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

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is

addressed. If you believe this e-mail was sent to you in error and the e-mail

contains patient information, please contact the Partners Compliance HelpLine at

http://www.partners.org/complianceline . If the e-mail was sent to you in error

but does not contain patient information, please contact the sender and properly

dispose of the e-mail.