > St. Louis, MO 63110 Email: > [email protected]<mailto:[email protected]> > > From: "Glasser, Matthew" <[email protected]<mailto:[email protected]>> > Date: Monday, January 22, 2018 at 12:58 PM > To: Darko Komnenić <[email protected]<mailto:[email protected]>>, > "Harms, Michael" <[email protected]<mailto:[email protected]>> > > Cc: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > Subject: Re: [HCP-Users] An error in Post-FreeSurfer Pipeline > > > ./FreeSurferPipelineBatch.sh > log.txt 2>&1 would collect both stderr and > stdout into a single file. One of the nice things about using SGE or a > similar software is they automatically put stderr and stdout into separate > log files. > > Peace, > > Matt. > > From: Darko Komnenić <[email protected]<mailto:[email protected]>> > Date: Monday, January 22, 2018 at 12:55 PM > To: "Harms, Michael" <[email protected]<mailto:[email protected]>> > Cc: Matt Glasser <[email protected]<mailto:[email protected]>>, > "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > Subject: Re: [HCP-Users] An error in Post-FreeSurfer Pipeline > > Thanks Michael and Matt. > I indeed ran it from the terminal, as described on this website: > https://github.com/Washington-University/Pipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage#structural-preprocessing > What would be your recommendation now? Rerun the pipelines but add a > modification like this? > > ./FreeSurferPipelineBatch.sh |& tee ~/filename.txt > > On Mon, Jan 22, 2018 at 7:38 PM, Harms, Michael > <[email protected]<mailto:[email protected]>> wrote: > > To expand on that slightly, the HCP Pipelines themselves don’t automatically > generate log files. You need to either capture the output to the terminal > (e.g., using the ‘tee’ command) if running in a terminal, or use appropriate > arguments in your compute cluster to capture the stderr and stdout. > > Cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid > Ave<https://maps.google.com/?q=660+South+Euclid+Ave&entry=gmail&source=g>. > Tel: 314-747-6173<tel:(314)%20747-6173> > St. Louis, MO 63110 Email: > [email protected]<mailto:[email protected]> > > From: > <[email protected]<mailto:[email protected]>> > on behalf of "Glasser, Matthew" > <[email protected]<mailto:[email protected]>> > Date: Monday, January 22, 2018 at 12:35 PM > To: Darko Komnenić <[email protected]<mailto:[email protected]>> > Cc: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > Subject: Re: [HCP-Users] An error in Post-FreeSurfer Pipeline > > I don’t know how you launched the pipelines. If you used SGE you would look > in the stderr or stdout log files (e and o). If you just ran this in a > terminal and closed the terminal, the logs may no longer be available. > > Peace, > > Matt. > > From: Darko Komnenić <[email protected]<mailto:[email protected]>> > Date: Monday, January 22, 2018 at 12:03 PM > To: Matt Glasser <[email protected]<mailto:[email protected]>> > Cc: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > Subject: Re: [HCP-Users] An error in Post-FreeSurfer Pipeline > > Hi Matt, > not sure if I can't find it, or if it's just not there, but I don't see that > log anywhere in the subject folder. Attached are the screenshot of the T1w > folder for a particular participant, subfolder with the participant's name > inside the T1w folder, as well as "scripts" subfolder where recon-all logs > are found. Any idea where the complete log for FS Pipeline should be? > Thanks! > [line image 1][line image 2] > [line image 4] > > On Mon, Jan 22, 2018 at 6:22 PM, Glasser, Matthew > <[email protected]<mailto:[email protected]>> wrote: > That is not a complete FreeSurfer run, so you need to look at the log of the > FreeSurfer HCP Pipeline itself. > > Peace, > > Matt. > > From: Darko Komnenić <[email protected]<mailto:[email protected]>> > Date: Monday, January 22, 2018 at 11:18 AM > > To: Matt Glasser <[email protected]<mailto:[email protected]>> > Cc: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > Subject: Re: [HCP-Users] An error in Post-FreeSurfer Pipeline > > Thanks! > In the ${StudyFolder}/${Subject}/T1w/${Subject}/Scripts folder, there are > recon-all.log and recon-all-status.log files (which is what I assume I > should be looking at since recon-all is the main part of the FS pipeline). > The latter just lists the times when certain steps were completed, but the > former is really massive, and I'm not sure where to start looking. At the > very end it says that it finished without error, but in the middle there are > some things that seem like warnings, but I can't really understand them. If > someone could take a look, I would be very grateful! > Thanks a lot in advance! > Darko > > On Mon, Jan 22, 2018 at 6:11 PM, Glasser, Matthew > <[email protected]<mailto:[email protected]>> wrote: > Look inside the FreeSurfer folder in > ${StudyFolder}/${Subject}/T1w/${Subject} > > Peace, > > Matt. > > From: Darko Komnenić <[email protected]<mailto:[email protected]>> > Date: Monday, January 22, 2018 at 11:08 AM > To: Matt Glasser <[email protected]<mailto:[email protected]>> > Cc: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > Subject: Re: [HCP-Users] An error in Post-FreeSurfer Pipeline > > 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]<mailto:[email protected]>> wrote: > I would look into the logs for the FreeSurfer pipeline. Perhaps it did not > complete correctly. > > Peace, > > Matt. > > From: > <[email protected]<mailto:[email protected]>> > on behalf of Darko Komnenić > <[email protected]<mailto:[email protected]>> > Date: Monday, January 22, 2018 at 10:59 AM > To: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[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]<mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[email protected]> > 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. 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