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Merged
merged 4 commits into from
May 18, 2023
Merged

[ENH] Transfer all atlases to spm atlas #100

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2702f53
prepare visfatlas
Remi-Gau May 18, 2023
227e736
transfer visatlas
Remi-Gau May 18, 2023
31b03cf
copy wang atlas to spm atlas dir
Remi-Gau May 18, 2023
f071c64
fix texts
Remi-Gau May 18, 2023
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2 changes: 1 addition & 1 deletion atlas/Glasser/space-MNI152ICBM2009anlin_atlas-glasser_dseg.xml
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@@ -1,7 +1,7 @@
<?xml version="1.0" encoding="ISO-8859-1"?>
<atlas version="2.0">
<header>
<name>space-MNI152ICBM2009anlin_atlas-glasser_dseg</name>
<name>A multi-modal parcellation of human cerebral cortex. Glasser 2016</name>
<version>1.0</version>
<description>space-MNI152ICBM2009anlin_atlas-glasser_dseg</description>
<url></url>
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41 changes: 41 additions & 0 deletions atlas/space-MNI_atlas-wang_dseg.xml
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@@ -0,0 +1,41 @@
<atlas version="2.0">
<header>
<name>Probabilistic Maps of Visual Topography in Human Cortex. Wang 2015.</name>
<version>1.0</version>
<description>space-MNI_atlas-wang_dseg</description>
<url />
<licence />
<coordinate_system>MNI</coordinate_system>
<type>Label</type>
<images>
<imagefile>space-MNI_atlas-wang_dseg.nii</imagefile>
</images>
</header>
<data>
<label><index>1</index><name>V1v</name></label>
<label><index>2</index><name>V1d</name></label>
<label><index>3</index><name>V2v</name></label>
<label><index>4</index><name>V2d</name></label>
<label><index>5</index><name>V3v</name></label>
<label><index>6</index><name>V3d</name></label>
<label><index>7</index><name>hV4</name></label>
<label><index>8</index><name>VO1</name></label>
<label><index>9</index><name>VO2</name></label>
<label><index>10</index><name>PHC1</name></label>
<label><index>11</index><name>PHC2</name></label>
<label><index>12</index><name>MST</name></label>
<label><index>13</index><name>hMT</name></label>
<label><index>14</index><name>LO2</name></label>
<label><index>15</index><name>LO1</name></label>
<label><index>16</index><name>V3b</name></label>
<label><index>17</index><name>V3a</name></label>
<label><index>18</index><name>IPS0</name></label>
<label><index>19</index><name>IPS1</name></label>
<label><index>20</index><name>IPS2</name></label>
<label><index>21</index><name>IPS3</name></label>
<label><index>22</index><name>IPS4</name></label>
<label><index>23</index><name>IPS5</name></label>
<label><index>24</index><name>SPL1</name></label>
<label><index>25</index><name>FEF</name></label>
</data>
</atlas>
5 changes: 2 additions & 3 deletions atlas/update_atlas_xml.py
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Expand Up @@ -7,16 +7,15 @@

lut_file = (
Path(__file__).parent
/ "Glasser"
/ "visual_topography_probability_atlas"
/ "LUT.csv"
)

df = pd.read_csv(lut_file, sep=",")

xml_file = (
Path(__file__).parent
/ "Glasser"
/ "space-MNI152ICBM2009anlin_atlas-glasser_dseg.xml"
/ "space-MNI_atlas-wang_dseg.xml"
)

