gedit with bash shell highlighting (sh). Matt
On 1/29/18, 11:50 AM, "Darko Komnenić" <[email protected]> wrote: >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:hcp-users-bounces@humanconn >>ectome.org>> >> 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-No >>tes,-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:hcp-users-bounces@humanconn >>ectome.org>> >> 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:hcp-users-bounces@humanconn >>ectome.org>> >> 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_me >>sh_atlases >> >> >>--grayordinatesdir=/home/lisak/Desktop/Pipelines/global/templates/91282_G >>reyordinates >> --grayordinatesres=2 --hiresmesh=164 --lowresmesh=32 >> >>--subcortgraylabels=/home/lisak/Desktop/Pipelines/global/config/FreeSurfe >>rSubcorticalLabelTableLut.txt >> >> >>--freesurferlabels=/home/lisak/Desktop/Pipelines/global/config/FreeSurfer >>AllLut.txt >> >> >>--refmyelinmaps=/home/lisak/Desktop/Pipelines/global/templates/standard_m >>esh_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. 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 >> [email protected]<mailto:[email protected]> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
