Make PROFUMO/MELODIC locations more explicit

In essence, this commit moves some of the hard coded paths out of the helper
functions and into `RunTests.m`, where things are a bit easier to track.

IO/loadMELODIC.m

-function [ Pg ] = loadMELODIC( outputDir, params )
+function [ Pg ] = loadMELODIC( melodicDir, params )
 
-Pg = read_avw(fullfile(outputDir, 'MELODIC.gica', 'melodic_IC.nii.gz'));
+Pg = read_avw(fullfile(melodicDir, 'melodic_IC.nii.gz'));
 Pg = reshape(Pg, params.V, params.iN);
 
 end

IO/loadPROFUMO.m

-function [ Pg, P, A, pcA ] = loadPROFUMO( outputDir, params )
+function [ Pg, P, A, pcA ] = loadPROFUMO( pfmDir, params )
 
-pfmDir = fullfile(outputDir, 'PROFUMO.pfm', 'FinalModel');
+pfmDir = fullfile(pfmDir, 'FinalModel');
 
 % Load group maps
 mPg = h5read(fullfile(pfmDir, 'GroupSpatialModel', 'SignalMeans.post', ...

Methods/MELODIC.sh

@@ -8,10 +8,15 @@ nifti_dir=$2
 dim=$3
 TR=$4
 
+mkdir "${output_dir}"
+
+# Run all FSL commands locally
+unset SGE_ROOT
+
 # Run MELODIC
-melodic -i ${nifti_dir}/MELODIC_SpecFile.txt \
-    -o ${output_dir}/MELODIC.gica \
+melodic -i "${nifti_dir}/MELODIC_SpecFile.txt" \
+    -o "${output_dir}" \
     --tr=${TR} -a concat -d ${dim} \
     --migpN=300 --nobet --nomask \
     --maxrestart=5 --verbose \
-    > ${output_dir}/MELODIC_Output.txt
+    > "${output_dir}/TerminalOutput.txt"

Methods/PROFUMO.sh

@@ -8,11 +8,14 @@ nifti_dir=$2
 dim=$3
 TR=$4
 
+mkdir "${output_dir}"
+
 # Run PROFUMO (need to make sure we're on jalapeno18!)
-nice -n 20 ~samh/bin/PROFUMO \
-    ${nifti_dir}/PROFUMO_SpecFile.json \
+#nice -n 20 PROFUMO \
+PROFUMO \
+    "${nifti_dir}/PROFUMO_SpecFile.json" \
     ${dim} \
-    ${output_dir}/PROFUMO.pfm \
+    "${output_dir}" \
     --useHRF ${TR} --hrfFile ~samh/PROFUMO/HRFs/Default.phrf \
     --covModel Run --lowRankData 150 -d 0.5 --nThreads 10 \
-    > ${output_dir}/PROFUMO_Output.txt
+    > "${output_dir}/TerminalOutput.txt"

RunTests.m

@@ -362,11 +362,12 @@ for n = 1:params.nRepeats
     %% Run MELODIC %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     
     try
+        melodicDir = fullfile(repeatDir, 'MELODIC.gica');
         system(sprintf( ...
             'sh Methods/MELODIC.sh %s %s %d %1.2f', ...
-            repeatDir, niftiDir, params.iN, params.TR));
+            melodicDir, niftiDir, params.iN, params.TR));
         
-        icadr_Pg = loadMELODIC(repeatDir, params);
+        icadr_Pg = loadMELODIC(melodicDir, params);
         [icadr_P, icadr_A] = runDR(D, icadr_Pg, params);
         icadr_pcA = calculateNetmats(icadr_A, params);
         
@@ -379,11 +380,12 @@ for n = 1:params.nRepeats
     %% Run PROFUMO %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     
     try
+        pfmDir = fullfile(repeatDir, 'PROFUMO.pfm');
         system(sprintf( ...
             'sh Methods/PROFUMO.sh %s %s %d %1.2f', ...
-            repeatDir, niftiDir, params.iN, params.TR));
+            pfmDir, niftiDir, params.iN, params.TR));
         
-        [pfm_Pg, pfm_P, pfm_A, pfm_pcA] = loadPROFUMO(repeatDir, params);
+        [pfm_Pg, pfm_P, pfm_A, pfm_pcA] = loadPROFUMO(pfmDir, params);
         
         scores.PROFUMO(n) = calculateDecompositionAccuracy( ...
                 P, pfm_P, A, pfm_A, pcA, pfm_pcA, params);