[FieldTrip] Creating an 8K sourcemodel from freesurfer files

Ioannis Zorzos gianof at hotmail.com
Wed Oct 23 11:22:43 CEST 2019

Dear fieldtripers again,

I found the problem, it was on the name of my subject. It should not contain dots (.) because it messes with the tok function that the ft_read_headshape uses. With some changes, I was able to fix the problem.

Thank you,
Zorzos Ioannis
Phd Candidate
National Technical University of Athens

From: fieldtrip <fieldtrip-bounces at science.ru.nl> on behalf of Ioannis Zorzos <gianof at hotmail.com>
Sent: Wednesday, October 23, 2019 11:24:34 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: [FieldTrip] Creating an 8K sourcemodel from freesurfer files

Dear fieldtripers,

I am trying to create a source model for source-reconstruction according to the provided documentation ( http://www.fieldtriptoolbox.org/tutorial/sourcemodel/ ).

I have completed all the required steps. But at the end, when I try to load the sourcemodel files, from the created by the HCP-workbench folder, my loaded sourcemodel contains only the following fields: pos, tri brainstructure, brainstructurelabel.

However, I downloaded the example sourcemodel file created by the tutorial and this file contains 4 more important fields: sulc, curv, thickness, atlasroi (converted to inside).

What can I do to import these fields as well (as in the documentation).

The files created by the ft_postfreesurfer.sh (for the 8k example) are:

06.07.18_TsK.8k_fs_LR.wb.spec 06.07.18_TsK.L.aparc.8k_fs_LR.label.gii 06.07.18_TsK.L.aparc.a2009s.8k_fs_LR.label.gii 06.07.18_TsK.L.ArealDistortion_FS.8k_fs_LR.shape.gii 06.07.18_TsK.L.atlasroi.8k_fs_LR.shape.gii 06.07.18_TsK.L.curvature.8k_fs_LR.shape.gii 06.07.18_TsK.L.inflated.8k_fs_LR.surf.gii 06.07.18_TsK.L.midthickness.8k_fs_LR.surf.gii 06.07.18_TsK.L.pial.8k_fs_LR.surf.gii 06.07.18_TsK.L.sphere.8k_fs_LR.surf.gii 06.07.18_TsK.L.sulc.8k_fs_LR.shape.gii 06.07.18_TsK.L.thickness.8k_fs_LR.shape.gii 06.07.18_TsK.L.very_inflated.8k_fs_LR.surf.gii 06.07.18_TsK.L.white.8k_fs_LR.surf.gii 06.07.18_TsK.R.aparc.8k_fs_LR.label.gii 06.07.18_TsK.R.aparc.a2009s.8k_fs_LR.label.gii 06.07.18_TsK.R.ArealDistortion_FS.8k_fs_LR.shape.gii 06.07.18_TsK.R.atlasroi.8k_fs_LR.shape.gii 06.07.18_TsK.R.curvature.8k_fs_LR.shape.gii 06.07.18_TsK.R.inflated.8k_fs_LR.surf.gii 06.07.18_TsK.R.midthickness.8k_fs_LR.surf.gii 06.07.18_TsK.R.pial.8k_fs_LR.surf.gii 06.07.18_TsK.R.sphere.8k_fs_LR.surf.gii 06.07.18_TsK.R.sulc.8k_fs_LR.shape.gii 06.07.18_TsK.R.thickness.8k_fs_LR.shape.gii 06.07.18_TsK.R.very_inflated.8k_fs_LR.surf.gii 06.07.18_TsK.R.white.8k_fs_LR.surf.gii

I understand that the missing fields are there, somewhere, but the ft_read_headshape cannot read .shape.gii files. What can I do to create the proper sourcemodel?

Thank you a lot,

Zorzos Ioannis

Phd Candidate,

National Technical University of Athens

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