Thanks, Tim, I'll try that and let you know if it worked. On Sat, Feb 24, 2018 at 12:21 AM, Timothy Coalson <[email protected]> wrote:
> The error message appears to be from syntax in a bash script, so it should > be possible to track it down. > > If you put "set -x" at the top of the script it fails in and rerun it, it > will tell you each command before executing it, which should help narrow > down which line is the problem. If the line is calling or sourcing another > script, do the same with that script. This should help you find which bash > script has the unmatched quote. > > Tim > > > On Fri, Feb 23, 2018 at 1:03 PM, Darko Komnenić <[email protected]> > wrote: > >> Alright, thank you! >> Darko >> >> On Fri, Feb 23, 2018 at 6:20 PM, Glasser, Matthew <[email protected]> >> 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 <[email protected]> >>> Date: Friday, February 23, 2018 at 6:25 AM >>> >>> To: Matt Glasser <[email protected]> >>> Cc: "[email protected]" <[email protected]> >>> 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 <[email protected]> >>> 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 <[email protected]> >>>> Date: Thursday, February 22, 2018 at 4:49 AM >>>> To: Matt Glasser <[email protected]> >>>> >>>> Cc: "[email protected]" <[email protected]> >>>> 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 <[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/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 >>>>> SetUpHCPPipeline 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:ko >>>>>> [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:hcp-users@humanconnect >>>>>> ome.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 >>>>>> >> <[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-bo >>>>>> unces@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:hcp-users@humanconnect >>>>>> ome.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 >>>>>> >> <[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:gla >>>>>> [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:hcp-users@humanconnect >>>>>> ome.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 <[email protected]<mailto:ko >>>>>> [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:hcp-users@humanconnect >>>>>> ome.org>" >>>>>> >> <[email protected]<mailto:hcp-users@humanconnect >>>>>> ome.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 >>>>>> >> <[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-bo >>>>>> unces@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:hcp-users@humanconnect >>>>>> ome.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 <[email protected]<mailto:ko >>>>>> [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:hcp-users@humanconnect >>>>>> ome.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 >>>>>> >> <[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:ko >>>>>> [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:hcp-users@humanconnect >>>>>> ome.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 >>>>>> >> <[email protected]<mailto:[email protected]>> wrote: >>>>>> >> Look inside the FreeSurfer folder in >>>>>> >> ${StudyFolder}/${Subject}/T1w/${Subject} >>>>>> >> >>>>>> >> Peace, >>>>>> >> >>>>>> >> Matt. >>>>>> >> >>>>>> >> From: Darko Komnenić <[email protected]<mailto:ko >>>>>> [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:hcp-users@humanconnect >>>>>> ome.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 >>>>>> >> <[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-bo >>>>>> unces@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:hcp-users@humanconnect >>>>>> ome.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/SetUpHCPPipel >>>>>> ine.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 >> > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
