Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
249 changed files
with
18,795 additions
and
18,533 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,87 +1,87 @@ | ||
| % AA module | ||
| % Use the Anatomical Transformation Toolbox to normalise the structural to | ||
| % a template image | ||
|
|
||
| function [aap,resp]=aamod_ANTS_EPIwarp(aap,task,subj,sess) | ||
|
|
||
| resp=''; | ||
|
|
||
| switch task | ||
| case 'doit' | ||
|
|
||
| warning off | ||
|
|
||
| % Set the ANTS path | ||
| setenv('ANTSPATH', aap.directory_conventions.ANTSdir) | ||
| warpANTSpath = [fullfile(getenv('ANTSPATH'), 'bin', 'WarpImageMultiTransform') ' ']; | ||
|
|
||
| % Dimension number (always 3 for structural) | ||
| Ndim = [num2str(3) ' ']; | ||
|
|
||
| %% Get ANTs warps | ||
| ANTSimg = aas_getfiles_bystream(aap,subj,'ANTs'); | ||
| % Get structural directory for this subject | ||
| Spth = fileparts(ANTSimg(1,:)); | ||
|
|
||
| %% Template image | ||
| % [AVG] Changed to allow specification of any T1 template, does not | ||
| % need to be in the SPM folder any more... | ||
| sTimg = aap.directory_conventions.T1template; | ||
| if ~exist(sTimg, 'file') | ||
| aas_log(aap, true, sprintf('Couldn''t find template T1 image %s.', Timg)); | ||
| end | ||
|
|
||
| %% Get EPI images (or meanEPI, or...) | ||
|
|
||
| streams=aap.tasklist.currenttask.inputstreams; | ||
|
|
||
| % find out what streams we should normalise | ||
| streams=streams.stream(~[strcmp('ANTs',streams.stream)]); | ||
|
|
||
| % Is session specified in task header (used for meanepi, which only | ||
| % occurs in session 1) | ||
| if (isfield(aap.tasklist.currenttask.settings,'session')) | ||
| sess=aap.tasklist.currenttask.settings.session; | ||
| end | ||
|
|
||
| for streamind=1:length(streams) | ||
|
|
||
| % Images to warp | ||
| if (exist('sess','var')) | ||
| P = aas_getfiles_bystream(aap,subj,sess,streams{streamind}); | ||
| else | ||
| P = aas_getfiles_bystream(aap,subj,streams{streamind}); | ||
| end; | ||
|
|
||
| wimgs=[]; | ||
|
|
||
| for c=1:size(P,1) | ||
| [pth fn ext]=fileparts(P(c,:)); | ||
| wimgs = strvcat(wimgs,fullfile(pth,['w' fn ext])); | ||
|
|
||
| % delete previous because otherwise nifti write routine doesn't | ||
| % save disc space when you reslice to a coarser voxel | ||
| [s w]=aas_shell(['rm ' fullfile(pth,['w' fn ext])],true); % quietly | ||
|
|
||
| %% Use ANTS to normalise the stream! | ||
| warpANTS_command = [ warpANTSpath Ndim ... % dimension number | ||
| P(c,:) ' ' fullfile(pth, ['w' fn ext]) ... % moving image & output | ||
| ' -R ' sTimg ' '... % reference image | ||
| fullfile(Spth, 'antsWarp.nii')]; % transform | ||
| if exist(fullfile(Spth,'antsAffine.txt'), 'file') | ||
| warpANTS_command = [warpANTS_command ' ' fullfile(Spth, 'antsAffine.txt')]; % and affine, if this exists... | ||
| end | ||
|
|
||
| [s w] = aas_shell(warpANTS_command); | ||
| end | ||
|
|
||
| %% describe outputs | ||
|
|
||
| if (exist('sess','var')) | ||
| aap=aas_desc_outputs(aap,subj,sess,streams{streamind},wimgs); | ||
| else | ||
| aap=aas_desc_outputs(aap,subj,streams{streamind},wimgs); | ||
| end | ||
| end | ||
| end | ||
| % AA module | ||
| % Use the Anatomical Transformation Toolbox to normalise the structural to | ||
| % a template image | ||
|
|
||
| function [aap,resp]=aamod_ANTS_EPIwarp(aap,task,subj,sess) | ||
|
|
||
| resp=''; | ||
|
|
||
| switch task | ||
| case 'doit' | ||
|
|
||
| warning off | ||
|
|
||
| % Set the ANTS path | ||
| setenv('ANTSPATH', aap.directory_conventions.ANTSdir) | ||
| warpANTSpath = [fullfile(getenv('ANTSPATH'), 'bin', 'WarpImageMultiTransform') ' ']; | ||
