did you copy it to "flirt.fsl"? Did you rehash afterwards?
On 11/06/2013 10:42 AM, Christophe de Bezenac wrote:
It was not in $FREESURFER_HOME/bin so I copied the <flirt> unix executable from the fsl/bin and pasted it into $FREESURFER_HOME/bin. It still fails at the flirt.fsl command?
Thanks, Christophe
On 6 Nov 2013, at 15:20, Douglas N Greve wrote:
oops, sorry I just noticed that you did respond to the list!
On 11/06/2013 10:16 AM, Douglas N Greve wrote:
That should also be in $FREESURFER_HOME/bin. If not, just copy or symlink your flirt program to it. doug
ps. Please remember to post to the FS list and not to me personally. thanks!
On 11/06/2013 05:11 AM, Christophe de Bezenac wrote:
Thanks for responding Doug,
<reg-feat2anat> is in my path. I've actually now managed to run <reg-feat2anat> till the <flirt.fsl> command which produces the error (Command not found).
/Users/chdebezenac flirt.fsl -ref /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/refvol.fslregister.nii -in /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/exf2anat.init.fsl.mat flirt.fsl: Command not found. ERROR: flirt
Do you know why this might be?
Thanks again, Christophe
On 5 Nov 2013, at 23:18, Douglas N Greve wrote:
Is reg-feat2anat in your path? It should be in $FREESURFER_HOME/bin/reg-feat2anat doug On 11/05/2013 12:15 PM, Christophe de Bezenac wrote:
Hi everyone,
I am very new to freesurfer/qdec. What I would like to do is examine the results of a feat analysis in qdec and then perform further between-subject analyses with behavioural data (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer). I've run against problems at the first stage (registration) (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomic...). I imagine something is not set up right?
Christophe-de-Bezenacs-MacBook-Pro:~ chdebezenac$ tcsh setenv FREESURFER_HOME freesurfer [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv FREESURFER_HOME freesurfer [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% source freesurfer/SetUpFreeSurfer.csh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME freesurfer FSFAST_HOME freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR freesurfer/subjects MNI_DIR freesurfer/mni FSL_DIR /usr/local/fsl [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv SUBJECTS_DIR freesurferX/subjects [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% cd scan1Cor.feat [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] chdebezenac% ln -s $SUBJECTS_DIR/fsaverage ln: ./fsaverage: File exists [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] chdebezenac% ln -s $SUBJECTS_DIR/S1 ln: ./S1: File exists [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] chdebezenac% reg-feat2anat --feat scan1Cor.feat --subject S1 reg-feat2anat: Command not found. [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] chdebezenac% cd [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% ls S1 S4 fbert lh.EC_average scan1Cor.feat S2 S5 fbert2.feat qdec S3 bert fsaverage rh.EC_average [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% reg-feat2anat --feat scan1Cor.feat --subject S1 reg-feat2anat: Command not found. [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac%
Any help would be greatly appreciated,
Christophe
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