Alright, thank you! Darko On Fri, Feb 23, 2018 at 6:20 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
> No we don’t use python in that pipeline. I am afraid that no one else has > reported this and so I think the issue must be unique to your system. You > might trying on another computer/or in a VM where you install stuff from > scratch and see if the issue persists. > > Peace, > > Matt. > > From: Darko Komnenić <komnen...@gmail.com> > Date: Friday, February 23, 2018 at 6:25 AM > > To: Matt Glasser <glass...@wustl.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] An error in Post-FreeSurfer Pipeline > > Hi Matt, > Yes, I believe so. It is the FreeSurfer 5.3.0-HCP. > I also downloaded the latest version of that script and compared it with > the one I have in my Pipelines folder and they seem identical. > Could it maybe be python issue? Is FreeSurferHighResWhite written in > python2? Because I had some issues with that before. > Thanks, > Darko > > On Fri, Feb 23, 2018 at 1:29 AM, Glasser, Matthew <glass...@wustl.edu> > wrote: > >> Is your FreeSurfer set up correctly? I just checked the current git >> master version of FreeSurferHighResWhite and there was no syntax issue or >> missing “ >> >> Peace, >> >> Matt. >> >> From: Darko Komnenić <komnen...@gmail.com> >> Date: Thursday, February 22, 2018 at 4:49 AM >> To: Matt Glasser <glass...@wustl.edu> >> >> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Subject: Re: [HCP-Users] An error in Post-FreeSurfer Pipeline >> >> Hi Matt, >> yes, I am using bash. >> >> On Wed, Feb 21, 2018 at 9:56 PM, Glasser, Matthew <glass...@wustl.edu> >> wrote: >> >>> That is the shell command to source a script. Are you using bash as >>> your shell? >>> >>> Peace, >>> >>> Matt. >>> >>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Darko >>> Komnenić <komnen...@gmail.com> >>> Date: Wednesday, February 21, 2018 at 2:20 PM >>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>> >>> 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/Deskt >>> op/NMDA_HCP/controls/VIMS_HC_070/T1w >>> --t1=/home/lisak/Desktop/NMDA_HCP/controls/VIMS_HC_070/T1w/T >>> 1w_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/T >>> 2w_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 <glass...@wustl.edu> >>> wrote: >>> >>>> gedit with bash shell highlighting (sh). >>>> >>>> Matt >>>> >>>> On 1/29/18, 11:50 AM, "Darko Komnenić" <komnen...@gmail.com> 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 <glass...@wustl.edu> 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 <komnen...@gmail.com<mailto:komnen...@gmail.com >>>> >> >>>> >> Date: Friday, January 26, 2018 at 11:58 AM >>>> >> To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> >>>> >> Cc: >>>> >>"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" >>>> >> <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org >>>> >> >>>> >> 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 >>>> >> <komnen...@gmail.com<mailto:komnen...@gmail.com>> 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 >>>> >> <glass...@wustl.edu<mailto:glass...@wustl.edu>> 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: >>>> >> >>>> >><hcp-users-boun...@humanconnectome.org<mailto:hcp-users-bo >>>> unces@humanconn >>>> >>ectome.org>> >>>> >> on behalf of Darko Komnenić >>>> >> <komnen...@gmail.com<mailto:komnen...@gmail.com>> >>>> >> Date: Friday, January 26, 2018 at 10:58 AM >>>> >> >>>> >> Cc: >>>> >>"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" >>>> >> <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org >>>> >> >>>> >> 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 >>>> >> <mha...@wustl.edu<mailto:mha...@wustl.edu>> 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: >>>> >> mha...@wustl.edu<mailto:mha...@wustl.edu> >>>> >> >>>> >> From: "Glasser, Matthew" <glass...@wustl.edu<mailto:gla >>>> ss...@wustl.edu>> >>>> >> Date: Monday, January 22, 2018 at 12:58 PM >>>> >> To: Darko Komnenić <komnen...@gmail.com<mailto:komnen...@gmail.com >>>> >>, >>>> >> "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> >>>> >> >>>> >> Cc: >>>> >>"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" >>>> >> <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org >>>> >> >>>> >> 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 <komnen...@gmail.com<mailto:komnen...@gmail.com >>>> >> >>>> >> Date: Monday, January 22, 2018 at 12:55 PM >>>> >> To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> >>>> >> Cc: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, >>>> >> "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org >>>> >" >>>> >> <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org >>>> >> >>>> >> 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 >>>> >> <mha...@wustl.edu<mailto:mha...@wustl.edu>> 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: >>>> >> mha...@wustl.edu<mailto:mha...@wustl.edu> >>>> >> >>>> >> From: >>>> >> >>>> >><hcp-users-boun...@humanconnectome.org<mailto:hcp-users-bo >>>> unces@humanconn >>>> >>ectome.org>> >>>> >> on behalf of "Glasser, Matthew" >>>> >> <glass...@wustl.edu<mailto:glass...@wustl.edu>> >>>> >> Date: Monday, January 22, 2018 at 12:35 PM >>>> >> To: Darko Komnenić <komnen...@gmail.com<mailto:komnen...@gmail.com>> >>>> >> Cc: >>>> >>"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" >>>> >> <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org >>>> >> >>>> >> 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 <komnen...@gmail.com<mailto:komnen...@gmail.com >>>> >> >>>> >> Date: Monday, January 22, 2018 at 12:03 PM >>>> >> To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> >>>> >> Cc: >>>> >>"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" >>>> >> <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org >>>> >> >>>> >> 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 >>>> >> <glass...@wustl.edu<mailto:glass...@wustl.edu>> 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 <komnen...@gmail.com<mailto:komnen...@gmail.com >>>> >> >>>> >> Date: Monday, January 22, 2018 at 11:18 AM >>>> >> >>>> >> To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> >>>> >> Cc: >>>> >>"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" >>>> >> <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org >>>> >> >>>> >> 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 >>>> >> <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: >>>> >> Look inside the FreeSurfer folder in >>>> >> ${StudyFolder}/${Subject}/T1w/${Subject} >>>> >> >>>> >> Peace, >>>> >> >>>> >> Matt. >>>> >> >>>> >> From: Darko Komnenić <komnen...@gmail.com<mailto:komnen...@gmail.com >>>> >> >>>> >> Date: Monday, January 22, 2018 at 11:08 AM >>>> >> To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> >>>> >> Cc: >>>> >>"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" >>>> >> <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org >>>> >> >>>> >> 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 >>>> >> <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: >>>> >> 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-bo >>>> unces@humanconn >>>> >>ectome.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/templa >>>> tes/standard_me >>>> >>sh_atlases >>>> >> >>>> >> >>>> >>--grayordinatesdir=/home/lisak/Desktop/Pipelines/global/te >>>> mplates/91282_G >>>> >>reyordinates >>>> >> --grayordinatesres=2 --hiresmesh=164 >>>> --lowresmesh=32 >>>> >> >>>> >>--subcortgraylabels=/home/lisak/Desktop/Pipelines/global/c >>>> onfig/FreeSurfe >>>> >>rSubcorticalLabelTableLut.txt >>>> >> >>>> >> >>>> >>--freesurferlabels=/home/lisak/Desktop/Pipelines/global/co >>>> nfig/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 >>>> >> 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<mailto:HCP-Users@humanconnectome.org> >>>> >> 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 >>>> >> 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 >>> >>> >> > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
