Hello,
I am having a similar problem to that posted several times previously. I get an error when running reg-feat2anat to register FSL feat files to the freesurfer reconstruction, see:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-June/038437.html
because the subjectsfeatfolder.feat/reg/freesurfer/tmp/refvol.fslregister.nii file does not seem to make itself.
I'm wondering where I can find an active link to an updated reg-feat2anat, as all the links I find in threads are not working.
I did find a potential workaround: if I create the /mri/tmp directory and convert the .mgz file from the freesurfer output to .nii here, as explained on this website (http://wikis.la.utexas.edu/imagelab/book/how-convert-mgz-structural-files-ni...) I can create the missing nii file and rerun the registration, however, I'm uncertain about the orientation parameters as although the orientation of the nii matches that of my original T1, the resulting registration in freesurer is nonsense.
Example of the command I am using to manually convert the .mgz to nii:
mri_convert --in_type mgz --out_type nii subjectsfreesurferfolder/mri/brainmask.mgz --out_orientation RAS subjectsfeatfolder.feat/reg/freesurfer/tmp/refvol.fslregister.nii
Any suggestions on either the updated file location or the workaround much appreciated!
Notes:
I am running this version of FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 On Linux: Ubuntu 12.04.5 LTS
Emily