Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found

[Timothy B. Brown]

Hi,

I'm curious to know more about the file systems in use that would cause 
the symbolic link operation to not be supported.


I /think/ you would be getting this "Operation not supported" error if 
the file system in which your SUBJECTS_DIR exists is a "non-Unix" or 
"non-Unix-standard" file system (maybe a "Windows" file system like 
FAT32 or NTFS, or some other Mac standard file system that also doesn't 
support symbolic links). If that is the case, moving your 
FREESURFER_HOME (FreeSurfer installation directory) over to the file 
system where your subject data is stored will not do you any good. If 
symbolic links are not supported on that file system, moving more files 
to that file system will not help.


If this is the case, then moving the subject data to a file system that 
/does/ support symbolic links might be a good move. Do you manage the 
file system that appears to be mounted at /mnt/macdata?  Can you move 
the subject data elsewhere to a file system that does support symbolic 
links?


Assuming that the file system in which FreeSurfer is installed is one 
that /does/ support symbolic links, then moving the subject data over to 
that file system might be another way to alleviate the current problem. 
But as you wrote, you may have a space limit that prevents moving all 
the subject data over to that file system.


If that is the case, then temporarily moving the data for a subject that 
is being processed through the pipelines over to the same file system on 
which FreeSurfer is installed might do the trick. (Move or copy the data 
for a subject to be processed, run the pipelines on that subject, and 
then move the data back to where it was.) This will, of course, add 
significant copying time to the beginning and end of each of your 
pipeline runs.


Another option would be to try to take advantage of the fact that 
recon-all doesn't try to create the symbolic link if there is already an 
fsaverage directory in your 
.../HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w directory.  
Before processing the data, copy the appropriate fsaverage directory 
from the FreeSurfer installation directory into an fsaverage directory 
for your subject ($SUBJECTS_DIR/fsaverage).


However, a very brief look through the recon-all script indicates that 
this is just one case in which it relies on being able to create a 
symbolic link. I haven't specifically determined if those other uses of 
symbolic links are ones that are invoked by the HCP Pipeline scripts. 
But this option would only really deal with one of those cases. It seems 
clear to me that recon-all is written with the expectation that your 
data resides on a file system that supports symbolic links. So moving in 
that direction (either by moving all your data to such a file system or 
temporarily moving the data for each subject as it is processed) is, I 
think, the way to go.


Hope that is helpful,

  Tim

On 06/29/2017 12:18 PM, Mandelli, Maria Luisa wrote:

Hi! I think I found the problem and I saw that someone else had the 
same issues before


when it tries to create the symbolic link it fails. Here


ln -s $FREESURFER_HOME/subjects/fsaverage .
ln: failed to create symbolic link `./fsaverage': Operation not supported

In old post someone suggest to set the SUBJECTs_DIR to be on the same 
file system as $FREESURFER_HOME...I can try one case but eventually if 
I have more subjects I dont think I can because of space limit


Let me know if you have suggestions!

Thank you very much


*/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:* Glasser, Matthew <glass...@wustl.edu>
*Sent:* Wednesday, June 28, 2017 4:30:28 PM
*To:* Mandelli, Maria Luisa; Brown, Tim; hcp-users@humanconnectome.org
*Cc:* Dierker, Donna
*Subject:* Re: [HCP-Users] pipeline structural PostFreesurfer wmparc 
not found
If you were to delete everything and run again do you get the same error?

Peace,

Matt.