mytree = ET.parse(xml_file)
Expand Down
49 changes: 49 additions & 0 deletions atlas/visfAtlas/space-MNI_atlas-visfAtlas_dseg.xml
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@@ -0,0 +1,49 @@
<atlas version="2.0">
<header>
<name>A probabilistic functional parcellation of human occipito-temporal cortex. Rosenke 2020.</name>
<version>1.0</version>
<description>space-MNI_atlas-visfAtlas_dseg</description>
<url />
<licence />
<coordinate_system>MNI</coordinate_system>
<type>Label</type>
<images>
<imagefile>space-MNI_atlas-visfAtlas_dseg.nii</imagefile>
</images>
</header>
<data>
<label><index>1</index><name>lh_mFus</name></label>
<label><index>2</index><name>lh_pFus</name></label>
<label><index>3</index><name>lh_IOG</name></label>
<label><index>4</index><name>lh_OTS</name></label>
<label><index>5</index><name>lh_ITG</name></label>
<label><index>6</index><name>lh_MTG</name></label>
<label><index>7</index><name>lh_LOS</name></label>
<label><index>8</index><name>lh_pOTS</name></label>
<label><index>9</index><name>lh_IOS</name></label>
<label><index>10</index><name>lh_CoS</name></label>
<label><index>11</index><name>lh_hMT</name></label>
<label><index>12</index><name>lh_v1d</name></label>
<label><index>13</index><name>lh_v2d</name></label>
<label><index>14</index><name>lh_v3d</name></label>
<label><index>15</index><name>lh_v1v</name></label>
<label><index>16</index><name>lh_v2v</name></label>
<label><index>17</index><name>lh_v3v</name></label>
<label><index>18</index><name>rh_mFus</name></label>
<label><index>19</index><name>rh_pFus</name></label>
<label><index>20</index><name>rh_IOG</name></label>
<label><index>21</index><name>rh_OTS</name></label>
<label><index>22</index><name>rh_ITG</name></label>
<label><index>23</index><name>rh_MTG</name></label>
<label><index>24</index><name>rh_LOS</name></label>
<label><index>25</index><name>rh_CoS</name></label>
<label><index>26</index><name>rh_TOS</name></label>
<label><index>27</index><name>rh_hMT</name></label>
<label><index>28</index><name>rh_v1d</name></label>
<label><index>29</index><name>rh_v2d</name></label>
<label><index>30</index><name>rh_v3d</name></label>
<label><index>31</index><name>rh_v1v</name></label>
<label><index>32</index><name>rh_v2v</name></label>
<label><index>33</index><name>rh_v3v</name></label>
</data>
</atlas>
2 changes: 2 additions & 0 deletions initCppRoi.m
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Expand Up @@ -31,6 +31,8 @@ function initCppRoi()
copyAtlasToSpmDir('HCPex', 'verbose', true);
copyAtlasToSpmDir('AAL', 'verbose', true);
copyAtlasToSpmDir('Glasser', 'verbose', true);
copyAtlasToSpmDir('Wang', 'verbose', true);
copyAtlasToSpmDir('visfAtlas', 'verbose', true);

CPP_ROI_INITIALIZED = true();

Expand Down
93 changes: 67 additions & 26 deletions src/atlas/copyAtlasToSpmDir.m
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Expand Up @@ -6,7 +6,8 @@ function copyAtlasToSpmDir(varargin)
%
% copyAtlasToSpmDir(atlas, 'verbose', false)
%
% :param atlas: Any of ``{'AAL'}``. Defaults to ``'AAL'``
% :param atlas: Any of ``{'aal', 'hcpex', 'glasser', 'visfatlas', 'wang'}``.
% Defaults to ``'AAL'``
% :type atlas: char
%
% :param verbose: Defaults to ``false``
Expand All @@ -16,8 +17,6 @@ function copyAtlasToSpmDir(varargin)

