What should I use instead of cd?

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Eva Balgova
Eva Balgova on 10 Oct 2019
Edited: Stephen23 on 10 Oct 2019
Hello,
I have a piece of code (see below) that works but needs optimising. Any advice on what should be used insted of cd? The fullfile command would not work. Any other tips and suggestions on how to optimise the code are welcome. Thanks!
%%% This script will acess the SPM.mat result files of individual subjects and save
%%% their activation maps as binary maps as well as rename and copy them to
%%% a new file. The script needs optimising.
clear;
basedir = 'D:\ToM_1_REANALYSED';
spm_dir = 'C:\spm12';
addpath(spm_dir);
Subjectids = {'ToM_001_dicom','ToM_002_dicom','ToM_004_dicom','ToM_005_dicom','ToM_006_dicom','ToM_007_dicom','ToM_008_dicom','ToM_010_dicom','ToM_011_dicom','ToM_013_dicom','ToM_014_dicom','ToM_016_dicom','ToM_017_dicom','ToM_018_dicom','ToM_019_dicom','ToM_021_dicom','ToM_022_dicom','ToM_024_dicom','ToM_025_dicom','ToM_026_dicom','ToM_027_dicom','ToM_028_dicom','ToM_029_dicom','ToM_030_dicom'};
data_dirs = {'ANALYSIS_PLANNED_REG_P001','ANALYSIS_PLANNED_REG_P002','ANALYSIS_PLANNED_REG_P004','ANALYSIS_PLANNED_REG_P005','ANALYSIS_PLANNED_REG_P006','ANALYSIS_PLANNED_REG_P007','ANALYSIS_PLANNED_REG_P008','ANALYSIS_PLANNED_REG_P010','ANALYSIS_PLANNED_REG_P011','ANALYSIS_PLANNED_REG_P013','ANALYSIS_PLANNED_REG_P014','ANALYSIS_PLANNED_REG_P016','ANALYSIS_PLANNED_REG_P017','ANALYSIS_PLANNED_REG_P018','ANALYSIS_PLANNED_REG_P019','ANALYSIS_PLANNED_REG_P021','ANALYSIS_PLANNED_REG_P022','ANALYSIS_PLANNED_REG_P024','ANALYSIS_PLANNED_REG_P025','ANALYSIS_PLANNED_REG_P026','ANALYSIS_PLANNED_REG_P027','ANALYSIS_PLANNED_REG_P028','ANALYSIS_PLANNED_REG_P029','ANALYSIS_PLANNED_REG_P030'};
%%%Matlab batch for saving binary maps from single subject results
for n=1:length(Subjectids)
cd ([basedir '\' Subjectids{n} '\' data_dirs{n} '\' 'TOM']) % works fine with cd, but try to think about better ways of doing this...
%%% fullfile ([basedir '\' Subjectids{n} '\' data_dirs{n} '\' 'TOM' '\'])
spm('defaults', 'FMRI');
spm_jobman('initcfg');
matlabbatch{1}.spm.stats.results.spmmat ={'SPM.mat'}
matlabbatch{1}.spm.stats.results.conspec.titlestr = '';
matlabbatch{1}.spm.stats.results.conspec.contrasts = 1;
matlabbatch{1}.spm.stats.results.conspec.threshdesc = 'none';
matlabbatch{1}.spm.stats.results.conspec.thresh = 0.001;
matlabbatch{1}.spm.stats.results.conspec.extent = 0;
matlabbatch{1}.spm.stats.results.conspec.conjunction = 1;
matlabbatch{1}.spm.stats.results.conspec.mask.none = 1;
matlabbatch{1}.spm.stats.results.units = 1;
matlabbatch{1}.spm.stats.results.export{1}.ps = true;
matlabbatch{1}.spm.stats.results.export{2}.binary.basename = '_binary_activation_map';
spm_jobman('run', matlabbatch);
movefile (['spmT_0001__binary_activation_map.nii'], [Subjectids{n} '_binary_activation_map.nii'])
copyfile([Subjectids{n} '_binary_activation_map.nii'],'\\fs-root-w\home-005\sepa70\Windows_Data\Desktop\PHD OFFICE\1_PROJECTS\TOM_TMS\TOM_peak_activations_from_fMRI_data\Single_Subject_Activation_Maps')
cd ../../../..
end

