But of course, Bruce says the .nii.gz format should have worked, so it does not need to be type mgz format. I would trust Bruce. Sorry for not cc'ing the mailing list earlier.

Thanks, John

John Drozd Post-Doctoral Fellow Robarts Research Institute University of Western Ontario London, Ontario, Canada http://publish.uwo.ca/~jdrozd2

Begin forwarded message:

From: John Jan Drozd john.drozd@gmail.com Date: 1 August, 2011 5:10:07 PM EDT To: "Tax, C.M.W." c.m.w.tax@student.tue.nl Subject: Re: [Freesurfer] Problem loading nii

Hi,

I believe the image must be type mgz format for Freesurfer. (For FSL it needs to be type nii or nii.gz.)

Try typing:

gunzip t1.nii.gz mri_convert t1.nii t1.mgz tkmedit -f t1.mgz

John

John Drozd Post-Doctoral Fellow Robarts Research Institute University of Western Ontario London, Ontario, Canada http://publish.uwo.ca/~jdrozd2

On 2011-08-01, at 4:55 PM, "Tax, C.M.W." c.m.w.tax@student.tue.nl wrote:

...

Dear Sir/Madam,

I would like to use freesurfer for cortical flattening, working with the nii format. When I try to load the nii.gz file as described on http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html, I get the following error:

student@BMT-PC125:~$ tkmedit -f t1.nii.gz niiRead(): error opening file ./t1.nii.gz

Error: Loading volume t1.nii.gz

Couldn't read the anatomical volume.

Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.

This image t1.nii.gz was obtained by converting DICOM images with dcm2nii. I also tried to load a example dataset downloaded from http://nifti.nimh.nih.gov/nifti-1/data, but still I get the same error. FSL was able to load both datasets without problems.

Please could you help me with this problem?

Thank you in advance,

Kindest Regards

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