% (C) Copyright 2022 CPP ROI developers

SUPPORTED_ATLASES = {'aal', 'hcpex'};

args = inputParser;

addOptional(args, 'atlas', 'AAL', @ischar);
Expand All @@ -30,29 +29,7 @@ function copyAtlasToSpmDir(varargin)

spmAtlasDir = fullfile(spm('dir'), 'atlas');

switch lower(atlas)

case 'aal'
sourceAtlasImage = fullfile(returnAtlasDir(), 'AAL3', 'AAL3v1_1mm.nii.gz');
sourceAtlasXml = fullfile(returnAtlasDir(), 'AAL3', 'AAL3v1_1mm.xml');

case 'hcpex'
unzipAtlas(lower(atlas));
sourceAtlasImage = fullfile(returnAtlasDir(lower(atlas)), 'HCPex.nii');
sourceAtlasXml = fullfile(returnAtlasDir(), 'HCPex.xml');

case 'glasser'
unzipAtlas(lower(atlas));
sourceAtlasImage = fullfile(returnAtlasDir(lower(atlas)), ...
'space-MNI152ICBM2009anlin_atlas-glasser_dseg.nii');
sourceAtlasXml = fullfile(returnAtlasDir(lower(atlas)), ...
'space-MNI152ICBM2009anlin_atlas-glasser_dseg.xml');

otherwise
error(['Only the following atlases can be copied to SPM atlas folder:\n', ...
bids.internal.create_unordered_list(SUPPORTED_ATLASES)]);

end
[sourceAtlasImage, sourceAtlasXml] = prepareFiles(atlas);

targetAtlasImage = fullfile(spmAtlasDir, spm_file(sourceAtlasImage, 'filename'));
targetAtlasXml = fullfile(spmAtlasDir, spm_file(sourceAtlasXml, 'filename'));
Expand Down Expand Up @@ -90,4 +67,68 @@ function copyAtlasToSpmDir(varargin)

end

if strcmpi(atlas, 'wang')
delete(sourceAtlasImage);
end

end

function [sourceAtlasImage, sourceAtlasXml] = prepareFiles(atlas)

SUPPORTED_ATLASES = {'aal', 'hcpex', 'glasser', 'visfatlas', 'wang'};

atlas = lower(atlas);
switch atlas

case 'aal'
sourceAtlasImage = fullfile(returnAtlasDir(), 'AAL3', 'AAL3v1_1mm.nii.gz');
sourceAtlasXml = fullfile(returnAtlasDir(), 'AAL3', 'AAL3v1_1mm.xml');

case 'hcpex'
sourceAtlasImage = fullfile(returnAtlasDir(atlas), 'HCPex.nii');
sourceAtlasXml = fullfile(returnAtlasDir(), 'HCPex.xml');

case 'visfatlas'
sourceAtlasImage = fullfile(returnAtlasDir(atlas), 'space-MNI_atlas-visfAtlas_dseg.nii');
sourceAtlasXml = fullfile(returnAtlasDir(atlas), 'space-MNI_atlas-visfAtlas_dseg.xml');

case 'glasser'

sourceAtlasImage = fullfile(returnAtlasDir(atlas), ...
'space-MNI152ICBM2009anlin_atlas-glasser_dseg.nii');
sourceAtlasXml = fullfile(returnAtlasDir(atlas), ...
'space-MNI152ICBM2009anlin_atlas-glasser_dseg.xml');

case 'wang'
sourceAtlasImage = fullfile(returnAtlasDir(atlas), ...
'subj_vol_all', ...
'space-MNI_atlas-wang_dseg.nii');
sourceAtlasXml = fullfile(returnAtlasDir(), ...
'space-MNI_atlas-wang_dseg.xml');

otherwise
error(['Only the following atlases can be copied to SPM atlas folder:\n', ...
bids.internal.create_unordered_list(SUPPORTED_ATLASES)]);

end

if ismember(atlas, {'hcpex', 'glasser', 'visfatlas', 'wang'})
if exist(sourceAtlasImage, 'file') ~= 2
unzipAtlas(atlas);
end
end

