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allow using existing native space ROIs instead of converting it in AFQ #1

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allow using existing native space ROIs instead of converting it in AFQ #1

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5d44288
using exsiting native ROIs instead of converting it in AFQ
Feb 14, 2020
0a48fda
using existing ROI instead of convert in AFQ
Feb 14, 2020
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4 changes: 2 additions & 2 deletions functions/AFQ_Create.m
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Original file line number Diff line number Diff line change
Expand Up @@ -334,8 +334,8 @@


% For some reason it is not going inside this loop, at least when testing in black the docker container
% if AFQ_get(afq,'use mrtrix')
if true
%if AFQ_get(afq,'use mrtrix')
if true
disp('use mrtrix is true')
for ii = 1:AFQ_get(afq,'num subs')
mrtrixdir = fullfile(afq.sub_dirs{ii},'mrtrix');
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72 changes: 42 additions & 30 deletions functions/AFQ_SegmentFiberGroups.m
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Expand Up @@ -324,41 +324,53 @@
fgCopy=fg; fgCopy.subgroup=[];
for roiID=1:size(moriRois, 1)
% Load the nifit image containing ROI-1 in MNI space
ROI_img_file=fullfile(tdir, 'MNI_JHU_tracts_ROIs', [moriRois{roiID, 1}]);
%% LMX: need to fix this hard code path for native space ROI
moridir = '/share/wandell/users/glerma/TESTDATA/FS/17_CAMINO_6835_2/pipeline/input'
ROI_img_file=fullfile(moridir, 'MORI', ['MORI_' moriRois{roiID, 1}]);
% Transform ROI-1 to an individuals native space
if recomputeROIs
% Default is to use the spm normalization unless a superior
% ANTS normalization was passed in
if exist('antsInvWarp','var') && ~isempty(antsInvWarp)
outfile = fullfile(fileparts(dt6File),'ROIs',moriRois{roiID, 1});
roi1(roiID) = ANTS_CreateRoiFromMniNifti(ROI_img_file, antsInvWarp, [], outfile);
else
[RoiFileName, invDef, roi1(roiID)]=dtiCreateRoiFromMniNifti(dt6File, ROI_img_file, invDef, true);
end
else
RoiFileName=fullfile(fileparts(dt6File), 'ROIs', [prefix(prefix(ROI_img_file, 'short'), 'short') '.mat']);
roi1(roiID) = dtiReadRoi(RoiFileName);
end
% if recomputeROIs
% % Default is to use the spm normalization unless a superior
% % ANTS normalization was passed in
% if exist('antsInvWarp','var') && ~isempty(antsInvWarp)
% outfile = fullfile(fileparts(dt6File),'ROIs',moriRois{roiID, 1});
% roi1(roiID) = ANTS_CreateRoiFromMniNifti(ROI_img_file, antsInvWarp, [], outfile);
% else
% [RoiFileName, invDef, roi1(roiID)]=dtiCreateRoiFromMniNifti(dt6File, ROI_img_file, invDef, true);
% end
% else
% RoiFileName=fullfile(fileparts(dt6File), 'ROIs', [prefix(prefix(ROI_img_file, 'short'), 'short') '.mat']);
% roi1(roiID) = dtiReadRoi(RoiFileName);
RoiFileName=fullfile(fileparts(dt6File), 'ROIs', [prefix(prefix(moriRois{roiID, 1}, 'short'), 'short') '.mat']);
roi1(roiID) = dtiImportRoiFromNifti(ROI_img_file);
if ~exist(fullfile(fileparts(dt6File), 'ROIs'), 'dir')
mkdir(fullfile(fileparts(dt6File), 'ROIs'))
end
dtiWriteRoi(roi1(roiID), RoiFileName)
% end
% Find fibers that intersect the ROI
[fgOut,contentiousFibers, keep1(:, roiID)] = dtiIntersectFibersWithRoi([], 'and', minDist, roi1(roiID), fg);
keepID1=find(keep1(:, roiID));
% Load the nifit image containing ROI-2 in MNI space
ROI_img_file=fullfile(tdir, 'MNI_JHU_tracts_ROIs', [moriRois{roiID, 2}]);
% Transform ROI-2 to an individuals native space
if recomputeROIs
[RoiFileName, invDef, roi]=dtiCreateRoiFromMniNifti(dt6File, ROI_img_file, invDef, true);
% Default is to use the spm normalization unless a superior
% ANTS normalization was passed in
if exist('antsInvWarp','var') && ~isempty(antsInvWarp)
outfile = fullfile(fileparts(dt6File),'ROIs',moriRois{roiID, 2});
roi2(roiID) = ANTS_CreateRoiFromMniNifti(ROI_img_file, antsInvWarp, [], outfile);
else
[RoiFileName, invDef, roi2(roiID)]=dtiCreateRoiFromMniNifti(dt6File, ROI_img_file, invDef, true);
end
else
RoiFileName=fullfile(fileparts(dt6File), 'ROIs', [prefix(prefix(ROI_img_file, 'short'), 'short') '.mat']);
roi2(roiID) = dtiReadRoi(RoiFileName);
end
ROI_img_file=fullfile(moridir, 'MORI', ['MORI_', moriRois{roiID, 2}]);

% % Transform ROI-2 to an individuals native space
% if recomputeROIs
% [RoiFileName, invDef, roi]=dtiCreateRoiFromMniNifti(dt6File, ROI_img_file, invDef, true);
% % Default is to use the spm normalization unless a superior
% % ANTS normalization was passed in
% if exist('antsInvWarp','var') && ~isempty(antsInvWarp)
% outfile = fullfile(fileparts(dt6File),'ROIs',moriRois{roiID, 2});
% roi2(roiID) = ANTS_CreateRoiFromMniNifti(ROI_img_file, antsInvWarp, [], outfile);
% else
% [RoiFileName, invDef, roi2(roiID)]=dtiCreateRoiFromMniNifti(dt6File, ROI_img_file, invDef, true);
% end
% else
% RoiFileName=fullfile(fileparts(dt6File), 'ROIs', [prefix(prefix(ROI_img_file, 'short'), 'short') '.mat']);
% roi2(roiID) = dtiReadRoi(RoiFileName);
roi2(roiID) = dtiImportRoiFromNifti(ROI_img_file);
RoiFileName=fullfile(fileparts(dt6File), 'ROIs', [prefix(prefix(moriRois{roiID, 2}, 'short'), 'short') '.mat']);
dtiWriteRoi(roi1(roiID), RoiFileName)
% end
%To speed up the function, we intersect with the second ROI not all the
%fibers, but only those that passed first ROI.
fgCopy.fibers=fg.fibers(keepID1(keepID1>0));
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2 changes: 2 additions & 0 deletions tmux-client-3598.log
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@@ -0,0 +1,2 @@
1581552296.322535 got 211 from server
1581552296.322600 got 203 from server