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Changed: Correction and cleanup of the CAT SPM preprocessing batch in
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          cat_conf_extopts, cat_run, cat_run_job[1639], and cat_main1639.
          Improved documentation and help and make batch visible for default
          users.
Changed:  Allowed to have empty template files to keep the SPM registration
          and have no specific probability maps for WMHs and lesions in
          cat_main[1639], cat_main_registration, and cat_run.
Fixed:    Corrected bug in testing for BIDS in cat_io_writenii.
Fixed:    Corrected bug in cat_main_report use in the retrospective CAT
          report pointed out by Thomas Stephan (issue #24).
Fixed:    Corrected bug in cat_long_report > cat_stat_homogeneity in case
          of BIDS setting with subdirs.
Changed paths:
 M CHANGES.txt
 M cat_conf_extopts.m
 M cat_io_writenii.m
 M cat_main.m
 M cat_main1639.m
 M cat_main_registration.m
 M cat_main_report.m
 M cat_main_reportstr.m
 M cat_run.m
 M cat_run_job.m
 M cat_run_job1639.m
 M cat_stat_homogeneity.m
 M tbx_cfg_cat.m
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@robdahn
robdahn committed May 8, 2024
1 parent 37c2919 commit 61fdd4c
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29 changes: 29 additions & 0 deletions CHANGES.txt
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Original file line number Diff line number Diff line change
@@ -1,4 +1,33 @@
------------------------------------------------------------------------
r2579 | dahnke | 2024-05-08 17:39:57

Changed paths:
M CHANGES.txt
M cat_conf_extopts.m
M cat_io_writenii.m
M cat_main.m
M cat_main1639.m
M cat_main_registration.m
M cat_main_report.m
M cat_main_reportstr.m
M cat_run.m
M cat_run_job.m
M cat_run_job1639.m
M cat_stat_homogeneity.m
M tbx_cfg_cat.m

Changed: Correction and cleanup of the CAT SPM preprocessing batch in
cat_conf_extopts, cat_run, cat_run_job[1639], and cat_main1639.
Improved documentation and help and make batch visible for default
users.
Changed: Allowed to have empty template files to keep the SPM registration
and have no specific probability maps for WMHs and lesions in
cat_main[1639], cat_main_registration, and cat_run.
Fixed: Corrected bug in testing for BIDS in cat_io_writenii.
Fixed: Corrected bug in cat_main_report use in the retrospective CAT
report pointed out by Thomas Stephan (issue #24).
Fixed: Corrected bug in cat_long_report > cat_stat_homogeneity in case
of BIDS setting with subdirs.------------------------------------------------------------------------
r2578 | gaser | 2024-05-07 16:03:00

Changed paths:
Expand Down
113 changes: 84 additions & 29 deletions cat_conf_extopts.m
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Original file line number Diff line number Diff line change
Expand Up @@ -52,31 +52,50 @@
darteltpm.tag = 'darteltpm';
darteltpm.name = 'Dartel Template';
darteltpm.def = @(val)cat_get_defaults('extopts.darteltpm', val{:});
darteltpm.num = [1 1];
darteltpm.num = [1-spmseg 1];
darteltpm.filter = 'image';
darteltpm.ufilter = 'Template_1';
darteltpm.help = {
'Select the first of six images (iterations) of a Dartel template. The Dartel template must be in multi-volume (5D) nifti format and should contain GM and WM segmentations. '
''
'Please note that the use of an own Dartel template will result in deviations and unreliable results for any ROI-based estimations because the atlases will differ and any ROI processing will be therefore deselected.'
''
};
if spmseg
darteltpm.help = {
'Select the first of six images (iterations) of a Dartel template. The Dartel template must be in multi-volume (5D) nifti format and should contain GM and WM segmentations. If the field is empty no Dartel registration will be perfor'
''
'Please note that the use of an own Dartel template will result in deviations and unreliable results for any ROI-based estimations because the atlases will differ and any ROI processing will be therefore deselected.'
''
};
else
darteltpm.help = {
'Select the first of six images (iterations) of a Dartel template. The Dartel template must be in multi-volume (5D) nifti format and should contain GM and WM segmentations. '
''
'Please note that the use of an own Dartel template will result in deviations and unreliable results for any ROI-based estimations because the atlases will differ and any ROI processing will be therefore deselected.'
''
};
end


%---------------------------------------------------------------------

shootingtpm = cfg_files;
shootingtpm.tag = 'shootingtpm';
shootingtpm.name = 'Shooting Template';
shootingtpm.def = @(val)cat_get_defaults('extopts.shootingtpm', val{:});
shootingtpm.num = [1 1];
shootingtpm.num = [1-spmseg 1];
shootingtpm.filter = 'image';
shootingtpm.ufilter = 'Template_0';
shootingtpm.help = {
'Select the first of five images (iterations) of a Shooting template. The Shooting template must be in multi-volume (5D) nifti format and should contain GM, WM, and background segmentations and have to be saved with at least 16 bit. '
''
'Please note that the use of an own Shooting template will result in deviations and unreliable results for any ROI-based estimations because the atlases will differ and any ROI processing will be therefore deselected.'
''
if spmseg
shootingtpm.help = {
'Select the first of five images (iterations) of a Shooting template. The Shooting template must be in multi-volume (5D) nifti format and should contain GM, WM, and background segmentations and have to be saved with at least 16 bit. If the field is empty no Dartel registration will be performed and the default SPM registration is used instead.'
''
'Please note that the use of an own Shooting template will result in deviations and unreliable results for any ROI-based estimations because the atlases will differ and any ROI processing will be therefore deselected.'
''
};
else
shootingtpm.help = {
'Select the first of five images (iterations) of a Shooting template. The Shooting template must be in multi-volume (5D) nifti format and should contain GM, WM, and background segmentations and have to be saved with at least 16 bit. '
''
'Please note that the use of an own Shooting template will result in deviations and unreliable results for any ROI-based estimations because the atlases will differ and any ROI processing will be therefore deselected.'
''
};
end

%------------------------------------------------------------------------

Expand All @@ -98,7 +117,12 @@
brainmask.name = 'Brainmask';
brainmask.filter = 'image';
brainmask.ufilter = 'brainmask';
brainmask.def = @(val)cat_get_defaults('extopts.brainmask', val{:});
if spmseg % in case of SPM this fields are not required yet
brainmask.val{1} = {''};
else
brainmask.def = @(val)cat_get_defaults('extopts.brainmask', val{:});
end
brainmask.hidden = ~spmseg || expert<2;
brainmask.num = [1 1];
brainmask.help = {
'Initial brainmask.'
Expand All @@ -111,10 +135,15 @@
T1.name = 'T1';
T1.filter = 'image';
T1.ufilter = 'T1';
T1.def = @(val)cat_get_defaults('extopts.T1', val{:});
T1.num = [1 1];
if spmseg % in case of SPM this fields are not required yet
T1.val{1}= {''};
else
T1.def = @(val)cat_get_defaults('extopts.T1', val{:});
end
T1.hidden = ~spmseg || expert<2;
T1.num = [1-spmseg 1];
T1.help = {
'Affine registration template.'
'Affine registration template. ' % Implement? >> If no image is give only the TPM is used for registration.
};

%------------------------------------------------------------------------
Expand All @@ -124,14 +153,18 @@
WMHtpm.name = 'WMH-TPM';
WMHtpm.filter = 'image';
WMHtpm.ufilter = '';
if isempty(cat_get_defaults('extopts.WMHtpm')) % default files without WMHtpm
WMHtpm.hidden = ~spmseg || expert<2;
if spmseg % in case of SPM this fields are not required yet
WMHtpm.val{1}= {''};
elseif isempty(cat_get_defaults('extopts.WMHtpm')) % default files without WMHtpm
WMHtpm.val{1}= spm_file(cat_get_defaults('extopts.T1'),'filename','cat_wmh_miccai2017.nii');
else
WMHtpm.def = @(val)cat_get_defaults('extopts.WMHtpm', val{:});
end
WMHtpm.num = [0 1];
WMHtpm.help = {
'White matter hyperintensity tissue probability map.'
'White matter hyperintensity tissue probability map. '
'If no image is give the WMH detection focus on atypical GM close to ventrile regions or within the WM that does not belong to subcortical structures without further prior weighting. '
};

%------------------------------------------------------------------------
Expand All @@ -141,14 +174,18 @@
BVtpm.name = 'BV-TPM';
BVtpm.filter = 'image';
BVtpm.ufilter = '';
if isempty(cat_get_defaults('extopts.BVtpm')) % default files without BVtpm
BVtpm.hidden = ~spmseg || expert<2;
if spmseg % in case of SPM this fields are not required yet
BVtpm.val{1}= {''};
elseif isempty(cat_get_defaults('extopts.BVtpm')) % default files without BVtpm
BVtpm.val{1}= spm_file(cat_get_defaults('extopts.T1'),'filename','cat_bloodvessels.nii');
else
BVtpm.def = @(val)cat_get_defaults('extopts.BVtpm', val{:});
end
BVtpm.num = [0 1];
BVtpm.help = {
'Blood vessel tissue probability map.'
'Blood vessel tissue probability map. '
'If no map is give the blood vessel detection focus on high intensity 1D structures without further prior weighting. '
};

%------------------------------------------------------------------------
Expand All @@ -158,7 +195,10 @@
SLtpm.name = 'SL-TPM';
SLtpm.filter = 'image';
SLtpm.ufilter = '';
if isempty(cat_get_defaults('extopts.SLtpm')) % default files without SLtpm
SLtpm.hidden = ~spmseg || expert<2;
if spmseg
SLtpm.val{1} = {''}; %<UNDEFINED>
elseif isempty(cat_get_defaults('extopts.SLtpm')) % default files without SLtpm
SLtpm.val{1}= spm_file(cat_get_defaults('extopts.T1'),'filename','cat_strokelesions_ATLAS303.nii');
else
SLtpm.def = @(val)cat_get_defaults('extopts.SLtpm', val{:});
Expand All @@ -177,7 +217,7 @@
bb.tag = 'bb';
bb.name = 'Bounding box';
bb.def = @(val)cat_get_defaults('extopts.bb', val{:});
bb.hidden = expert < 1;
bb.hidden = expert < 1 && ~spmseg;
bb.help = {
'The bounding box describes the dimensions of the volume to be written starting from the anterior commissure in mm. It should include the entire brain (or head in the case of the Boundary Box of the SPM TPM) and additional space for smoothing the image. The MNI 9-mm boundary box is optimized for CATs MNI152NLin2009cAsym template and supports filter cores up to 10 mm. Although this box support 12 mm filter sizes theoretically, slight interference could occur at the edges and larger boxes are recommended for safety. '
'Additionally, it is possible to use the boundary box of the TPM or the template for special (animal) templates with strongly different boundary boxes. '
Expand Down Expand Up @@ -523,7 +563,7 @@
vdist.labels = {'optimal (2)','fine (1)','extra fine (0.5)'};
vdist.values = {2 1 0.5};
vdist.def = @(val)cat_get_defaults('extopts.vdist', val{:});
vdist.hidden = expert<1;
vdist.hidden = expert<1 | (spmseg & expert<2);
vdist.help = {
['Higher mesh resolution may support indipendent measuresments but also increase the chance of self-intersections. ' ...
'For each level, the mesh resolution (number of elements) is doubled and accuracy is increased slightly (by the square root). ' ...
Expand Down Expand Up @@ -1135,7 +1175,12 @@
scale_cortex.name = 'Modify cortical surface creation';
scale_cortex.strtype = 'r';
scale_cortex.num = [1 1];
scale_cortex.def = @(val)cat_get_defaults('extopts.scale_cortex', val{:});
if spmseg
scale_cortex.hidden = true;
scale_cortex.val{1} = 0.5;
else
scale_cortex.def = @(val)cat_get_defaults('extopts.scale_cortex', val{:});
end
scale_cortex.help = {
'Scale intensity values for cortex to start with initial surface that is closer to GM/WM border to prevent that gyri/sulci are glued if you still have glued gyri/sulci (mainly in the occ. lobe). You can try to decrease this value (start with 0.6). Please note that decreasing this parameter also increases the risk of an interrupted parahippocampal gyrus.'
''
Expand All @@ -1146,7 +1191,12 @@
add_parahipp.name = 'Modify parahippocampal surface creation';
add_parahipp.strtype = 'r';
scale_cortex.num = [1 1];
add_parahipp.def = @(val)cat_get_defaults('extopts.add_parahipp', val{:});
if spmseg
add_parahipp.hidden = true;
add_parahipp.val{1} = 0;
else
add_parahipp.def = @(val)cat_get_defaults('extopts.add_parahipp', val{:});
end
add_parahipp.help = {
'Increase values in the parahippocampal area to prevent large cuts in the parahippocampal gyrus (initial surface in this area will be closer to GM/CSF border if the parahippocampal gyrus is still cut. You can try to increase this value (start with 0.15).'
''
Expand All @@ -1157,7 +1207,12 @@
close_parahipp.name = 'Initial morphological closing of parahippocampus';
close_parahipp.labels = {'No','Yes'};
close_parahipp.values = {0 1};
close_parahipp.def = @(val)cat_get_defaults('extopts.close_parahipp', val{:});
if spmseg
close_parahipp.hidden = true;
close_parahipp.val{1} =0;
else
close_parahipp.def = @(val)cat_get_defaults('extopts.close_parahipp', val{:});
end
close_parahipp.help = {
'Apply initial morphological closing inside mask for parahippocampal gyrus to minimize the risk of large cuts of parahippocampal gyrus after topology correction. However, this may also lead to poorer quality of topology correction for other data and should be only used if large cuts in the parahippocampal areas occur.'
''
Expand Down Expand Up @@ -1193,7 +1248,7 @@
surface = cfg_branch;
surface.tag = 'surface';
surface.name = 'Surface Options';
surface.val = {pbtres pbtver SRP reduce_mesh vdist scale_cortex add_parahipp close_parahipp};
surface.val = {pbtres pbtver SRP vdist scale_cortex add_parahipp close_parahipp};
surface.hidden = expert<1;
surface.help = {'CAT12 parameter to control the surface processing.';''};

Expand All @@ -1216,7 +1271,7 @@
if expert
extopts.val = {spmsegmentation,registration,surface,admin};
else
extopts.val = {vox,bb,surface,admin}; % bb is hidden
extopts.val = {vox,bb,registration,surface,admin}; % bb is hidden
end
end
extopts.help = {'Using the extended options you can adjust special parameters or the strength of different corrections ("0" means no correction and "0.5" is the default value that works best for a large variety of data).'};
2 changes: 1 addition & 1 deletion cat_io_writenii.m
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Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,7 @@

pp = fileparts(V.fname);
if ~exist('folder','var'), folder = ''; end
if ~exist(fullfile(pp,folder),'dir'), mkdir(fullfile(pp,folder)); end
if ~exist(spm_file(fullfile(pp,folder),'fpath'),'dir'), mkdir(spm_file(fullfile(pp,folder),'fpath')); end


% deal with label maps
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