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spDist_extractROIdata.m
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spDist_extractROIdata.m
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% spvDist_extractROIdata.m
%
% saves data into ROI files for each subj, session; training & testing data
% saved separately within each file; concatenates L and R hemis
%
% ZSCORES right now (run-level)
%
% also, extract pRF fits, R2, etc.
%
%
%
function spDist_extractROIdata(subj,sess,ROIs)
task_dir = 'spDist';
root = spDist_loadRoot;
if nargin < 1 || isempty(subj)
%subj = {'AY','CC','KD','MR','XL'};
subj = {'XL'}
end
if nargin < 2 || isempty(subj)
% TODO: if no defined sessions, use all....
sess_template = {'spDist2'};
sess = cell(length(subj),1); for ss = 1:length(subj); sess{ss} = sess_template; end
clear sess_template
end
% heuristic for defining RF session - can make more explicit, but this
% should work ok
sess_rf = cell(length(subj),1);
for ss = 1:length(subj)
if ~strcmpi(subj{ss},'EK') % only subj EK has RF2 as their target ret
sess_rf{ss} = 'RF1';
else
sess_rf{ss} = 'RF2';
end
end
% should work...
root_rf = sprintf('%s/../vRF_tcs/',root);
%root_rf = '/deathstar/data/vRF_tcs/';
% in case ROIs live somewhere else...
root_ROI = root;
%root_ROI = '/deathstar/data/wmChoose_scanner/';
if nargin < 3 || isempty(ROIs)
ROIs = {'V1','V2','V3','V3AB','hV4','VO1','VO2','LO1','LO2','TO1','TO2','IPS0','IPS1','IPS2','IPS3','sPCS','iPCS', {'V1','V2','V3'},{'TO1','TO2'},{'LO1','LO2'},{'VO1','VO2'},{'IPS0','IPS1'},{'IPS2','IPS3'}};
end
roi_str = cell(size(ROIs));
%task_TRs = 372; % number of TRs in 'choose' task
% which functional files do we want? func or surf
func_type = 'surf'; % 'surf' or 'func'
func_file = sprintf('%s_volreg_normPctDet*.nii.gz',func_type); % search for this in SUBJ/SESS
% which RF file to load/store?
rf_nii = 'RF_surf_25mm-fFit.nii.gz'; % unsmoothed data; smoothed ersion (C2F enabled) used to make ROIs
% where to look in the RF file for params (is there a way to pull this out
% dynamically from nii? doesn't seem stored anywhere...)
RF_paramIdx.phase = 1;
RF_paramIdx.ve = 2;
RF_paramIdx.ecc = 3;
RF_paramIdx.sigma = 4;
RF_paramIdx.exp = 5;
RF_paramIdx.x0 = 6;
RF_paramIdx.y0 = 7;
RF_paramIdx.b = 8;
rf_fields = fieldnames(RF_paramIdx);
for ss = 1:length(subj)
% load all ROIs, RF data (/deathstar/data/vRF_tcs/MR/RF1/MR_RF1_vista//deathstar/data/vRF_tcs/KD/RF1/KD_RF1_vista/RF_surf_25mm-fFit.nii.gz
rf_file = sprintf('%s%s/%s/%s_%s_vista/%s',root_rf,subj{ss},sess_rf{ss},subj{ss},sess_rf{ss},rf_nii);
fprintf('Loading RF params from %s\n',rf_file);
rfnii = niftiRead(rf_file);
roi_nii = cell(length(ROIs),1);
%roi_rf_params = cell(length(ROIs),1);
roi_rf_struct = cell(length(ROIs),1);
for rr = 1:length(ROIs)
% is this ROI a cell? if not, make it a cell
if ~iscell(ROIs{rr})
this_ROIs = {ROIs{rr}};
else
this_ROIs = ROIs{rr};
end
% for saving files
roi_str{rr} = horzcat(this_ROIs{:});
roi_nii{rr} = cell(length(this_ROIs),1);
% initialize roi_rf_struct{rr} fields
roi_rf_struct{rr} = struct;
for ff = 1:length(rf_fields)
roi_rf_struct{rr}.(rf_fields{ff}) = [];
end
roi_rf_struct{rr}.coordIdx = [];
roi_rf_struct{rr}.ROIidx = []; % which ROI each voxel comes from (from thisROI)
for tt = 1:length(this_ROIs)
% updated TCS 9/14/2017 - ROIs will live w/in expt dir, not RF dir,
% because of different resolution...