Answers (2)

thoughtGarden
thoughtGarden on 10 Oct 2019
Your use of fullfile should be this:
fullfile(basedir, Subjectids{n}, data_dirs{n},'TOM')
Also, why are you trying to avoid using cd? cd is specifically designed to change folders, which it seems is your goal.
I suppose another option would be to copy the file to the desired folder using
copyfile
That way you aren't changing directories every loop.
  4 Comments
Eva Balgova
Eva Balgova on 10 Oct 2019
Thank you for your answer. Could you please provide an example or amendment to the code that would lead to achieving this? Thanks. Eva

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Stephen23
Stephen23 on 10 Oct 2019
Edited: Stephen23 on 10 Oct 2019
Your fullfile usage (which you commented out) does not make much sense, in particular:
  1. concatenating everything together before calling fullfile and explicitly providing the path separator characters completely defeats the point of fullfile.
  2. You do not seem to allocate fullfile's output to anything, and hence do not use it anywhere in your code.
Instead of this:
% fullfile ([basedir '\' Subjectids{n} '\' data_dirs{n} '\' 'TOM' '\'])
you need something like this:
P = fullfile(basedir,Subjectids{n},data_dirs{n},'TOM');
and then you need to actually use P in your code. Possibly you want something like this:
destdir = '\\fs-root-w\home-005\sepa70\Windows_Data\Desktop\PHD OFFICE\1_PROJECTS\TOM_TMS\TOM_peak_activations_from_fMRI_data\Single_Subject_Activation_Maps';
basedir = 'D:\ToM_1_REANALYSED';
Subjectids = {'ToM_001_dicom','ToM_002_dicom','ToM_004_dicom','ToM_005_dicom','ToM_006_dicom','ToM_007_dicom','ToM_008_dicom','ToM_010_dicom','ToM_011_dicom','ToM_013_dicom','ToM_014_dicom','ToM_016_dicom','ToM_017_dicom','ToM_018_dicom','ToM_019_dicom','ToM_021_dicom','ToM_022_dicom','ToM_024_dicom','ToM_025_dicom','ToM_026_dicom','ToM_027_dicom','ToM_028_dicom','ToM_029_dicom','ToM_030_dicom'};
data_dirs = {'ANALYSIS_PLANNED_REG_P001','ANALYSIS_PLANNED_REG_P002','ANALYSIS_PLANNED_REG_P004','ANALYSIS_PLANNED_REG_P005','ANALYSIS_PLANNED_REG_P006','ANALYSIS_PLANNED_REG_P007','ANALYSIS_PLANNED_REG_P008','ANALYSIS_PLANNED_REG_P010','ANALYSIS_PLANNED_REG_P011','ANALYSIS_PLANNED_REG_P013','ANALYSIS_PLANNED_REG_P014','ANALYSIS_PLANNED_REG_P016','ANALYSIS_PLANNED_REG_P017','ANALYSIS_PLANNED_REG_P018','ANALYSIS_PLANNED_REG_P019','ANALYSIS_PLANNED_REG_P021','ANALYSIS_PLANNED_REG_P022','ANALYSIS_PLANNED_REG_P024','ANALYSIS_PLANNED_REG_P025','ANALYSIS_PLANNED_REG_P026','ANALYSIS_PLANNED_REG_P027','ANALYSIS_PLANNED_REG_P028','ANALYSIS_PLANNED_REG_P029','ANALYSIS_PLANNED_REG_P030'};
for n = 1 :numel(Subjectids)
P = fullfile(basedir,Subjectids{n},data_dirs{n},'TOM');
old = fullfile(P,'spmT_0001__binary_activation_map.nii');
new = fullfile(P,[Subjectids{n},'_binary_activation_map.nii']);
movefile(old,new)
copyfile(new,destdir)
end

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