Sorry, I don't know why it is failing. We don't have a problem with it
and no one else has reported this. Check the location of the FSLDIR env
variable. Or maybe it is a new version of FSL that is not compatible
with the old?
On 6/20/14 5:25 PM, Alan Lee wrote:
[sorry, I may have sent this multiple times, but, because I'm not sure
if it got through because I got several "bounce-back" error messages,
I'm sending it out again...]
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/>
On Thu, Jun 19, 2014 at 9:03 PM, Alan Lee <alan....@ens.fr
<mailto:alan....@ens.fr>> 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/>
On Tue, Jun 17, 2014 at 4:54 PM, Douglas Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@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/>
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