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
hmmm, that should have worked. Do you want to email us the t1.nii.gz volume and we'll take a look?
On Mon, 1 Aug 2011, Tax, C.M.W. 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
What version of FS are you running and on what platform? Can you upload the file to me at our file drop below? doug
Tax, C.M.W. 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Tax, C.M.W.