Thank you very much, now it is working!
The backslash was there but there was no space just after the .dat
I report below the final commands that I have used in case somebody else
might find it useful.
Thanks again!
mris_preproc --target fsaverage --hemi lh \
--iv ${SUBJECTS_DIR}/sub01/stats/con_0
It looks like it is a scripting problem where you did not include a
backslash to indicate that the command line continued to the next line
and so it thinks that "-=-iv" is a command (I assume that "commande
introuvable" means something like "command not found")
On 11/9/17 12:39 PM, Elisa Cas
Thank you very much for your help,
that almost fixed the problem.. Indeed it seems like it worked well for the
first subject, but then it crashed for the second one..
this is the last part of what it typed on the command window:
%
Cleaning up
---
rm -r ./tmp
looks like you did not create the lta file properly. You can just pass
mris_preproc the .dat file instead of the lta.
On 11/07/2017 10:51 AM, Elisa Castaldi wrote:
> Yes, the output is in native functional space.
>
> On 7 November 2017 at 16:40, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.ed
Yes, the output is in native functional space.
On 7 November 2017 at 16:40, Douglas N Greve
wrote:
> Did you keep the spm output in native functional space?
>
>
> On 11/07/2017 09:23 AM, Elisa Castaldi wrote:
> > Yes,
> > this is what I have already done: I moved both the fsaverage and the
> > s
Did you keep the spm output in native functional space?
On 11/07/2017 09:23 AM, Elisa Castaldi wrote:
> Yes,
> this is what I have already done: I moved both the fsaverage and the
> subjects into SUBJECTS_DIR and the error I get is ERROR: source volume
> is neither source nor target of the regi
Yes,
this is what I have already done: I moved both the fsaverage and the
subjects into SUBJECTS_DIR and the error I get is ERROR: source volume is
neither source nor target of the registration.
On 7 November 2017 at 15:11, Douglas Greve
wrote:
> When you look in SUBJECTS_DIR, you should see fs
When you look in SUBJECTS_DIR, you should see fsaverage and all the
subjects being passed to mris_preproc. If not, you need to move them (or
sym link them) into that folder.
On 11/7/17 6:07 AM, Elisa Castaldi wrote:
Thanks for your answer.
If I don't specify the directory I get the following
Thanks for your answer.
If I don't specify the directory I get the following error
ERROR: cannot find fsaverage in SUBJECTS_DIR
and if I move fsaverage to SUBJECTS_DIR it says that it cannot find
manat_mp1 which is the name of the folder containing the results of recon
all for the subject sub01 (c
Use
--target fsaverage
instead of giving the full path
On 11/06/2017 01:27 PM, Elisa Castaldi wrote:
> Dear Freesurfer users,
>
> I would like to perform surface based fMRI gorup analysis in
> Freesurfer starting from SPM first level output files, but I am not
> succeding.
> I have already pr
Dear Freesurfer users,
I would like to perform surface based fMRI gorup analysis in Freesurfer
starting from SPM first level output files, but I am not succeding.
I have already preprocessed the data in spm and used Freesurfer for
boundary based registration, I have succesfully ran the recon -all
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