Changes for Revision 1: Updates to code (new spatial specificity anal…

…yses) and manuscript (more specific discussion, related to transferability of approach to other systems), README

.gitmodules

@@ -1,15 +1,21 @@
+[submodule "Code/Toolboxes/tnufmri"]
+ path = Code/Toolboxes/tnufmri
+ url = git@tnurepository.ethz.ch:lkasper/tnufmri.git
 [submodule "Code/Toolboxes/UniQC"]
  path = Code/Toolboxes/UniQC
  url = git@gitlab.ethz.ch:uniqc/uniqc-code.git
 [submodule "Code/Toolboxes/UniQC-Tasks"]
  path = Code/Toolboxes/UniQC-Tasks
  url = git@gitlab.ethz.ch:uniqc/uniqc-tasks.git
-[submodule "Code/Toolboxes/export_fig"]
- path = Code/Toolboxes/export_fig
- url = https://github.com/altmany/export_fig.git
+[submodule "Code/Toolboxes/PhysIO"]
+ path = Code/Toolboxes/PhysIO
+ url = git@tnurepository.ethz.ch:physio/physio-public.git
 [submodule "Code/Toolboxes/spm12"]
  path = Code/Toolboxes/spm12
  url = git@tnurepository.ethz.ch:SPM/spm12.git
-[submodule "Code/Toolboxes/TAPAS"]
- path = Code/Toolboxes/TAPAS
- url = https://github.com/translationalneuromodeling/tapas.git
+[submodule "Code/Toolboxes/export_fig"]
+ path = Code/Toolboxes/export_fig
+ url = https://github.com/altmany/export_fig.git
+[submodule "Code/Toolboxes/ismrmrd"]
+ path = Code/Toolboxes/ismrmrd
+ url = https://github.com/ismrmrd/ismrmrd.git

Code/.gitignore

@@ -0,0 +1,2 @@
+*.asv
+*.m~

Code/Analysis/spifi_compute_summary.m

@@ -11,14 +11,14 @@ function spifi_compute_summary(details)
 % spifi_compute_summary
 %
 % See also
- 
+
 % Author: Lars Kasper
 % Created: 2019-06-19
 % Copyright (C) 2019 Institute for Biomedical Engineering
 % University of Zurich and ETH Zurich
 %
 % This file is part of the TAPAS UniQC Toolbox, which is released
-% under the terms of the GNU General Public License (GPL), version 3. 
+% under the terms of the GNU General Public License (GPL), version 3.
 % You can redistribute it and/or modify it under the terms of the GPL
 % (either version 3 or, at your option, any later version).
 % For further details, see the file COPYING or
@@ -51,9 +51,11 @@ function spifi_compute_summary(details)
 copyfile(details.glm.tcon, details.summary.tcon);
 
 
-% copy warped and unbiased stuff
-copyfile(details.preproc.anat.warp2mni, details.summary.anat.warp2mni);
-copyfile(details.preproc.func.biascorrected, details.summary.func.biascorrected);
-copyfile(details.preproc.func.warp2mni, details.summary.func.warp2mni);
-copyfile(details.glm.warp2mni.tcon_differential1, ...
- details.summary.glm.warp2mni.tcon_differential1);
+% copy warped and unbiased stuff, don't mind, if it does not exist
+try
+ copyfile(details.preproc.anat.warp2mni, details.summary.anat.warp2mni);
+ copyfile(details.preproc.func.biascorrected, details.summary.func.biascorrected);
+ copyfile(details.preproc.func.warp2mni, details.summary.func.warp2mni);
+ copyfile(details.glm.warp2mni.tcon_differential1, ...
+ details.summary.glm.warp2mni.tcon_differential1);
+end

Code/Analysis/spifi_coreg_anat_to_func.m

@@ -19,7 +19,7 @@
 % University of Zurich and ETH Zurich
 
 X = MrImageSpm4D(coregOpts.source);
-meanX = mean(X);
+meanX = mean(X, 't');
 meanX.save('fileName', coregOpts.mean);
 
 Y = MrImageSpm4D(coregOpts.ref);

Code/Analysis/spifi_run_segment_anat.m

@@ -1,8 +1,8 @@
-function matlabbatch = spifi_run_segment_anat(fileAnat, templateBatch, savedBatch)
+function matlabbatch = spifi_run_segment_anat(fileAnat, templateBatch, savedBatch, biasFwhm)
 % Segments anatomical image and saves bias-corrected version, as well as
 % bias field and tissue probability maps
 %
-% matlabbatch = spifi_run_segment_anat(fileAnat, templateBatch, savedBatch)
+% matlabbatch = spifi_run_segment_anat(fileAnat, templateBatch, savedBatch, biasFwhm)
 %
 % IN
 %
@@ -25,8 +25,14 @@
 % For further details, see the file COPYING or
 % <http://www.gnu.org/licenses/>.
 %
+
+if nargin < 4
+ biasFwhm = 60;
+end
+
 run(templateBatch);
 matlabbatch{1}.spm.spatial.preproc.channel.vols{1} = fileAnat;
+matlabbatch{1}.spm.spatial.preproc.channel.biasfwhm = biasFwhm;
 tnufmri_convert_batch_mat_to_m(matlabbatch, savedBatch);
 spm_jobman('interactive', matlabbatch);
 spm_jobman('run', matlabbatch);