|
|
||
| % Dimension number (always 3 for structural) | ||
| Ndim = [num2str(3) ' ']; | ||
|
|
||
| %% Get ANTs warps | ||
| ANTSimg = aas_getfiles_bystream(aap,subj,'ANTs'); | ||
| % Get structural directory for this subject | ||
| Spth = fileparts(ANTSimg(1,:)); | ||
|
|
||
| %% Template image | ||
| % [AVG] Changed to allow specification of any T1 template, does not | ||
| % need to be in the SPM folder any more... | ||
| sTimg = aap.directory_conventions.T1template; | ||
| if ~exist(sTimg, 'file') | ||
| aas_log(aap, true, sprintf('Couldn''t find template T1 image %s.', Timg)); | ||
| end | ||
|
|
||
| %% Get EPI images (or meanEPI, or...) | ||
|
|
||
| streams=aap.tasklist.currenttask.inputstreams; | ||
|
|
||
| % find out what streams we should normalise | ||
| streams=streams.stream(~[strcmp('ANTs',streams.stream)]); | ||
|
|
||
| % Is session specified in task header (used for meanepi, which only | ||
| % occurs in session 1) | ||
| if (isfield(aap.tasklist.currenttask.settings,'session')) | ||
| sess=aap.tasklist.currenttask.settings.session; | ||
| end | ||
|
|
||
| for streamind=1:length(streams) | ||
|
|
||
| % Images to warp | ||
| if (exist('sess','var')) | ||
| P = aas_getfiles_bystream(aap,subj,sess,streams{streamind}); | ||
| else | ||
| P = aas_getfiles_bystream(aap,subj,streams{streamind}); | ||
| end; | ||
|
|
||
| wimgs=[]; | ||
|
|
||
| for c=1:size(P,1) | ||
| [pth fn ext]=fileparts(P(c,:)); | ||
| wimgs = strvcat(wimgs,fullfile(pth,['w' fn ext])); | ||
|
|
||
| % delete previous because otherwise nifti write routine doesn't | ||
| % save disc space when you reslice to a coarser voxel | ||
| [s w]=aas_shell(['rm ' fullfile(pth,['w' fn ext])],true); % quietly | ||
|
|
||
| %% Use ANTS to normalise the stream! | ||
| warpANTS_command = [ warpANTSpath Ndim ... % dimension number | ||
| P(c,:) ' ' fullfile(pth, ['w' fn ext]) ... % moving image & output | ||
| ' -R ' sTimg ' '... % reference image | ||
| fullfile(Spth, 'antsWarp.nii')]; % transform | ||
| if exist(fullfile(Spth,'antsAffine.txt'), 'file') | ||
| warpANTS_command = [warpANTS_command ' ' fullfile(Spth, 'antsAffine.txt')]; % and affine, if this exists... | ||
| end | ||
|
|
||
| [s w] = aas_shell(warpANTS_command); | ||
| end | ||
|
|
||
| %% describe outputs | ||
|
|
||
| if (exist('sess','var')) | ||
| aap=aas_desc_outputs(aap,subj,sess,streams{streamind},wimgs); | ||
| else | ||
| aap=aas_desc_outputs(aap,subj,streams{streamind},wimgs); | ||
| end | ||
| end | ||
| end | ||
| end |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,19 +1,19 @@ | ||
| <?xml version="1.0" encoding="utf-8"?> | ||
| <aap> | ||
| <tasklist> | ||
| <currenttask domain='session' desc='Use ANTS to warp EPI to template based on structural warp' modality='MRI'> | ||
|
|
||
| <permanenceofoutput>1</permanenceofoutput> | ||
|
|
||
| <inputstreams> | ||
| <stream>epi</stream> | ||
| <stream>ANTs</stream> | ||
| </inputstreams> | ||
|
|
||
| <outputstreams> | ||
| <stream>epi</stream> | ||
| </outputstreams> | ||
|
|
||
| </currenttask> | ||
| </tasklist> | ||
| <?xml version="1.0" encoding="utf-8"?> | ||
| <aap> | ||
| <tasklist> | ||
| <currenttask domain='session' desc='Use ANTS to warp EPI to template based on structural warp' modality='MRI'> | ||
|
|
||
| <permanenceofoutput>1</permanenceofoutput> | ||
|
|
||
| <inputstreams> | ||
| <stream>epi</stream> | ||
| <stream>ANTs</stream> | ||
| </inputstreams> | ||
|
|
||
| <outputstreams> | ||
| <stream>epi</stream> | ||
| </outputstreams> | ||
|
|
||
| </currenttask> | ||
| </tasklist> | ||
| </aap> |
Oops, something went wrong.