Update to make life easier for multiUsers

-pathFile.mat will now store the personal folder paths for the auto
pipeline
-other files modified to work accordingly

zUsers/Adrien/automatedPipeline2015_1.m

@@ -1,4 +1,4 @@
-function automatedPipeline2015_1
+function automatedPipeline2015_1(subjectID)
 % ------------------------------------------------------------------------------------------------------------
 % fMRI processing pipeline whose goal is to automatize steps as much as
 % possible
@@ -10,9 +10,20 @@
 clc
 % ------------------------------------------------------------------------------------------------------------
 % REPLACE THE FOLLOWING VARIABLE WITH YOUR VALUES
-subject_folder = '/Users/adrienchopin/Desktop/Big_data_STAM/RN31/pre1/NewPipeline'; %no end slash
-megavista_folder = '/Users/adrienchopin/Desktop/Megavista'; %no end slash
-subjectID='RN31test';
+disp('At that stage, DICOM files should be in the subject folder in a folder called 01_Raw_DICOM and the par files in the folder 01_PAR')
+disp('Epi should be called epi01-whatever, epi02-whatever, ..., gems should be called gems-whatever and mprage, gems_mprage-whatever.')
+answer = input('You should be in the subject folder for the subject that you want to analyse. 1 = ESC; any other key = OK ');
+if answer == 1; error('ESCAPE'); end
+%subject_folder = '/Users/adrienchopin/Desktop/Big_data_STAM/RN31/pre1/NewPipeline'; %no end slash
+subject_folder = cd;
+
+if ~exist('subjectID','var'); subjectID = 'default'; disp('Defaults subject ID...'); end
+
+%Write the following line (not commented, with your correct path) in the
+%command line to save the variable in a file called pathFile - move that
+%file to your zUsers folder
+%megavista_folder = '/Users/adrienchopin/Desktop/Megavista'; %no end slash
+load('pathFile','megavista_folder')
 % ------------------------------------------------------------------------------------------------------------
 
 
@@ -193,7 +204,7 @@
                     answer = input('Figure: Is everything OK? (y)es / (n)o: ', 's');
                     if strcmp(answer, 'n')==1; error('Something went wrong, according to you...');end
                 else %NOT GOOD
-                    error('python motioncorrect.py: Something went wrong with last step')
+                    error('python motionparams.py: Something went wrong with last step')
                 end
         else %NOT GOOD
             error('python motioncorrect.py: Something went wrong with last step')

zUsers/Adrien/extractPARfile.m

@@ -41,6 +41,7 @@ function extractPARfile(stamFile,rootEpi)
         end
     else
         disp('Only one epi found')
+        dataSplit = data;
     end
 
     fixationDuration = 15.7;
@@ -98,8 +99,8 @@ function extractPARfile(stamFile,rootEpi)
 
         parfileCorrelated
         parfileUncorrelated
-        writeMatToFile(parfileCorrelated,[rootEpi,sprintf('%02.f',run),'_Correlated.txt'])
-        writeMatToFile(parfileUncorrelated,[rootEpi,sprintf('%02.f',run),'_Uncorrelated.txt'])
+        writeMatToFile(parfileCorrelated,[rootEpi,sprintf('%02.f',run),'_Correlated.par'])
+        writeMatToFile(parfileUncorrelated,[rootEpi,sprintf('%02.f',run),'_Uncorrelated.par'])
     end
 end
 

zUsers/Sara/automatedPipeline2015_1.m

@@ -16,9 +16,12 @@
 clc
 % ------------------------------------------------------------------------------------------------------------
 % REPLACE THE FOLLOWING VARIABLE WITH YOUR VALUES
-subject_folder = '/Users/localadmin/Desktop/EM21/Pre1'; %no end slash
-megavista_folder = '/Users/localadmin/megavista'; %no end slash
-subjectID='EM21';
+% subject_folder = '/Users/localadmin/Desktop/EM21/Pre1'; %no end slash
+% megavista_folder = '/Users/localadmin/megavista'; %no end slash
+% subjectID='EM21';
+subject_folder = '/Users/adrienchopin/Desktop/Big_data_STAM/RN31/pre1/NewPipeline'; %no end slash
+megavista_folder = '/Users/adrienchopin/Desktop/Megavista'; %no end slash
+subjectID='RN31test';
 % ------------------------------------------------------------------------------------------------------------
 
 
@@ -232,7 +235,8 @@
                     %added because deleting this folder manually everytime
                     %i wanted to redo this step during debugging was very
                     %annoying -- Sara Popham
-                    [success, status]=rmdir([subject_folderMocoCheck,'/',mocoCheckFolder,'_nifti'],'s'); if success; disp('Deleted');else error(status); end
+                    %ERROR HERE - [success, status]=rmdir([subject_folderMocoCheck,'/',mocoCheckFolder,'_nifti'],'s'); if success; disp('Deleted');else error(status); end
+                    [success, status]=rmdir(subject_folderMocoCheck,'s'); if success; disp('Deleted');else error(status); end
                 case {2} %dont go, move to next step
                     doMotionCorrectionCheck = 0;
                     disp('Skipped');
@@ -253,9 +257,9 @@
             [success, status]=copyfile([subject_folderMoco,'/*_mcf.nii.gz'],[subject_folderMocoCheck,'/',mocoCheckFolder,'_nifti']); if success; disp('Done');else error(status); end
             [success, status]=copyfile([subject_folderDICOM,'/epi01*'],[subject_folderMocoCheck,'/',mocoCheckFolder,'_dicom']); if success; disp('Done');else error(status); end
         %rename epi_01_whatever to epi_01_whatever_mcf
-            epiFolder = dir([subject_folderMocoCheck,'/',mocoCheckFolder,'_dicom/epi01*']);
-            movefile([subject_folderMocoCheck,'/',mocoCheckFolder,'_dicom/',epiFolder.name],[subject_folderMocoCheck,'/',mocoCheckFolder,'_dicom/',epiFolder.name,'_mcf']);
-        disp('Starting motioncorrect.py in:'); 
+           epiFolder = dir([subject_folderMocoCheck,'/',mocoCheckFolder,'_dicom/epi01*']);
+           movefile([subject_folderMocoCheck,'/',mocoCheckFolder,'_dicom/',epiFolder.name],[subject_folderMocoCheck,'/',mocoCheckFolder,'_dicom/',epiFolder.name,'_mcf']);
+         disp('Starting motioncorrect.py in:'); 
             cd(preprocessPath);
             success = system(['python motioncorrect.py ', subject_folderMocoCheck]); 
         if success==0 %GOOD