Code/Analysis/spifi_warp2mni_func_anat.m

@@ -23,7 +23,7 @@
 matlabbatch{1}.spm.spatial.normalise.write.subj.def{1} = ...
  opts.forwardDeformationField;
 matlabbatch{1}.spm.spatial.normalise.write.subj.resample = ...
- opts.source;
+ opts.source(isfile(opts.source)); % only warp existing files
 tnufmri_convert_batch_mat_to_m(matlabbatch, opts.saveBatch)
 spm_jobman('interactive', matlabbatch);
 spm_jobman('run', matlabbatch);

Code/Attic/check_quality.m

@@ -0,0 +1,44 @@
+function qcImages = check_quality(fileNameNifti)
+% Computes Quality Control measures for nifti time series and plots the
+% relevant ones
+%
+% qcImages = check_quality(fileNameNifti)
+%
+% IN
+%
+% OUT
+% qcImages cell(nImages,1) of MrImage, relevant quality control
+% images, e.g., mean/tsnr/maxdiffabs etc.
+%
+% EXAMPLE
+% check_quality
+%
+% See also
+%
+% Author: Lars Kasper
+% Created: 2018-05-23
+% Copyright (C) 2018 Institute for Biomedical Engineering
+% University of Zurich and ETH Zurich
+%
+% This file is part of the TAPAS UniQC Toolbox, which is released
+% under the terms of the GNU General Public License (GPL), version 3. 
+% You can redistribute it and/or modify it under the terms of the GPL
+% (either version 3 or, at your option, any later version).
+% For further details, see the file COPYING or
+% <http://www.gnu.org/licenses/>.
+%
+% $Id: new_function2.m 354 2013-12-02 22:21:41Z kasperla $
+
+Y = MrImage(fileNameNifti);
+
+Y.mean.plot()
+Y.std.plot()
+Y.snr.plot()
+
+plot(abs(Y-mean(Y)), 'useSlider', 'true');
+
+plot(image2k(Y-mean(Y)), 'useSlider', 'true');
+
+
+
+qcImages{1} = Y;

Code/Attic/glm_uniqc.m

@@ -0,0 +1,39 @@
+%% model specification
+TR = 3.128
+physio_path = ...
+fileExplicitMask = '';% fullfile(data_path, 'masks', 'brain_mask.nii');
+
+% timing in seconds
+data.glm.timingUnits = 'secs';
+% repetition time
+data.glm.repetitionTime = TR;
+% model derivatives
+data.glm.hrfDerivatives = [0 0]; %[1 1];
+% noise model FAST
+data.glm.serialCorrelations = 'FAST';
+% add conditions
+% specify block length first
+block_length = 18;
+% specify first condition
+first_condition = [1 5 7 11 13 17];
+first_condition_onsets = first_condition*block_length;
+% specify second condition
+second_condition = [2 4 8 10 14 16];
+second_condition_onsets = second_condition*block_length;
+% add to glm
+data.glm.conditions.names = {'simple', 'complex'};
+data.glm.conditions.onsets = {second_condition_onsets, first_condition_onsets};
+% add durations
+data.glm.conditions.durations = {block_length, block_length};
+% add confound regressors
+confound_regressors = load(fullfile(physio_path,'multiple_regressors.txt')); 
+data.glm.regressors.other = confound_regressors;
+% add an explicit mask
+data.glm.explicitMasking = fileExplicitMask;
+% turn of inplicit masking threshold;
+data.glm.maskingThreshold = -Inf;
+
+% compute stat images
+data.compute_stat_images;
+% estimate
+data.specify_and_estimate_1st_level;

Code/Representation/Revision1/create_figure_readout_duration_t2star.m

@@ -0,0 +1,39 @@
+function fhArray = create_figure_readout_duration_t2star()
+%Compares full spiral readout to cropped one (1mm, 37ms) to show effect of
+%longer readout under T2*
+%
+% fhArray = create_figure_readout_duration_t2star()
+%
+% Note: This needs to run SPIFI_0007_MainReconstructImages of
+% recon-scripts-spifi (git@tnurepository.ethz.ch:laymm/recon-scripts-spifi.git)
+% at commit 8a79c10886f27fc83419d720ddf936f9cf026a69 before
+%
+% IN
+%
+% OUT
+%
+% EXAMPLE
+% create_figure_readout_duration_t2star
+%
+% See also
+
+% Author: Lars Kasper
+% Created: 2020-06-18
+% Copyright (C) 2020 Institute for Biomedical Engineering
+% University of Zurich and ETH Zurich
+%
+% This file is part of the TAPAS UniQC Toolbox, which is released
+% under the terms of the GNU General Public License (GPL), version 3. 
+% You can redistribute it and/or modify it under the terms of the GPL
+% (either version 3 or, at your option, any later version).
+% For further details, see the file COPYING or
+% <http://www.gnu.org/licenses/>.
+%
+
+X = MrImage
+X.read_data_from_graphics_handle(21)
+Y = MrImage
+Y.read_data_from_graphics_handle(14)
+X.plot
+Y.plot
+plot(abs(X./max(X)-Y./max(Y)))

Code/Representation/create_figure_spm_subject.m

@@ -149,7 +149,7 @@
  zI(end-1:end), ...
  'selectedSlices', figOptions.selectedSlice, ...
  sharedParameters_tra{:}, ...
- 'nRows', 1);
+ 'nRows', 4);
  case 'sag'
  %% sagittal plot
  zI = resizedUnderlay.crop_all({'x', [100 100]}, Y(nFiles+[-1 0]));