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- Original Message -
From: Bruce Fischl
Date: Thursday, February 18, 2010 8:47 am
Subject: Re: [Freesurfer] converting nifti to .mgz files - command
To: Freesurfer Local Archive
Cc: Jenessa Price , freesurfer@nmr.mgh.harvard.edu
> you should a
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 s
Jenessa,
Try the following steps:
1. In the $SUBJECTS_DIR create separate folders for each subject
2. 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/SUBJE
Can you please tell me the exact mri_convert command for converting
nifti to .mgz?
We had originally done it using .img/.hdr files, but there were errors
with the recon because the orientation wasn't correct. We then were
able to get a correct orientation using the .nii format but could not
conve
