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 convert to .mgz with the mri_convert command.
Thank you!
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/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
^..^<
Jacek Jonca-Jasinski Texas Tech University
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
^..^<
Jacek Jonca-Jasinski Texas Tech University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The following command line works for me:
recon-all -i $FREESURFER_HOME/subjects/<subject folder with .nii file>/<filename>.nii -subjid <name of new folder for FS to create/write to>
Julie E. McEntee, M.A., C.C.R.P. Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./ Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676
----- Original Message ----- From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: Thursday, February 18, 2010 8:47 am Subject: Re: [Freesurfer] converting nifti to .mgz files - command To: Freesurfer Local Archive freesurfer@jonca.org Cc: Jenessa Price jenessaprice@gmail.com, freesurfer@nmr.mgh.harvard.edu
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
^..^<
Jacek Jonca-Jasinski Texas Tech University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Freesurfer Local Archive -
Jenessa Price -
Julie E McEntee