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 >>>>> $FREESURFER_HOME/bin/reg-feat2anat >>>>> doug >>>>> On 11/05/2013 12:15 PM, Christophe de Bezenac wrote: >>>>>> Hi everyone, >>>>>> >>>>>> I am very new to freesurfer/qdec. What I would like to do is examine the >>>>>> results of a feat analysis in qdec and then perform further >>>>>> between-subject analyses with behavioural data >>>>>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer). >>>>>> I've run against problems at the first stage (registration) >>>>>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical). >>>>>> I imagine something is not set up right? >>>>>> >>>>>> Christophe-de-Bezenacs-MacBook-Pro:~ chdebezenac$ 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 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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. >>>>> >> -- >> 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 > >
-- 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