%roifn = sprintf('%s%s/%s/%s_%s_vista/roi/bilat.%s.nii.gz',root_rf,subj{ss},sess_rf{ss},subj{ss},sess_rf{ss},ROIs{rr});
roifn = sprintf('%s%s/rois/bilat.%s.nii.gz',root_ROI,subj{ss},this_ROIs{tt});
fprintf('Loading ROI data from %s\n',roifn);
roi_nii{rr}{tt} = niftiRead(roifn);
% extract RF params from that ROI
roi_rf_params = niftiExtract(rfnii,roi_nii{rr}{tt});
for ff = 1:length(rf_fields)
roi_rf_struct{rr}.(rf_fields{ff}) = horzcat(roi_rf_struct{rr}.(rf_fields{ff}),roi_rf_params(RF_paramIdx.(rf_fields{ff}),:));
end
% for putting back into RAI nii file
roi_rf_struct{rr}.coordIdx = horzcat(roi_rf_struct{rr}.coordIdx, find(roi_nii{rr}{tt}.data(:)~=0).');
roi_rf_struct{rr}.ROIidx = horzcat(roi_rf_struct{rr}.ROIidx,ones(1,size(roi_rf_params,2))*tt);
clear roifn;
end
end
% hmmm....we're goign to want to put everything together
% eventually...but I guess for now I'll save out different mat files
% per session; can fix later on
for sess_idx = 1:length(sess{ss})
% loop through all funcPrefix files within subj, sess and determine
% which is map and which is task based on num TRs
this_func_files = dir(sprintf('%s%s/%s/%s',root,subj{ss},sess{ss}{sess_idx},func_file));
sess_nii = cell(length(this_func_files),1);
for ff = 1:length(this_func_files)
thisfn = sprintf('%s%s/%s/%s',root,subj{ss},sess{ss}{sess_idx},this_func_files(ff).name);
fprintf('loading %s\n',thisfn);
sess_nii{ff} = niftiRead(thisfn);
clear thisfn;
end
% handle _Long mode...
if strfind(sess{ss}{sess_idx},'Long')
task_TRs = 432;
else
task_TRs = 372;
end
% get # of TRs from each run this session
nTRs = cellfun(@(x) x.dim(4),sess_nii);
this_task_runs = find(nTRs==task_TRs);
r_all = nan(task_TRs*numel(this_task_runs),2); % run, subrun
sess_all = sess_idx * ones(task_TRs*numel(this_task_runs),1);
% extract, for each ROI, the time series from each mapping run &
% concatenate
fn_all = cell(length(this_task_runs),1); % empty for now
for rr = 1:length(ROIs)
% since we're indexing into original ROIs, need to turn
% single-ROIs into cells again (like above)
if ~iscell(ROIs{rr})
this_ROIs = {ROIs{rr}};
else
this_ROIs = ROIs{rr};
end
d_all = nan(task_TRs*numel(this_task_runs),size(roi_rf_struct{rr}.coordIdx,2));
d_allz = nan(task_TRs*numel(this_task_runs),size(roi_rf_struct{rr}.coordIdx,2));
startidx_TR = 1;
for tt = 1:length(this_task_runs)
fprintf('TASK (spatial distractor) %i: %s\n',tt,sess_nii{this_task_runs(tt)}.fname);
% which TRs we're extracting
thisidx = startidx_TR:(startidx_TR+task_TRs-1);
%
if rr == 1
fn_all{tt} = sess_nii{this_task_runs(tt)}.fname; % save the files we loaded from
end
for subroi_idx = 1:length(this_ROIs)
mdata = niftiExtract(sess_nii{this_task_runs(tt)},roi_nii{rr}{subroi_idx});
d_all( thisidx,roi_rf_struct{rr}.ROIidx==subroi_idx) = mdata; % no manipulation
d_allz(thisidx,roi_rf_struct{rr}.ROIidx==subroi_idx) = zscore(mdata,0,1); % Z-SCORE!!!
r_all(thisidx) = tt;
clear mdata;
end
startidx_TR = thisidx(end)+1;
clear thisidx;
end
% save
rf = roi_rf_struct{rr};
fn2s = sprintf('%s/%s_ROIdata/%s_%s_%s_%s.mat',root,task_dir,subj{ss},sess{ss}{sess_idx},roi_str{rr},func_type);
fprintf('saving to %s...\n',fn2s);
save(fn2s,'d_all','d_allz','r_all','sess_all','r_all','fn_all','rf_file','rf','func_file');
clear rf d_all d_allz;
end
end
end