Re: [Freesurfer] Retinotopic mapping using selxavg3-sess

Yes. I'm surprised that FSL would run at all without that defined. doug

On 06/23/2014 12:44 PM, Alan Lee wrote:

Yes, I've installed FSL already. I can launch FSL by typing "fslview" in the command window.

However, it seems that the $FSLDIR is not defined. Should I define it manually using setenv before running selxavg3-sess?

-- Alan Lee sites.google.com/site/alanlflee/ http://sites.google.com/site/alanlflee/

On Mon, Jun 23, 2014 at 4:03 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Do you have FSL installed? If so, what is your $FSLDIR?


On 06/19/2014 03:03 PM, Alan Lee wrote:
>
> Thanks, Doug. I think I've kind of sorted that one out by creating a
> folder called "Retinotopy" under
> freesurfer/subjects/Retinotopy/33333/, which contains the 001/, ...
> 004/ folders containing those their corresponding (polar and eccen)
> rtopy.par and f.nii files.
>
> But now I have another problem. When I run
>
> selxavg3-sess -a Retintopy.33333.lh -s 33333
>
> , it runs up to the point as below, where it's "using FSL's BET to
> Extract Brain".
>
> # ---------- Using FSL's BET to Extract Brain------------------ #
> /usr/local/freesurfer/subjects/Retinotopy/33333/Retinotopy
> bet.fsl /tmp/mkbrainmask_9112/in.nii /tmp/mkbrainmask_9112/brain
-m -f 0.1
> /usr/local/freesurfer//bin/bet.fsl: 1:
> /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found
> /usr/local/freesurfer//bin/bet.fsl: 1:
> /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found
> /usr/local/freesurfer//bin/bet.fsl: 1:
> /usr/local/freesurfer//bin/bet.fsl: /bin/imtest: not found
> /usr/local/freesurfer//bin/bet.fsl: 153: [: =: unexpected operator
> /usr/local/freesurfer//bin/bet.fsl: 231:
> /usr/local/freesurfer//bin/bet.fsl: /bin/bet2: not found
>
> Then I realized that the program looks for those not-found
> files (remove_ext, imtest, bet2) in /bin/, but actually they're
all in
> /usr/lib/fsl/5.0/.
>
> What I did next was to copy those files from /usr/lib/fsl/5.0/ to
> /bin/, but then I got this error:
>
> # ---------- Using FSL's BET to Extract Brain------------------ #
> /usr/local/freesurfer/subjects/Retinotopy/33333/Retinotopy
> bet.fsl /tmp/mkbrainmask_12619/in.nii
/tmp/mkbrainmask_12619/brain -m
> -f 0.1
> /bin/bet2: error while loading shared libraries: libfslvtkio.so:
> cannot open shared object file: No such file or directory
> mri_binarize --i /tmp/mkbrainmask_12619/brain_mask.nii --min .01 --o
> /tmp/mkbrainmask_12619/brain_mask.nii
> niiRead(): error opening file /tmp/mkbrainmask_12619/brain_mask.nii
>
> Again, I tried copying the file libfslvtkio.so from /usr/lib/fsl/5.0
> to /bin/, but it keeps giving me the same error.
>
> So I have two questions:
> 1) I suspect that selxavg3-sess should be looking for the files in
> /usr/lib/fsl/5.0 instead of in /bin/. Why does it do that? And
how can
> I direct it to look for files in the former location instead?
> 2) As a quick fix, is it OK for me to copy all the files from
> /usr/lib/fsl/5.0 to /bin/? Will it solve the problem? The folder
/bin/
> contains something else and I don't really feel like messing
with it.
>
> Many thanks,
> Alan
>
>
>
>
>
> --
> Alan Lee
> sites.google.com/site/alanlflee/
<http://sites.google.com/site/alanlflee/>
<http://sites.google.com/site/alanlflee/>
>
>
> On Tue, Jun 17, 2014 at 4:54 PM, Douglas Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:
>
>
>     It looks for it in the current folder. You must run this
from the
>     same folder you ran mkanalysis-sess from (which should be your
>     project folder)
>
>
>
>
>     On 6/17/14 4:13 PM, Alan Lee wrote:
>>     Hello,
>>
>>     I'm using freesurfer to do retinotopic mapping. I've completed
>>     the recon-all, mkanalysis-sess, mri-convert and preproc-sess
>>     steps. Now when I run the selxavg3-sess (my subject name is
33333):
>>
>>     selxavg3-sess -a Retinotopy.33333.lh -s 33333
>>
>>     I got the following message:
>>     "ERROR:
>> /usr/local/freesurfer/subjects/Retinotopy/33333/Retinotopy does
>>     not exist"
>>
>>     It seems to look for a Retintopy folder within
>>     /Retinotopy/33333/. I suppose the Retinotopy folder should be
>>     placed under freesurfer/subjects/ ? Am I missing something
here?
>>
>>     Any help would be greatly appreciated.
>>
>>     Many thanks,
>>     Alan
>>
>>     =====================
>> debian:/usr/local/freesurfer/subjects/Retinotopy# selxavg3-sess
>>     -a Retinotopy.33333.lh -s 33333
>>     Surface data self lh
>> --------------------------------------------------------------
>>     selxavg3-sess logfile is
>>
/usr/local/freesurfer/subjects/Retinotopy/log/selxavg3-sess-Retinotopy-Retinotopy.33333.lh-140617154401.log
>> --------------------------------------------------------------
>>     preproc-sess -s 33333 -d
>>     /usr/local/freesurfer/subjects/Retinotopy -a
Retinotopy.33333.lh
>>     -nolog
>> --------------------------------------------------------------
>>     preproc-sess logfile is /dev/null
>> --------------------------------------------------------------
>>     $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
>>     root
>>     setenv FREESURFER_HOME /usr/local/freesurfer/
>>     setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/Structural
>>     Linux debian 3.2.0-4-486 #1 Debian 3.2.57-3+deb7u1 i686
GNU/Linux
>>     /usr/local/freesurfer/subjects/Retinotopy
>> /usr/local/freesurfer//fsfast/bin/preproc-sess
>>     -s 33333 -d /usr/local/freesurfer/subjects/Retinotopy -a
>>     Retinotopy.33333.lh -nolog
>>     Tue Jun 17 15:44:05 CEST 2014
>>     instem   f
>>     mc   1     f fmcpr
>>     stc  0     fmcpr
>>     sm   0
>>     mask 1   brain
>>     33333 Template -----------------------------
>>     mktemplate-sess -s 33333 -d
>>     /usr/local/freesurfer/subjects/Retinotopy -fsd Retinotopy
-nolog
>>     -update
>>     Session: /usr/local/freesurfer/subjects/Retinotopy/33333
>>     ----------------
>>     Tue Jun 17 15:44:06 CEST 2014
>>     ERROR:
/usr/local/freesurfer/subjects/Retinotopy/33333/Retinotopy
>>     does not exist
>>
>>     =====================
>>
>>
>>     --
>>     Alan Lee
>> sites.google.com/site/alanlflee/
<http://sites.google.com/site/alanlflee/>
>>     <http://sites.google.com/site/alanlflee/>
>>
>>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
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