From: "Mandelli, Maria Luisa" <marialuisa.mande...@ucsf.edu 
<mailto:marialuisa.mande...@ucsf.edu>>
Date: Wednesday, June 28, 2017 at 6:18 PM
To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>, 
"Brown, Tim" <tbbr...@wustl.edu <mailto:tbbr...@wustl.edu>>, 
"hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>>
Cc: "Dierker, Donna" <do...@wustl.edu <mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not 
found

this is the version

freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP


and yes I m running the HCP Pipelines


*/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:* Glasser, Matthew <glass...@wustl.edu <mailto:glass...@wustl.edu>>
*Sent:* Wednesday, June 28, 2017 4:10:27 PM
*To:* Mandelli, Maria Luisa; Brown, Tim; hcp-users@humanconnectome.org 
<mailto:hcp-users@humanconnectome.org>
*Cc:* Dierker, Donna
*Subject:* Re: [HCP-Users] pipeline structural PostFreesurfer wmparc 
not found
That’s weird as I change the subject directory in the pipelines but 
don’t normally have this error.  FreeSurfer just makes a symlink. 
 What version of FreeSurfer are you using?  Are you calling it using 
the HCP Pipelines?

Peace,

Matt.

From: "Mandelli, Maria Luisa" <marialuisa.mande...@ucsf.edu 
<mailto:marialuisa.mande...@ucsf.edu>>
Date: Wednesday, June 28, 2017 at 6:06 PM
To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>, 
"Brown, Tim" <tbbr...@wustl.edu <mailto:tbbr...@wustl.edu>>, 
"hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>>
Cc: "Dierker, Donna" <do...@wustl.edu <mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not 
found

Hi!thank you for your help!

the error is in the log file


Invalid argument
ERROR reading 
/mnt/macdata/groups/language/malu-cloud/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label
Linux mmandelli-vm 3.2.0-126-virtual #169-Ubuntu SMP Fri Mar 31 
14:47:56 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

So actually it s true I dont have the fsaverage directory in my 
subject folder but it s in ${FREESURFER_HOME}/subjects/fsaverage


Now the my $SUBJECT_DIR is set where are my data not $FREESURFER_HOME....


am I missing a link somewhere?


*/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:* Glasser, Matthew <glass...@wustl.edu <mailto:glass...@wustl.edu>>
*Sent:* Wednesday, June 28, 2017 4:00:56 PM
*To:* Brown, Tim; hcp-users@humanconnectome.org 
<mailto:hcp-users@humanconnectome.org>; Mandelli, Maria Luisa
*Cc:* Dierker, Donna
*Subject:* Re: [HCP-Users] pipeline structural PostFreesurfer wmparc 
not found
Perhaps I missed it but I don’t actually see the error messages you 
are getting.

Peace,

Matt.

From: <hcp-users-boun...@humanconnectome.org 
<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Timothy 
B. Brown" <tbbr...@wustl.edu <mailto:tbbr...@wustl.edu>>
Organization: Washington University in St. Louis
Date: Wednesday, June 28, 2017 at 5:00 PM
To: "hcp-users@humanconnectome.org 
<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org 
<mailto:hcp-users@humanconnectome.org>>, "marialuisa.mande...@ucsf.edu 
<mailto:marialuisa.mande...@ucsf.edu>" <marialuisa.mande...@ucsf.edu 
<mailto:marialuisa.mande...@ucsf.edu>>
Cc: "Dierker, Donna" <do...@wustl.edu <mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not 
found

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:*hcp-users-boun...@humanconnectome.org<hcp-users-boun...@humanconnectome.org> 
on behalf of Mandelli, Maria Luisa <marialuisa.mande...@ucsf.edu>
*Sent:* Monday, June 26, 2017 1:52:02 PM
*To:* Dierker, Donna
*Cc:* hcp-users@humanconnectome.org
*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 <do...@wustl.edu>
*Sent:* Monday, June 26, 2017 11:54:40 AM
*To:* Mandelli, Maria Luisa
*Cc:* hcp-users@humanconnectome.org
*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 
<marialuisa.mande...@ucsf.edu> 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
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users


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--
/Timothy B. Brown
Business & Technology Application Analyst III
Pipeline Developer (Human Connectome Project)
tbbrown(at)wustl.edu
/
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--
/Timothy B. Brown
Business & Technology Application Analyst III
Pipeline Developer (Human Connectome Project)
tbbrown(at)wustl.edu
/
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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.

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