First iteration of cell array ok, then it is empty until manually "evaluate selection" of previous segment

Hello,

I posted about this script earlier but it was quite long and I am unable to provide the data due to size limitations. However, I think I may have found the problematic segment early on in the script. Basically, the script pulls ID numbers from a csv, then matches those ID numbers with other data in the main source_path folder. So, the goal is to match an ID number with various .ima files, and then a .nii file, then run a software command. This works fine for the first iteration, but fails in the second. I think the issue is in this first portion of the code- specifically at the variables NII_list, NII_foldername, tmp_nii, and tmp_nii_foldername..

At the second iteration the script stops, and when I index tmp_nii and tmp_nii_foldername they come up empty. Whereas in the first iteration tmp_nii matched the ID and was able to find the nii file associated with that participant ID. The participant ID (cur_scan_code) changes correctly with the second iteration. However, when I go up and manually "evaluate selection" in the command window for

NII_foldername = cell(length(NII_list),1); %cell struct w length (rows) of nii_list x 1 column

for i = 1:length(dicom_list) %for the length of ^, get ith name from dicom list
    dicom_foldername{i} = dicom_list(i).name; %setting dicom_foldername to the name of the list. This gives us contents
                                              %of the folder where the dicoms are (source_path)

end

for i = 1:length(NII_list)
    NII_foldername{i} = NII_list(i).name; %setting NII_foldername (which is empty before this) to contain the names/files from NII_list
                                          %after this NII_foldername should have the nii files (ex 'RAN133-1a3_T1.nii')

end;

and then index tmp_nii and tmp_nii_foldername in the command window, I get the correct values. That is, the correct .nii file matched from the correct iteration of participant ID. The relevant portion of the code is below.

Thanks for the help. I hope this makes sense, I am quite stuck. I just don't know why it works after "evaluate selection" and not in the script. Is something causing this?

clc;
clear;
addpath (pwd);

%%Paths- source and final
    source_path = 'B:\BBA\Gannet\Tests\8.13.18_testManualBatchScript'; %where the dicoms are; Can be a larger list, even if we are currently only doing a newer/smaller
                                                    %batch. The excel list document will take care of only what we want
    %fit_path = 'B:\BBA\Gannet\TAP\TEMP\GannetFit_output'; %used for renaming MRS_struct
    MRS_struct_path = 'B:\BBA\Gannet\Tests\8.13.18_testManualBatchScript'; %location of MRS_struct file that will be renamed
    NII_path = 'B:\BBA\Gannet\Tests\8.13.18_testManualBatchScript\NII_files'; %folder of NII files

      scan_code_filename = 'List_to_analyze.csv'; % this is the .csv we look through to get scan codes
                                                           % change per analysis, keep this in VOI folder

%%Keywords + setup
    %analysis_name = 'BBA_ALC'    

      study_name = 'RAN'; %change per study/ analysis

      %These keywords are from the DICOM files- to set file_water and file_metab
      water_keyword = 'TEMP GABA H2O svs_se'; %these should be the same for RAN vs TAP etc.
      metab_keyword = 'TEMP GABA svs_edit_RFA'; %most of them with this
      NII_keyword = '_T1'; %this may work but need to test
      %metab_keyword = 'TEMP GABA svs_edit_859A'; %use this for PRE RAN 69

     % count = 0;    

%%read the scan code     
cd(source_path);

% look through CSV file. Open, look through (comma delim), close
fid = fopen(scan_code_filename);
scan_code_file_text = textscan(fid, '%s', 'Delimiter', ',');
fclose(fid);

% extract the list of scan codes from the CSV file

scan_code_exp = strcat(study_name,'\d\d\d-\d');                              
scan_code_array = regexp(scan_code_file_text{1},scan_code_exp, 'match'); %look for scan_code_exp within scan_code_file_text (.csv file)
       %list of PIDs from .csv file  

%put scan codes into final array
scan_code_array = scan_code_array(~cellfun('isempty', scan_code_array)); %making a usable array here and below

for i = 1:length(scan_code_array) %for loop to deal with cell array structure?

      scan_code_array{i} = scan_code_array{i}{1};

end

scan_code_array = unique(scan_code_array); %make sure each ID is unique

%%Go to dicom location and find files-- LOOP Start

cd(source_path)

display ('Find DICOM files and set water/metab files');

% make an array for dicom folder name
dicom_list = dir(source_path); %top of layer where all dicom FOLDERS are stored (in TEMP/INS folders)
                                %DICOM folders
dicom_foldername = cell(length(dicom_list),1); %cell struct w length of dicom list X 1

% make an array for nii folder name
NII_list = dir([NII_path, '/*.nii']);%list all conent from location of NIFTI files
%%%NII_list = dir(NII_path); %location where nii files are

NII_foldername = cell(length(NII_list),1); %cell struct w length (rows) of nii_list x 1 column

for i = 1:length(dicom_list) %for the length of ^, get ith name from dicom list
    dicom_foldername{i} = dicom_list(i).name; %setting dicom_foldername to the name of the list. This gives us contents
                                              %of the folder where the dicoms are (source_path)

end

for i = 1:length(NII_list)
    NII_foldername{i} = NII_list(i).name; %setting NII_foldername (which is empty before this) to contain the names/files from NII_list
                                          %after this NII_foldername should have the nii files ('RAN133-1a3_T1.nii')

end;

% find the files
for i = 1: length(scan_code_array) %length of # of scancodes in list/array (.csv input file)
    display ('inside for loop');
    cur_scan_code = scan_code_array{i};  %current scan code is the ith of scan code array

      %Setup dicom search via cur_scan_code (PID) 
      tmp = strfind(dicom_foldername, cur_scan_code); %find current scan code ^ (PID) within dicom folders
      tmp_foldername = dicom_foldername(~cellfun('isempty', tmp)); %folders from with MATCHING SCAN CODE (should return metab and water)

      %Setup nii search via cur_scan_code (PID)
      tmp_nii = strfind(NII_foldername, cur_scan_code); %find current scan code ^^ (PID) within folder with NII files
      tmp_nii_foldername = NII_foldername(~cellfun('isempty',tmp_nii)); %folders from ^ scan code (should return .nii file)

[Amal George M]

Hi Holly,

This issue might be originating from the last ' for loop' in the shared code. Check whether any of the involved variables 'NII_foldername' or 'scan_code_array' are being modified inside the loop. Try debugging the 'for loop' by inserting breakpoints.

If you are new to Matlab, here is a link on using the debugger tool .