Hi Matt, yes, I am using bash. On Wed, Feb 21, 2018 at 9:56 PM, Glasser, Matthew <[email protected]> wrote:
> That is the shell command to source a script. Are you using bash as your > shell? > > Peace, > > Matt. > > From: <[email protected]> on behalf of Darko Komnenić > <[email protected]> > Date: Wednesday, February 21, 2018 at 2:20 PM > Cc: "[email protected]" <[email protected]> > > Subject: Re: [HCP-Users] An error in Post-FreeSurfer Pipeline > > Dear HCP experts, > I wrote to this mailing list about a month ago with a problem that the > FreeSurfer Pipeline would get interrupted after finishing recon-all, and > starting FreeSurferHiResWhite script. The error log showed > START: FreeSurferHighResWhite > Unmatched ". > and below > set -- --subject=VIMS_HC_070 --subjectDIR=/home/lisak/ > Desktop/NMDA_HCP/controls/VIMS_HC_070/T1w > --t1=/home/lisak/Desktop/NMDA_HCP/controls/VIMS_HC_070/T1w/ > T1w_acpc_dc_restore.nii.gz --t1brain=/home/lisak/Desktop/ > NMDA_HCP/controls/VIMS_HC_070/T1w/T1w_acpc_dc_restore_brain.nii.gz > --t2=/home/lisak/Desktop/NMDA_HCP/controls/VIMS_HC_070/T1w/ > T2w_acpc_dc_restore.nii.gz --printcom= > . /home/lisak/Desktop/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh > > > The suggestion I got was that I probably removed or added a quote > somewhere while editing the scripts. However, after looking carefully and > multiple times at FreeSurferPipelineBatch.sh, FreeSurferPipeline.sh, as > well as FreeSurferHiresWhite.sh, I have not been able to find any unmatched > quotes. > > Looking at the message above the only thing that seems a bit weird is a > dot between the equal sign and the beginning of the file path for the SetUp > HCPPipeline script, after the --printcom segment. We don't see that dot > and space after other headings, such as subject, t1, etc. However, I > haven't been able to identify what is causing that space and dot to appear > only after printcom. The corresponding segments of my script files seem > identical to the scripts that are in the latest release from the GitHub > website. > > Does this seem like a reasonable line of thought (that a space and a dot > between the equal sign and the beginning of the path are not normal)? And > if so, do you have any idea what might be causing it? > Thanks in advance for any suggestions! > Best, > Darko > > > On Mon, Jan 29, 2018 at 10:39 PM, Glasser, Matthew <[email protected]> > wrote: > >> 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 >> <https://maps.google.com/?q=8134+%0D+%3E%3E+660+South+Euclid+%0D+%3E%3E+%0D+%3E%3EAve&entry=gmail&source=g> >> >> 660 South Euclid >> <https://maps.google.com/?q=8134+%0D+%3E%3E+660+South+Euclid+%0D+%3E%3E+%0D+%3E%3EAve&entry=gmail&source=g> >> >> >> >>Ave >> <https://maps.google.com/?q=8134+%0D+%3E%3E+660+South+Euclid+%0D+%3E%3E+%0D+%3E%3EAve&entry=gmail&source=g> >> <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 >> <https://maps.google.com/?q=8134+%0D+%3E%3E+660+South+Euclid+%0D+%3E%3E+%0D+%3E%3EAve&entry=gmail&source=g> >> >> 660 South Euclid >> <https://maps.google.com/?q=8134+%0D+%3E%3E+660+South+Euclid+%0D+%3E%3E+%0D+%3E%3EAve&entry=gmail&source=g> >> >> >> >>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/templa >> tes/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/templ >> ates/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 > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
