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 <komnen...@gmail.com> wrote:

> 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:ko
>>>>> mnen...@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:ko
>>>>> mnen...@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:ko
>>>>> mnen...@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:ko
>>>>> mnen...@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:ko
>>>>> mnen...@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/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
>>>>> >> HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
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