From 90950e7758c6b22474018087f148859ee1913519 Mon Sep 17 00:00:00 2001 From: Helge <47348963+HJZollner@users.noreply.github.com> Date: Mon, 11 Mar 2024 10:37:33 -0400 Subject: [PATCH] Multiple external .BASIS files - Added a feature to allow for two separate .BASIS files to be defined for MEGA-PRESS --- exampledata/sdat/MEGA/jobSDAT_MEGA_LCModel.m | 15 ++++++++++++--- exampledata/sdat/UnEdited/jobSDAT_LCModel.m | 2 +- fit/code/osp_fitInitialise.m | 4 ++-- 3 files changed, 15 insertions(+), 6 deletions(-) diff --git a/exampledata/sdat/MEGA/jobSDAT_MEGA_LCModel.m b/exampledata/sdat/MEGA/jobSDAT_MEGA_LCModel.m index ed1b6dd9..2a78866f 100644 --- a/exampledata/sdat/MEGA/jobSDAT_MEGA_LCModel.m +++ b/exampledata/sdat/MEGA/jobSDAT_MEGA_LCModel.m @@ -194,9 +194,18 @@ opts.fit.FWHMcoMM3 = 14; -% Optional: In case the automatic basisset picker is not working you can manually -% select the path to the basis set in the osprey/fit/basis, i.e.: -% opts.fit.basisSetFile = 'osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat'; +%%% ----- LCMODEL FITTING OPTIONS ----- +% Specify LCModel-format basis set (.BASIS) +% If no basis set file is provided Osprey will generate the .BASIS file +% from Osprey's database +% opts.fit.basisSetFile = {which('3T_megapress_Philips_68ms_noMM_A.BASIS'), +% which('3T_megapress_Philips_68ms_noMM_diff1.BASIS')}; + + +% Specify LCModel-type control file (.CONTROL) +% This is optional: If you leave this field blank, Osprey will create a +% minimum control file for you. +% opts.fit.controlFile = ''; % Optional: Deface the strucutral images in the Coreg/Seg figures for HIPAA % compliance diff --git a/exampledata/sdat/UnEdited/jobSDAT_LCModel.m b/exampledata/sdat/UnEdited/jobSDAT_LCModel.m index 98c78366..79923462 100644 --- a/exampledata/sdat/UnEdited/jobSDAT_LCModel.m +++ b/exampledata/sdat/UnEdited/jobSDAT_LCModel.m @@ -191,7 +191,7 @@ % Specify LCModel-format basis set (.BASIS) % If no basis set file is provided Osprey will generate the .BASIS file % from Osprey's database -opts.fit.basisSetFile = which('3T_PRESS_Philips_35ms_noMM.BASIS'); +% opts.fit.basisSetFile = {which('3T_press_Philips_35ms_noMM.BASIS')}; % Specify LCModel-type control file (.CONTROL) diff --git a/fit/code/osp_fitInitialise.m b/fit/code/osp_fitInitialise.m index 0c93f12b..356a41cc 100644 --- a/fit/code/osp_fitInitialise.m +++ b/fit/code/osp_fitInitialise.m @@ -53,7 +53,7 @@ % Find the right basis set (provided as *.mat file in Osprey basis set % format) -if ~(isfield(MRSCont.opts.fit,'basisSetFile') && ~isempty(MRSCont.opts.fit.basisSetFile) && ~isfolder(MRSCont.opts.fit.basisSetFile)) +if ~(isfield(MRSCont.opts.fit,'basisSetFile') && ~isempty(MRSCont.opts.fit.basisSetFile) && ~isfolder(MRSCont.opts.fit.basisSetFile{1})) % Intercept non-integer echo times and replace the decimal point with % an underscore to avoid file extension problems @@ -164,7 +164,7 @@ % Clear existing basis set MRSCont.fit.basisSet = []; -if ~isfile(MRSCont.opts.fit.basisSetFile) && (ismcc || isdeployed) +if ~isfile(MRSCont.opts.fit.basisSetFile(1)) && (ismcc || isdeployed) if ~strcmp(MRSCont.opts.fit.basisSetFile(1),filesep) MRSCont.opts.fit.basisSetFile = [filesep MRSCont.opts.fit.basisSetFile]; end