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brain_radius fix #29

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merged 4 commits into from
Oct 4, 2024
Merged

brain_radius fix #29

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1f32bf2
Update dcan_signal_processing.m
madisoth Sep 21, 2024
6c0d853
Update filtered_movement_regressors.m
madisoth Sep 21, 2024
a3a14c1
Update dcan_bold_proc.py
madisoth Sep 21, 2024
20e0add
recompile binaries after making brain radius fixes
Sep 24, 2024
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3 changes: 2 additions & 1 deletion dcan_bold_proc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -486,7 +486,7 @@ def interface(subject, output_folder, task=None, fd_threshold=None,
input_spec['movement_regressors'], str(repetition_time),
str(motion_filter_option), str(motion_filter_order),
str(band_stop_min), motion_filter_type, str(band_stop_min),
str(band_stop_max), filtered_movement_regressors]
str(band_stop_max), str(brain_radius), filtered_movement_regressors]

subprocess.call(cmd)
# update input movement regressors
Expand Down Expand Up @@ -530,6 +530,7 @@ def interface(subject, output_folder, task=None, fd_threshold=None,
'motion_filename': os.path.basename(
output_spec['output_motion_numbers']),
'skip_seconds': skip_seconds,
'brain_radius_in_mm': brain_radius,
'result_dir': output_spec['result_dir']
}
# write input json for matlab script
Expand Down
6 changes: 4 additions & 2 deletions matlab_code/dcan_signal_processing.m
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Expand Up @@ -27,6 +27,8 @@ function dcan_signal_processing(config_path)
motion_filename= conf_json.motion_filename;
skip_seconds= conf_json.skip_seconds;
result_dir= conf_json.result_dir;
brain_radius_in_mm = conf_json.brain_radius_in_mm
brain_radius_in_cm= brain_radius_in_mm * 0.1;
int_method= 'linear';
%silence warnings
warning('off', 'all')
Expand Down Expand Up @@ -64,14 +66,14 @@ function dcan_signal_processing(config_path)
%% read mov_reg and calculate Friston regressors
MR = dlmread(file_mov_reg);
MR = MR(:, [1 2 3 4 5 6]);
FR = make_friston_regressors(MR);
FR = make_friston_regressors(MR, brain_radius_in_cm);

%% Calculate residuals (regression)
[r, c] = size(X');
Rr = zeros(r,c);

%% Create FD.mat
FD = calc_FD_HCP(file_mov_reg);
FD = calc_FD_HCP(file_mov_reg, brain_radius_in_mm);
save([result_dir filesep 'FD.mat'], 'FD', '-v7')
txt_FD_file=[path_ex_sum filesep 'FD_' fMRIName '.txt'];
save(txt_FD_file, 'FD','-ascii')
Expand Down
8 changes: 5 additions & 3 deletions matlab_code/filtered_movement_regressors.m
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
function filtered_movement_regressors(path_mov_reg, TR, filt_option, order, LP_freq_min, filt_type, fc_RR_min, fc_RR_max, output)
function filtered_movement_regressors(path_mov_reg, TR, filt_option, order, LP_freq_min, filt_type, fc_RR_min, fc_RR_max, brain_radius, output)
%% This function applies a low pas filter to the motion numbers and save it with a different number

% %% Input arguments
Expand All @@ -8,7 +8,8 @@ function filtered_movement_regressors(path_mov_reg, TR, filt_option, order, LP_f
% order order of the filter to be applied
% LP_freq_min Low pass frequency (in minutes) to be filtered
%% defaults
head_ratio_cm = 5;
% head_ratio_cm = 5;


%% when compiling comment out paths and uncomment this section
TR = str2num(TR);
Expand All @@ -17,6 +18,7 @@ function filtered_movement_regressors(path_mov_reg, TR, filt_option, order, LP_f
LP_freq_min = str2num(LP_freq_min);
fc_RR_min = str2num(fc_RR_min);
fc_RR_max = str2num(fc_RR_max);
head_ratio_cm = str2num(brain_radius) * 0.1;

%% filter design

Expand Down Expand Up @@ -83,7 +85,7 @@ function filtered_movement_regressors(path_mov_reg, TR, filt_option, order, LP_f
% Read motion numbers
file_mov_reg = [path_contents(i).folder filesep path_contents(i).name]; %-- for MATLAB USE
MR = dlmread(file_mov_reg);
MR_ld=make_friston_regressors(MR);%% Using this function to only get the linear displacements
MR_ld=make_friston_regressors(MR, head_ratio_cm);%% Using this function to only get the linear displacements
MR_ld=MR_ld(:,1:6);

switch filt_option
Expand Down