The MNI directory directly under freesurfer is there, but the MNI_PERL5
directory is not. e.g,
bash-3.2$ echo $MNI_PERL5LIB
/Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6
bash-3.2$ cd $MNI_PERL5LIB
bash: cd: /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6: No
such file
Hi Michelle
is the MNI stuff installed? If seems like ti can't find
"MNI/Startup.pm". Mine is under: $MNI_PERL5LIB/MNI/Startup.pm
cheers
Bruce
On Sun, 21 Jul
2013, Michelle W. Voss wrote:
Hi, I seem to be having the same error, recon all is crashing out with the
mri_nu_correct.mni comman
Hi, I seem to be having the same error, recon all is crashing out with the
mri_nu_correct.mni command, e.g., if I run in the mri directory of a
subject, I get what is pasted below. Any ideas for the fix?
bash-3.2$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
--no-rescale --i orig.mgz
>
> Hi Doug,
>
> The command runs a bit further now but then exits with errors.
> Unfortunately this time there is no specific stated error. The last few
> lines of the log are:
>
> INFO: extension is mgz
> #
> #@# Talairach Tue Jun 4 13:22:08 EDT 2013
>
That dcmunpack command will put the data into a file called
unpack3/MPRAGE/002/struct.nii
It needs to be put into upack3/mri/orig/002.mgz
doug
On 06/04/2013 11:22 AM, Nitenson, Adam wrote:
> Hi Doug,
>
> When I try the command as you suggested:
> recon-all -all -s unpack3
> I get the following
Hi Doug,
When I try the command as you suggested:
recon-all -all -s unpack3
I get the following error:
ERROR: no run data found in
/gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri. Make sure to
have a volume called 001.mgz in
/gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri/ori
Hi Adam, if the subject folder exists and you pass recon-all a -i flag,
then it will exit with error saying that the data exist (otherwise it
would overwrite what is there). However, just because the subject folder
exists does not mean that there is any data sitting in subject/mri/orig.
Then it
Hello users,
I am trying to get Freesurfer (5.2) working properly off-site and am
encountering errors I did not have while working at the Martinos center. We
use the same Siemens 3T Tim Trio scanner at Brown, so I would hope the data
is similar to work with.
I have been using dcmunpack since unpa
