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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
