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/
> 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 <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-
>> bounces@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:glass...@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-
>> bounces@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-
>> bounces@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/
>> 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
>> >> HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
>> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> >>
>> >>
>> >>
>> >>
>> >> _______________________________________________
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>> >> HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
>> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> >>
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