No idea why. What is the difference in the headers? Can you post the terminal output of both your mri_vol2surf commands? Also, you can try using MRIread.m and MRIwrite.m (these use load_nifti and save_nifti under the hood but also do some things to the header).

doug

On 11/20/2013 08:46 AM, Leila Reddy wrote:

Hi,

I am trying to save a nifti file using save_nifti. I'm running into a strange problem that I describe below.

I have a nifti file (subj_mask.nii) created by a colleague using Nibabel (http://nipy.sourceforge.net/nibabel/). This volume is in the MNI305 space.

Step1: In a first step I wanted to convert this volume to the fsaverage surface format. To do that I used :

mri_vol2surf --src subj_mask.nii --hemi rh --out_type mgh --float2int round --o blah9-rh.mgh --projfrac 0.5 --trgsubject fsaverage --regheader fsaverage.

I load it in tksurfer and when I do view-> configure->overlay, I see a range of values (as expected) and am able to set the min and max thresholds as I want.

Step 2: In a second step I loaded this nifti file into matlab using load_nifti and had to alter the volume a little bit as below: hdr=load_nifti('subj_mask.nii'); vol=hdr.vol; vol(find(vol<4))=0; hdr.vol=vol; save_nifti(hdr,'new_mask.nii').

I convert the volume to fsaverage surface space as before but when I view it in tksurfer I am not able to set a min and max threshold with configure->overlay. Instead, there is no distribution of values plotted in the configure overlay window and I get the following error message: % ERROR updating histo: impossible limits (min 0.55556 >= max 0.55556) for axis "x"

I finally managed to solve this problem by loading the header information from a FS-FAST created nifti:

hdr_fsfast = load_nifti('bold/analysis.mni/mask.nii.gz'); hdr_fsfast.vol=vol; save_nifti(hdr_fsfast,'new_mask.nii').

Now I am able to see the distribution of values in the configure overlay window and am able to set the thresholds.

The headers for FS-FAST and Nibabel generated niftis are indeed slightly different but why do I not have the problem in step 1 when I use the Nibabel file, but only in step 2 after I use save_nifti with the Nibabel header ?

I use the load_nifti and save_nifti commands very often (and haven't had problems before because I was only using FS-FAST generated files) so I would really appreciate it if someone could point out what is going on so that I understand what to do in future.

Thanks, Leila

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