Re: [Freesurfer] convert multiple Analyze to single 4D nifti

Thanks, Doug and Kara, mri_concat is very handy.

Xu

On Fri, Oct 24, 2008 at 11:40 AM, Doug Greve greve@nmr.mgh.harvard.eduwrote:

one way to do it is with mri_concat, something like

mri_concat f???.img --o f.nii.gz

if your individual volumes are f000.img f001.img etc

Kara Dyckman wrote:

I'm not sure. When I just tried it, it converted to .nii.gz. Maybe it

...

has to do with the version of fsl being used? I'm posting this to the freesurfer listserv to see if anyone else has ideas.

Xu Cui wrote:

Thanks Kara. I tried fslmerge on my images and the result is a single

...

.img / .hdr pair, not a nii or nii.gz file. Do you have any clue? The reason to convert to nii is that fsfast seems to require nii file.

Thanks, Xu

On Thu, Oct 23, 2008 at 2:20 PM, Kara Dyckman <kara@nmr.mgh.harvard.edumailto: kara@nmr.mgh.harvard.edu> wrote:

If I remember correctly, you can use the fslmerge command to merge all the .hdr files into one nifti file.

Try this in the directory where your analyze files are: fslmerge -t outputname *.hdr

outputname is whatever you want to call your new nifti file

The result will be outputname.nii.gz

Hope that helps! Kara

Xu Cui wrote:

   Does anybody know how to convert a series of Analyze files
   into a single nii file?  Each analyze file is a single 3D
   volume at a time point; the nii file would be 4d.

   Thanks,
   Xu

   --

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   Xu Cui
   Department of Psychiatry and Behavioral Sciences
   Stanford University
   ----------------------------------------------------------------

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-- Kara A. Dyckman, Ph.D. Postdoctoral Fellow, Manoach Lab Psychiatric Neuroimaging Massachusetts General Hospital Charlestown Navy Yard 149 13th St. Charlestown, MA 02129 email: kara@nmr.mgh.harvard.edu mailto:kara@nmr.mgh.harvard.edu phone: 617-724-4604 fax: 617-726-4078

http://nmr.mgh.harvard.edu/manoachlab

--

Xu Cui Department of Psychiatry and Behavioral Sciences Stanford University

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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