Hi Maria,
My bet is that the error you are seeing is coming from the last call to
recon-all in the FreeSurferPipeline.sh script. This would be in the
statements that look like:
#Final Recon-all Steps
log_Msg "Final Recon-all Steps"
recon-all -subjid $SubjectID -sd $SubjectDIR -surfvolume -parcstats
-cortparc2 -parcstats2 -cortparc3 -parcstats3 -cortribbon -segstats
-aparc2aseg -wmparc -balabels -label-exvivo-ec -openmp ${num_cores}
${seed_cmd_appendix}
log_Msg "Completed"
In particular, it would be the line that is shown in red above. (Note,
depending on the version of the HCP Pipelines you are using, your
version of the recon-all command may not have the -openmp ${num_cores}
or the ${seed_cmd_appendix} in it.)
The -balabels option is asking the recon-all command to "Create Brodmann
area labels by mapping from fsaverage".
You probably won't have an fsaverage directory in the subject directory
which you are processing (in your case the
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w directory). In
that case, recon-all creates one for you as a symbolic link to the
$FREESURFER_HOME/subjects/fsaverage directory.
It is in a subdirectory of that created fsaverage directory that files
like lh.BA1.label should be found.
So, the first things that needs to be determined in your case are:
* At the time of this failure, does the
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage
directory exist at all?
* If it does exist, is it a symbolic link to somewhere in your
FreeSurfer installation? (I believe it should be a link to the
${FREESURFER_HOME}/subjects/fsaverage directory.)
* What is the value of your FREESURFER_HOME environment variable?
Can you check into those things and let me know what you find?
Best Regards,
Tim
On 06/28/2017 09:41 AM, Mandelli, Maria Luisa wrote:
Hi!I installed the freesurfer-hcp and I got an error in the Freesurfer
pipeline here...in the label directory I dont see the file that the
script is looking for! (lh.BA1.label)
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
/usr/local/freesurfer/bin/recon-all
PWD
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/hcp350014/label
CMD mri_label2label --srcsubject fsaverage --srclabel
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label
--trgsubject hcp350014 --trglabel ./lh.BA1.label --hemi lh --regmethod
surface
*/Maria Luisa Mandelli, PhD/*
/Assistant Professional Researcher/
*University of California, San Francisco*
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center**
_http://memory.ucsf.edu/_
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
------------------------------------------------------------------------
*From:* [email protected]
<[email protected]> on behalf of Mandelli, Maria
Luisa <[email protected]>
*Sent:* Monday, June 26, 2017 1:52:02 PM
*To:* Dierker, Donna
*Cc:* [email protected]
*Subject:* Re: [HCP-Users] pipeline structural PostFreesurfer wmparc
not found
thank you very much!I have the standard Freesurfer version!
I m going to try to the HCP one now!
*/Maria Luisa Mandelli, PhD/*
/Assistant Professional Researcher/
*University of California, San Francisco*
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center**
_http://memory.ucsf.edu/_
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
------------------------------------------------------------------------
*From:* Dierker, Donna <[email protected]>
*Sent:* Monday, June 26, 2017 11:54:40 AM
*To:* Mandelli, Maria Luisa
*Cc:* [email protected]
*Subject:* Re: [HCP-Users] pipeline structural PostFreesurfer wmparc
not found
Many of the HCP experts are at OHBM, so replies might take longer.
I know from my own experience with HCP output to look here for the
Freesurfer subject directories:
subject-id/T1w/subject-id/label/*
subject-id/T1w/subject-id/mri/*
subject-id/T1w/subject-id/surf/*
…
Also see page 21 here:
http://humanconnectome.org/storage/app/media/documentation/s1200/HCP_S1200_Release_Appendix_III.pdf
Hopefully there is no problem! :)
But I must point out that there is a difference between the Freesurfer
v5.3 distribution and Freesurfer 5.3-HCP.
The latter uses both T1w & T2w images, which makes a big difference
(e.g., for myelin maps).
Not sure which you used, but it is an important difference.
> On Jun 26, 2017, at 12:27 PM, Mandelli, Maria Luisa
<[email protected]> wrote:
>
> Hi!
> I m running the structural HCP pipeline and I m using Freesurfer v5.3
> It seems that the job finished without errors but I dont see the
files in the T1w folder of the subject.
> For example the wmparc_1mm files
> I m not sure where is the problem!
> Thank you
>
>
> Maria Luisa Mandelli, PhD
> Assistant Professional Researcher
>
> University of California, San Francisco
> 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
>
> Language Neurobiology Lab
> http://albalab.ucsf.edu/
> Memory and Aging Center
> http://memory.ucsf.edu/
> UCSF Dyslexia Center
> http://dyslexia.ucsf.edu/
>
> _______________________________________________
> HCP-Users mailing list
> [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.
_______________________________________________
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
--
/Timothy B. Brown
Business & Technology Application Analyst III
Pipeline Developer (Human Connectome Project)
tbbrown(at)wustl.edu
/
------------------------------------------------------------------------
The material in this message is private and may contain Protected
Healthcare Information (PHI). 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]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
