what format did you save your estimates in? If you want to overlay it on the surface, it has to be a "volume" where the first dimension is the number of vertices in the surface, and the others are all 1. Unless it is nifti in which case you have to split up the first dimension since it is too big for the nifti format

cheers Bruce

On Tue, 19 Feb 2019, forsteca@hu-berlin.de wrote:

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Hello Freesurfer Community,

I want to view my cortical thickness estimates (I calculated standard deviations for different subjects) on a 3D file. I thought I could replace the lh.thickness part in the following code by my own estimations:

freeview -f \ /Datasets/sSUBJ_DAY_01_01/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ /Datasets/sSUBJ_DAY_01_01/surf/lh.pial:annot=aparc.a2009s.annot:name=pial_aparc_des:visible=0 \ /Datasets/SUBJ_DAY_01_01/surf/lh.inflated:overlay=lh.thickness.asc:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \ /Datasets/sSUBJ_DAY_01_01/surf/lh.inflated:visible=0 \ /Datasets/sSUBJ_DAY_01_01/surf/lh.white:visible=0 \ /Datasets/sSUBJ_DAY_01_01/surf/lh.pial \ --viewport 3d

I tried loading a binary mat, as lh.thickness is a binary file as well. I got the following error:

couldn't determine type of file

Can you clarify what file structure the thickness overlay file should be, so that Freesurfer is able to read the thickness information ?

Thank you so much.

(addional info: mat file 163842x1 double)

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