Dear Dianne,
Here is one way to generate a text file of all suprathreshold coordinates:
1) use the "write filtered" button to create an image file of the voxels
surviving your selected threshold (after displaying the glass brains from
the "results" button)
2) use the imcalc button to convert the newly produced write-filtered
image into a binary image with values set to 1 where the suprathreshold
voxels are, or set to 0 otherwise. To do that, select the write-filtered
image when asked for image to work on, and the enter the following formula:
i1>0
in the prompt.
3) use roi_list, a small program I'm attaching here, to produce a text
file of all the coordinates from the file produced in 2). The program will
crate a new file, containing a list of all voxels within an image that
have the maximum value for this image - e.g., for a binary image of 0s and
1s, it will list all voxels having a value of 1.
Hope this works.
Best wishes,
Kalina
On Sat, 1 Sep 2001, Dianne Patterson wrote:
> Dear spm group,
>
> I am working with the very interesting mrGray and mrFlatmesh programs to
> analyze fMRI data and I have encountered a difficulty: I need to be able
> to generate a text file containing the x,y,z coordinates and colormap of
> all suprathreshold voxels.
>
> mrGray can read in a text file representing functional activations. What
> it needs is to know the color table associated with the activations (In
> my example below, the first row tells mrGray that there are two entries
> in the color table.
> The second row tells mrGray that the first color is red [r=255, g=0, b=0]).
>
> The last 3 rows tell mrGray the x,y,z coordinates (on the structural image)of
> the overlaid suprathreshold voxels AND the row from the color table that
> mrGray should use to represent that suprathreshold voxel (In my example,
> the second row from the bottom, the voxel specified is at position 90 [x,
> coronal], by position 89 [y, axial], by position 91 [z, sagittal] and it
> should be colored using the first color in the color table, red (1).
>
> 2
> 255 0 0
> 0 255 0
> 90 90 90 1
> 90 89 91 1
> 90 88 90 2
>
> I have looked through the archives and see evidence that people have generated
> text files containing information about the locations of suprathreshold
> voxel, but I didn't find quite what I was looking for. Has anyone out there
> written code to do this or something very similar to this?
>
> Thankyou,
>
> Dianne Patterson
> CNL
>
_____________________________________________________________________________
Kalina Christoff, Ph.D. Email: [log in to unmask]
Office: Rm.422; (650) 725-0797
Department of Psychology Home: (408) 245-2579
Jordan Hall, Main Quad Fax: (650) 725-5699
Stanford, CA 94305-2130 http://www-psych.stanford.edu/~kalina/
_____________________________________________________________________________
