Hi,
The first line of the error indicates that your FSLDIR environment
variable is not set correctly. Please check that you followed the
installation instructions carefully and have started a new terminal
since installing.
As for your later questions - the statistical images are in native space
at the first level and MNI space at higher levels. You will always
interact with voxel coordinates if you load into MATLAB, *but* they
will be MATLAB-style coordinates, so that the first value is 1, not 0.
If all you want to do is look at your images and see coordinates then
I would recommend using FSLView, not MATLAB.
All the best,
Mark
On 6 Mar 2010, at 13:07, Emma Liang wrote:
> Dear FSLers,
>
> I was trying to load the FSL .nii file on Matlab with read_avw, but
> it alway prompted: (I use Mac OS, FSL 4.12, Matlab 2009a)
>
> sh: /etc/fslconf/fsl.sh: No such file or directory
> ??? Error using ==> fread
> Invalid file identifier. Use fopen to generate a valid file
> identifier.
>
> Error in ==> read_avw_hdr at 17
> testval = fread(fid,1,'int32');
>
> Error in ==> read_avw at 33
> [dims,scales,bpp,endian,datatype]= read_avw_hdr(tmpname);
>
> I add the path /etc/fslconf to Matlab as well. I'm not good at
> Matlab and FSL commands. Could anyone tell me what the wrong is?
>
> And, I want to load the z-score map to Matlab. If read_avw works,
> what the coordinates and values from file
> rendered_thresh_zstat*.nii.gz are? Are the coordinates transfered
> and registered to standard MNI imaging in unit mm? If not, how
> should I do it? Thanks!
>
> Best wishes,
> Emma
|