[Eeglablist] Image Segmentation Saving

[Zeynep Akalin Acar]

You need to do Freesurfer pre-processing before loading an MR image:

Freesurfer pre-processing:

mri_convert -i fine_name.nii -ot analyze -o test1.img
mri_nu_correct.mni --i test1.img --o t1c.img --n 2
mri_convert -i t1c.img --conform_size 1 --out_orientation PSR -ot analyze
-o test2.img

It will arrange the orientation and the dimension of the image.

Thanks,
Zeynep.

On Tue, May 17, 2016 at 12:49 PM, Greg Mierzwinski <gmierz1 at live.ca> wrote:

> Hi,
>
>
> I seem to be receiving an error whenever I try to save either the
> "Filtered Image" or "Segmentation" image from the Image Segmentation
> sub-menu of NFT. I'm wondering if I am causing this problem by not having
> something set correctly or if this is a bug? Here is the error I get:
>
>
>
> ------------------------------------------------------------------------------------------------------------
>
> Subscripted assignment dimension mismatch.
>
> Error in Segmentation>pushbuttonSaveFiltered_Callback (line 957)
>    filt_im(:,:,i) = rot90(filt_im(:,:,i),3);
>
> Error in gui_mainfcn (line 75)
>         feval(varargin{:});
>
> Error in Segmentation (line 61)
>     gui_mainfcn(gui_State, varargin{:});
>
> Error in
>
> @(hObject,eventdata)Segmentation('pushbuttonSaveFiltered_Callback',hObject,eventdata,guidata(hObject))
>
>
> Error while evaluating uicontrol Callback
>
>
> ----------------------------------------------------------------------------------------------------------
>
>
> The image I am trying to segment has dimensions 290x200x290.
>
>
> I did some more digging into the |pushbuttonSaveFiltered_Callback| and
> noticed that 'i' was 1 when it stopped working but the value of M was 290. From
> what I can see here, the image should be in a saggital orientation, but it
> seems as if it should work with or without the specific orientation.
>
>
> Thanks,
>
> Greg
>
>
>
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