Volume source: aparc+aseg atlas

thhinault · August 8, 2018, 1:22pm

Hi everyone,
I used a volume source estimation on MEG resting-state data. Now I would like to import the Freesurfer atlases to get scout time series. Everything works fine for the aseg atlas but I get weird results when I try to import the aparc+aseg atlas (see attached for an example with the Thalamus ROI).

I say yes to apply the standard transformation Freesurfer --> Brainstorm (I used the Freesurfer folder to import my individual anatomies).

Is this a bug or am I missing something ?

Thanks

Thomas

thalamus

Francois · August 13, 2018, 7:21am

Hi Thomas,

There is no attachment in your message.
How are you trying to import this atlas and for which purpose?

Francois

thhinault · August 13, 2018, 10:39am

Below is the Thalamus ROIs I was referring to in the previous post.
I used Atlas>New atlas to import the subject specific atlases from the Freesurfer folder. I say "yes" when asked to apply the standard transformation Freesurfer-->Brainstrom. I tried to refuse to apply the standard transformation but it does not help.
Again, it works when I import the aseg atlas but not for any of the aparc atlases.
The goal is to define volume scouts to extract scout time series.
It seems that a part of the problem is that several ROIs are grouped together, see attached. Indeed when I import the Aparc atlas I only get 23 scouts when the atlas is supposed to include 68 of them.
1/The Thalamus ROI

2/One of the cortical ROI, with various regions that seem to be grouped together.

Thanks,

Thomas

Francois · August 13, 2018, 2:29pm

Hi Thomas,

Indeed, there was a bug in the code. The values from the atlas were read correctly, but then they were normalized as we do for regular MRI volumes, which makes no sense at all for an atlas.
I fixed this: https://github.com/brainstorm-tools/brainstorm3/commit/f7e851530653b7e2cc3fdcf175902d6cd18927a7

Please update Brainstorm and try again importing your atlases.

Cheers
Francois

thhinault · August 13, 2018, 4:16pm

Ok it works now.
Thanks !

Thomas

thhinault · August 13, 2018, 7:19pm

I also noticed that during the import several scouts remain unnamed, with just a number. Do you think this can be fixed as well ?

Thomas

Francois · August 15, 2018, 9:01am

The regions are named after a fixed list in panel_scouts.m. The labels correspond to what we find in aseg.mgz.
If you are interested, you can add the labels for the other regions and then open a pull request to submit your modifications.

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/gui/panel_scout.m#L5253


%% ===== ASEG LABELS =====

% Reference: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT

function Labels = GetAsegLabels(FsVersion)

% Parse inputs

if (nargin < 1) || isempty(FsVersion)

    FsVersion = 5;

end

% Classification depends on FreeSurfer version

switch FsVersion

    % Versions 5 and 6

    case 5

        Labels = {...

            0,  'Unknown'; ...

            1,  'Cortex ext L'; ...

            2,  'White L'; ...

            3,  'Cortex L'; ...

            4,  'Ventricle lat L'; ...

            5,  'Ventricle inf-lat L'; ...

            7,  'Cerebellum white L'; ...

            8,  'Cerebellum L'; ...

            9,  'Thalamus L'; ...

thhinault · August 15, 2018, 1:00pm

The ROIs from the Aseg atlas are correctly identified. Below are the corresponding names for the Aparc ROIs from the Freesurfer wiki. The only difference is that 1004 and 2004 (corpus callosum) are missing.

#No. Label Name:
1000 lh-unknown
1001 lh-bankssts
1002 lh-caudalanteriorcingulate
1003 lh-caudalmiddlefrontal
1004 lh-corpuscallosum
1005 lh-cuneus
1006 lh-entorhinal
1007 lh-fusiform
1008 lh-inferiorparietal
1009 lh-inferiortemporal
1010 lh-isthmuscingulate
1011 lh-lateraloccipital
1012 lh-lateralorbitofrontal
1013 lh-lingual
1014 lh-medialorbitofrontal
1015 lh-middletemporal
1016 lh-parahippocampal
1017 lh-paracentral
1018 lh-parsopercularis
1019 lh-parsorbitalis
1020 lh-parstriangularis
1021 lh-pericalcarine
1022 lh-postcentral
1023 lh-posteriorcingulate
1024 lh-precentral
1025 lh-precuneus
1026 lh-rostralanteriorcingulate
1027 lh-rostralmiddlefrontal
1028 lh-superiorfrontal
1029 lh-superiorparietal
1030 lh-superiortemporal
1031 lh-supramarginal
1032 lh-frontalpole
1033 lh-temporalpole
1034 lh-transversetemporal
1035 lh-insula
2000 rh-unknown
2001 rh-bankssts
2002 rh-caudalanteriorcingulate
2003 rh-caudalmiddlefrontal
2004 rh-corpuscallosum
2005 rh-cuneus
2006 rh-entorhinal
2007 rh-fusiform
2008 rh-inferiorparietal
2009 rh-inferiortemporal
2010 rh-isthmuscingulate
2011 rh-lateraloccipital
2012 rh-lateralorbitofrontal
2013 rh-lingual
2014 rh-medialorbitofrontal
2015 rh-middletemporal
2016 rh-parahippocampal
2017 rh-paracentral
2018 rh-parsopercularis
2019 rh-parsorbitalis
2020 rh-parstriangularis
2021 rh-pericalcarine
2022 rh-postcentral
2023 rh-posteriorcingulate
2024 rh-precentral
2025 rh-precuneus
2026 rh-rostralanteriorcingulate
2027 rh-rostralmiddlefrontal
2028 rh-superiorfrontal
2029 rh-superiorparietal
2030 rh-superiortemporal
2031 rh-supramarginal
2032 rh-frontalpole
2033 rh-temporalpole
2034 rh-transversetemporal
2035 rh-insula

Thomas

Francois · August 16, 2018, 2:49pm

github.com/brainstorm-tools/brainstorm3

New labels

opened 02:13PM - 16 Aug 18 UTC

closed 02:18PM - 29 Aug 18 UTC

thinault

enhancement

Labels = {... 1000, 'lh-unknown'; ... 1001, 'lh-bankssts'; ... 1002, 'lh-caud…alanteriorcingulate'; ... 1003, 'lh-caudalmiddlefrontal'; ... 1004, 'lh-corpuscallosum'; ... 1005, 'lh-cuneus'; ... 1006, 'lh-entorhinal'; ... 1007, 'lh-fusiform'; ... 1008, 'lh-inferiorparietal'; ... 1009, 'lh-inferiortemporal'; ... 1010, 'lh-isthmuscingulate'; ... 1011, 'lh-lateraloccipital'; ... 1012, 'lh-lateralorbitofrontal'; ... 1013, 'lh-lingual'; ... 1014, 'lh-medialorbitofrontal'; ... 1015, 'lh-middletemporal'; ... 1016, 'lh-parahippocampal'; ... 1017, 'lh-paracentral'; ... 1018, 'lh-parsopercularis'; ... 1019, 'lh-parsorbitalis'; ... 1020, 'lh-parstriangularis'; ... 1021, 'lh-pericalcarine'; ... 1022, 'lh-postcentral'; ... 1023, 'lh-posteriorcingulate'; ... 1024, 'lh-precentral'; ... 1025, 'lh-precuneus'; ... 1026, 'lh-rostralanteriorcingulate'; ... 1027, 'lh-rostralmiddlefrontal'; ... 1028, 'lh-superiorfrontal'; ... 1029, 'lh-superiorparietal'; ... 1030, 'lh-superiortemporal'; ... 1031, 'lh-supramarginal'; ... 1032, 'lh-frontalpole'; ... 1033, 'lh-temporalpole'; ... 1034, 'lh-transversetemporal'; ... 1035, 'lh-insula'; ... 2000, 'rh-unknown'; ... 2001, 'rh-bankssts'; ... 2002, 'rh-caudalanteriorcingulate'; ... 2003, 'rh-caudalmiddlefrontal'; ... 2004, 'rh-corpuscallosum'; ... 2005, 'rh-cuneus'; ... 2006, 'rh-entorhinal'; ... 2007, 'rh-fusiform'; ... 2008, 'rh-inferiorparietal'; ... 2009, 'rh-inferiortemporal'; ... 2010, 'rh-isthmuscingulate'; ... 2011, 'rh-lateraloccipital'; ... 2012, 'rh-lateralorbitofrontal'; ... 2013, 'rh-lingual'; ... 2014, 'rh-medialorbitofrontal'; ... 2015, 'rh-middletemporal'; ... 2016, 'rh-parahippocampal'; ... 2017, 'rh-paracentral'; ... 2018, 'rh-parsopercularis'; ... 2019, 'rh-parsorbitalis'; ... 2020, 'rh-parstriangularis'; ... 2021, 'rh-pericalcarine'; ... 2022, 'rh-postcentral'; ... 2023, 'rh-posteriorcingulate'; ... 2024, 'rh-precentral'; ... 2025, 'rh-precuneus'; ... 2026, 'rh-rostralanteriorcingulate'; ... 2027, 'rh-rostralmiddlefrontal'; ... 2028, 'rh-superiorfrontal'; ... 2029, 'rh-superiorparietal'; ... 2030, 'rh-superiortemporal'; ... 2031, 'rh-supramarginal'; ... 2032, 'rh-frontalpole'; ... 2033, 'rh-temporalpole'; ... 2034, 'rh-transversetemporal'; ... 2035, 'rh-insula'; ... };

Francois · August 29, 2018, 2:18pm

Done in: https://github.com/brainstorm-tools/brainstorm3/commit/40631a4f45ad262af4484fc69cb610dfa8564af0

Update Brainstorm and try again

thhinault · September 4, 2018, 11:52am

It works now.
Thanks!

Thomas