actually, on closer look, adding those lines to the FSL config did not fix
the problem. However, if I call bet2 by typing fsl5.0-bet2, then it works.
I am not sure why, but to call anything from fsl I have to first put
fsl5.0- first.




On Tue, Apr 16, 2013 at 2:40 PM, Corinna Bauer <corinna...@gmail.com> wrote:

> That's alright. I had to add these lines to my .bashrc file
> # get FSL config loaded
> if [ -f /usr/share/fsl/5.0/etc/fslconf/fsl.sh ]; then
>   . /usr/share/fsl/5.0/etc/fslconf/fsl.sh;
> fi
>
> but now, I get this error when running preproc-sess -per-run -fwhm 3
> -force -so up -surface self lhrh -s . -d . -fsd bold -rlf symm_runs
>
>  /usr/local/freesurfer/subjects/symmetry/functional
> mri_convert ERROR: could not determine file for
> /usr/local/freesurfer/subjects/symmetry/functional/lindsay_functional/mri/brainmask
> lindsay_functional/bold/006/tmp.bbregister.7574/fslregister/refvol.fslregister.nii
>
>
>
>
>
> On Tue, Apr 16, 2013 at 12:07 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu
> > wrote:
>
>>  Hi Corinna, I hate to pass the buck, but I think you'll have to contact
>> the FSL people to get it sorted out.
>> doug
>>
>>
>>
>> On 4/16/13 9:31 AM, Corinna Bauer wrote:
>>
>> Yes, if I just type bet2 I still get: libmeshclass.so: cannot open shared
>> object file: No such file or directory.
>>
>>
>>
>> On Fri, Apr 12, 2013 at 4:07 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu> wrote:
>>
>>> Hi Corinna, if you just run bet2 at the command line, do you get the
>>> same error?
>>> doug
>>>
>>> On 04/12/2013 03:56 PM, Corinna Bauer wrote:
>>> > Hello all, when running preproc-sess, I got this error message:
>>> > ERROR: could not determine file for
>>> >
>>> /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold/masks/brain
>>> > Try running mkbrainmask-sess with -per-run
>>> >
>>> > I then ran the mkbrainmask-sess as follows (kbrainmask-sess -s . -d .
>>> > -fsd bold
>>> > m) and got the output below, which shows a problem with a shared
>>> library?
>>> >
>>> > Any suggestions?
>>> >
>>> > Corinna
>>> >
>>> > ------------------------------------------------
>>> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test
>>> > Fri Apr 12 15:53:14 EDT 2013
>>> > mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil
>>> > 1 -nerode 0
>>> > FSLMATHS fslmaths.fsl
>>> > Scratch Dir is /tmp/mkbrainmask_9634
>>> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
>>> > mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii
>>> > mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii
>>> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>>> > reading from template.nii.gz...
>>> > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>>> > i_ras = (-0.996119, -0.0108587, 0.0873391)
>>> > j_ras = (0.000562893, 0.991553, 0.129698)
>>> > k_ras = (0.0880098, -0.129244, 0.9877)
>>> > writing to /tmp/mkbrainmask_9634/in.nii...
>>> > # ---------- Using FSL's BET to Extract Brain------------------ #
>>> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
>>> > bet.fsl /tmp/mkbrainmask_9634/in.nii /tmp/mkbrainmask_9634/brain -m -f
>>> 0.1
>>> > /usr/share/fsl/5.0/bin/bet2: error while loading shared libraries:
>>> > libmeshclass.so: cannot open shared object file: No such file or
>>> directory
>>> > mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min .01 --o
>>> > /tmp/mkbrainmask_9634/brain_mask.nii
>>> > niiRead(): error opening file /tmp/mkbrainmask_9634/brain_mask.nii
>>> >
>>> > $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
>>> > cwd /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
>>> > cmdline mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min
>>> > .01 --o /tmp/mkbrainmask_9634/brain_mask.nii
>>> > sysname  Linux
>>> > hostname lotfi
>>> > machine  x86_64
>>> > user     bauer
>>> >
>>> > input      /tmp/mkbrainmask_9634/brain_mask.nii
>>> > frame      0
>>> > nErode3d   0
>>> > nErode2d   0
>>> > output     /tmp/mkbrainmask_9634/brain_mask.nii
>>> > Binarizing based on threshold
>>> > min        0.01
>>> > max        +infinity
>>> > binval        1
>>> > binvalnot     0
>>> >
>>> >
>>> >
>>>  > _______________________________________________
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>
>>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Reply via email to