if strcmp(atlas, 'wang')
% merge left and right
files = spm_select('FPList', ...
fullfile(returnAtlasDir(lower(atlas)), 'subj_vol_all'), ...
'^space.*hemi.*nii$');
hdr = spm_vol(files);
vols = spm_read_vols(hdr);
vol = sum(vols, 4);
hdr = hdr(1);
hdr(1).fname = sourceAtlasImage;
spm_write_vol(hdr, vol);
end

end
4 changes: 3 additions & 1 deletion src/atlas/extractRoiFromAtlas.m
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Expand Up @@ -92,7 +92,9 @@
roiIdx = strcmp([hemisphere '_' roiName], lut.ROI);

case 'glasser'

warning(['The volumetric version of the Glasser atlas is not ideally suited ', ...
'to be used for standard brain-mapping approaches ', ...
'that use volumetric nonlinear deformations.']);
roiIdx = strcmp(roiName, lut.ROI);

end
Expand Down
55 changes: 43 additions & 12 deletions tests/test_copyAtlasToSpmDir.m
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Expand Up @@ -7,11 +7,39 @@
initTestSuite;
end

function test_copyAtlasToSpmDir_glasser()
function test_copyAtlasToSpmDir_wang()

if bids.internal.is_github_ci()
return
end
copyAtlasToSpmDir('wang', 'verbose', false);

targetAtlasImage = fullfile(spmAtlasDir(), ...
'space-MNI_atlas-wang_dseg.nii');
targetAtlasXml = fullfile(spmAtlasDir(), ...
'space-MNI_atlas-wang_dseg.xml');

assertEqual(exist(targetAtlasImage, 'file'), 2);
assertEqual(exist(targetAtlasXml, 'file'), 2);

cleanSpmAtlasDir();

end

function test_copyAtlasToSpmDir_visfatlas()

copyAtlasToSpmDir('visfatlas', 'verbose', false);

targetAtlasImage = fullfile(spmAtlasDir(), ...
'space-MNI_atlas-visfAtlas_dseg.nii');
targetAtlasXml = fullfile(spmAtlasDir(), ...
'space-MNI_atlas-visfAtlas_dseg.xml');

assertEqual(exist(targetAtlasImage, 'file'), 2);
assertEqual(exist(targetAtlasXml, 'file'), 2);

cleanSpmAtlasDir();

end

function test_copyAtlasToSpmDir_glasser()

copyAtlasToSpmDir('Glasser', 'verbose', false);

Expand All @@ -23,14 +51,12 @@ function test_copyAtlasToSpmDir_glasser()
assertEqual(exist(targetAtlasImage, 'file'), 2);
assertEqual(exist(targetAtlasXml, 'file'), 2);

cleanSpmAtlasDir();

end

function test_copyAtlasToSpmDir_basic()

if bids.internal.is_github_ci()
return
end

copyAtlasToSpmDir('AAL', 'verbose', false);

targetAtlasImage = fullfile(spmAtlasDir(), 'AAL3v1_1mm.nii');
Expand All @@ -39,14 +65,12 @@ function test_copyAtlasToSpmDir_basic()
assertEqual(exist(targetAtlasImage, 'file'), 2);
assertEqual(exist(targetAtlasXml, 'file'), 2);

cleanSpmAtlasDir();

end

function test_copyAtlasToSpmDir_HPCex()

if bids.internal.is_github_ci()
return
end

copyAtlasToSpmDir('HCPex', 'verbose', false);

targetAtlasImage = fullfile(spmAtlasDir(), 'HCPex.nii');
Expand All @@ -55,8 +79,15 @@ function test_copyAtlasToSpmDir_HPCex()
assertEqual(exist(targetAtlasImage, 'file'), 2);
assertEqual(exist(targetAtlasXml, 'file'), 2);

cleanSpmAtlasDir();

end

function value = spmAtlasDir()
value = fullfile(spm('dir'), 'atlas');
end

function cleanSpmAtlasDir()
delete(fullfile(spmAtlasDir, '*.nii'));
delete(fullfile(spmAtlasDir, '*.xml'));
end