you should also just be able to specify the nifti file to recon-all on the command line with -i the same way you would a dicom. If the extension is .nii is should recognize it and work properly
cheers Bruce On Wed, 17 Feb 2010, Freesurfer Local Archive wrote:
Jenessa,
Try the following steps:
- In the $SUBJECTS_DIR create separate folders for each subject
- in each subject's folder create a folders mri and mri/orig (e.g.
mkdir -p $SUBJECTS_DIR/SUBJECT-NAME/mri/orig) 3. Convert data from nii (or nii.gz) to mgz and place it in the $SUBJECTS_DIR/SUBJECT-NAME/mri/orig folder:
$FREESURFER_HOME/bin/mri_convert /PATH/TO/YOUR-IMAGE.nii $SUBJECTS_DIR/SUBJECT-NAME/mri/orig/001.mgz
If mri_convert is having trouble converting try more elaborate version of the same syntax:
$FREESURFER_HOME/bin/mri_convert --in_type nii --out_type mgz --input_volume /PATH/TO/YOUR-IMAGE.nii --output_volume $SUBJECTS_DIR/SUBJECT-NAME/mri/orig/001.mgz
Cheers,
Jacek
-- Jacek Jonca-Jasinski
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Jacek Jonca-Jasinski Texas Tech University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer