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License: Apache License 2.0
batch scripting files for neuroimaging
License: Apache License 2.0
Add robust settings for EPI skullstripping using bet
from FSL, in particular when there is strong signal bias.
update job_do_segmentCAT12
solution :
[,,idx_roi_in_netwok] = intersect(n.roi, ts_data.ts_table.abbreviation, 'stable')
this leads to pb when you have several sequences with different number of slices
n_outlier is printed, adding the ratio & percentage could help interpreting (even though the plot is very clear)
job_afni_proc_multi_echo
does not handle .nii.gz
file
TODO :
.nii.gz
or .nii
.nii.gz
or .nii
matvol/SPM/preproc/job_do_segmentCAT12.m
Line 143 in 597405a
At the moment, with an unedited cat_defaults.m
file, this cmd_prepend line is not enough to activate the expertgui option in the case if cluster execution.
solution
rgb_map_num = colormap(handles.axes);
solution : isfinite
logical(mask_global_Y(isfinite(mask_global_Y)));
matvol/SPM/preproc/job_coregister.m
Line 152 in 92eee73
this happens a lot during pilote study, its annoying...
Using cellfun(‘isempty’,…)
should be much faster than cellfun(@isempty,…)
Need to check that !
Create meinfo.mat
file for each subject.
+++ | --- |
---|---|
more flexible, no need to do a par.redo=1 | more disk access |
Disk access is neglectable I think, except if there are 100+ subjects, which is rare
fprintf(fid,'# on Diff card set b-value to b=%d \n', max(data(i).bval));
-> use the value after tolerance checkImageOrientationPatientDICOM
: if the values are not all integer, apply rotation to the vectors ?the code is done, need to wrap it in a function
matvol/DWI/gen_scheme2siemens.m
Line 144 in 627d816
Hi,
I am new to Github and relatively new to Matlab and was wondering whether you could give an example of how to use par as input for this function. Do you need to construct the variable beforehand? What if you would like to use the default?
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