Hi,
You can use the Renderhighres_gui to transform all your
first level stats to MNI space.
All the best,
Mark
On 7 Mar 2010, at 06:44, Emma Liang wrote:
> Thanks Harish! It works.
>
> Any help on the registration to MNI?
>
> Best wishes,
> Emma
>
> On Sun, Mar 7, 2010 at 5:11 PM, Harish kumar <[log in to unmask]
> > wrote:
>
> Hi..
>
> I am totally agreed with Mark Jenkison. Without setting the
> FSLDIR environment setting, it cannot run in Matlab. please find
> the attached startup.m file and put into matlab main directory and
> Change the directory setting in the first line of code.
>
> Regards
> Harish
>
>
>
>
>
>
> On Sun, Mar 7, 2010 at 1:06 PM, Emma Liang <[log in to unmask]> wrote:
> Hi Mark,
>
> Thanks for answer. But my FSL works very well, which means FSLDIR
> environment setting is ok, right?
>
> I want to calculate the distance between individual's and group's
> activated areas(thresholded z-map), so I want to register the first
> level result to MNI space to compare. How should I make it? Thanks.
>
> Best wishes,
> Emma
>
> On Sun, Mar 7, 2010 at 7:09 AM, Mark Jenkinson <[log in to unmask]>
> wrote:
> 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
>
>
>
>
> --
> With Kind Regards
> Harish Kumar
>
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