Thanks, Tim, I'll try that and let you know if it worked.

On Sat, Feb 24, 2018 at 12:21 AM, Timothy Coalson <tsc...@mst.edu> 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 <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
>>>>> 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 <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@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
>>>>>> >> <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@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
>>>>>> >> <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@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 <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@humanconnect
>>>>>> ome.org>"
>>>>>> >> <hcp-users@humanconnectome.org<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
>>>>>> >> <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@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 <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@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
>>>>>> >> <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@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
>>>>>> >> <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@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
>>>>>> >> <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@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
>>>>>> >> 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
>>
>
>

_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Reply via email to