Hi Arman,
Thanks for your suggestion. Sadly, the command
source /usr/share/fsl/5.0/etc/fslconf/fsl.sh
doesn't work and I've got the error:
FSLDIR=/usr/share/fsl/5.0: Command not found.
POSSUMDIR=/usr/lib/fsl/5.0: Command not found.
Bad : modifier in $ (/).
Do you think removing FSL altogether
I think that there must be a problem with your FSL install. I hate to
pass the buck, but did you contact the FSL list?
doug
On 07/13/2014 01:36 PM, Alan Lee wrote:
Hi Doug,
When I run the following:
/usr/lib/fsl/5.0/bin/bet2
it gives me the following error:
bet2: error while loading
Hi Alan,
I can guess there are several problems here with your fsl installation. Are
you on Neurodebian? For some historical reasons fsl5.0-command format for
usual fsl commands were used so that when people wanted to use both fsl 4
and 5 at the time there wouldn't be any confusion. Anyway you
Hi Doug,
When I run the following:
/usr/lib/fsl/5.0/bin/bet2
it gives me the following error:
bet2: error while loading shared libraries: libfslvtkio.so: cannot open
shared object file: No such file or directory
When I run
fsl
it says
fsl: Command not found.
However, the command
fslview
If you just run bet2 (ie, /usr/lib/fsl/5.0/bin/bet2) outside of FS, do
you still get the error? Can you use any of the other FSL commands?
On 07/04/2014 06:26 AM, Alan Lee wrote:
Hello freesurferers,
I ran this command (3 is my subject name):
selxavg3-sess -a Retinotopy.3.lh -s
Hello freesurferers,
I ran this command (3 is my subject name):
selxavg3-sess -a Retinotopy.3.lh -s 3
and got this error message:
# -- Using FSL's BET to Extract Brain-- #
/usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy
bet.fsl
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/
On Mon, Jun 23, 2014 at 4:03 PM,
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
[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
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
Thanks, Doug. I think I've kind of sorted that one out by creating a folder
called Retinotopy under freesurfer/subjects/Retinotopy/3/, 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.
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 3):
selxavg3-sess -a Retinotopy.3.lh -s 3
I got the following message:
ERROR:
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,
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