It looks right. Make sure that you have specified "self" when you run mkanalysis-sess to make sure the analysis is on the subject's own anatomy where you have MT defined doug

On 04/20/2014 08:35 AM, Reza Rajimehr wrote:

Hi,

For my dataset, it appears to be easier to do an ROI analysis in Matlab (instead of using funcroi commands). I just want to make sure the procedure described below is right:

1. I have a label/ROI on the right hemisphere surface of a subject (e.g.

MT from the motion localizer). I convert it to a mask file (MT.mask.nii.gz). I load it to Matlab using MRIread.

In an fMRI experiment, I have 3 conditions. For the right hemisphere vertices of the subject, I compute cespct.nii.gz for the contrasts of each condition vs. baseline (1_vs_0 , 2_vs_0 , 3_vs_0). Then I load the three cespct files to Matlab using MRIread.

3. For the vertices that are 1 in the MT.mask.nii.gz, I calculate the

averaged cespct across those vertices, in each contrast. So I will have % signal change values for the three conditions.

4. I repeat this for all subjects and do statistics across subjects.

Any comments?

Reza _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer