Fix bugs in external calls to FSL binaries in Matlab scripts used in …

…ReApplyFix

ReApplyFix/ReApplyFixPipeline.sh

@@ -216,7 +216,15 @@ main()
 	cd ${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_hp${HighPass}.ica
 
 	if [ -f ../${fmri_orig}_Atlas${RegString}.dtseries.nii ] ; then
+		log_Msg "FOUND FILE: ../${fmri_orig}_Atlas${RegString}.dtseries.nii"
+		log_Msg "Performing imln"
 		$FSLDIR/bin/imln ../${fmri_orig}_Atlas${RegString}.dtseries.nii Atlas.dtseries.nii
+
+
+		log_Msg "START: Showing linked files"
+		ls -l ../${fmri_orig}_Atlas${RegString}.dtseries.nii
+		ls -l Atlas.dtseries.nii
+		log_Msg "END: Showing linked files"
 	fi
 
 	$FSLDIR/bin/imln ../$fmri filtered_func_data

ReApplyFix/scripts/fix_3_clean_no_vol.m

@@ -24,13 +24,20 @@ function fix_3_clean(fixlist,aggressive,domot,hp)
 CIFTI=getenv('FSL_FIX_CIFTIRW');
 WBC=getenv('FSL_FIX_WBC');
 
+func_name='fix_3_clean';
+fprintf('%s - fixlist: "%s"\n', func_name, fixlist);
+fprintf('%s - aggressive: %d\n', func_name, aggressive);
+fprintf('%s - domot: %d\n', func_name, domot);
+fprintf('%s - hp: %d\n', func_name, hp);
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 %%%%  read set of bad components
 DDremove=load(fixlist);
 
 %%%%  find TR of data
 [grot,TR]=call_fsl('fslval filtered_func_data pixdim4'); TR=str2num(TR)
+fprintf('%s - After "fslval filtered_func_data pixdim4" - TR: %d\n', func_name, TR);
 
 %%%%  read and highpass CIFTI version of the data if it exists
 DObrainord=0;
@@ -46,7 +53,12 @@ function fix_3_clean(fixlist,aggressive,domot,hp)
     meanBO=mean(BO.cdata,2);
     BO.cdata=BO.cdata-repmat(meanBO,1,size(BO.cdata,2));
     save_avw(reshape([BO.cdata ; zeros(100*BOdimZnew-BOdimX,BOdimT)],10,10,BOdimZnew,BOdimT),'Atlas','f',[1 1 1 TR]);
-    call_fsl(sprintf('fslmaths Atlas -bptf %f -1 Atlas',0.5*hp/TR));
+
+%   call_fsl(sprintf('fslmaths Atlas -bptf %f -1 Atlas',0.5*hp/TR));
+    cmd_str=sprintf('fslmaths Atlas -bptf %f -1 Atlas',0.5*hp/TR);
+    fprintf('%s - About to execute: %s\n',func_name,cmd_str);
+    system(cmd_str);
+
     grot=reshape(read_avw('Atlas'),100*BOdimZnew,BOdimT);  BO.cdata=grot(1:BOdimX,:);  clear grot; BO.cdata=BO.cdata+repmat(meanBO,1,size(BO.cdata,2));
     ciftisave(BO,'Atlas_hp_preclean.dtseries.nii',WBC); % save out noncleaned hp-filtered data for future reference, as brainordinates file
   end

ReApplyFix/scripts/fix_3_clean_no_vol.prj

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <deployment-project plugin="plugin.deploytool" plugin-version="1.0">
-  <configuration target="target.standalone" target-name="Standalone Application" name="fix_3_clean_no_vol" location="/home/tbrown01/ReApplyFix" file="/home/tbrown01/ReApplyFix/fix_3_clean_no_vol.prj" build-checksum="1715923563">
+  <configuration target="target.standalone" target-name="Standalone Application" name="fix_3_clean_no_vol" location="/home/tbrown01/ReApplyFix" file="/home/tbrown01/ReApplyFix/fix_3_clean_no_vol.prj" build-checksum="1819143838">
     <param.project.name>/home/tbrown01/ReApplyFix/fix_3_clean_no_vol.prj</param.project.name>
     <param.target.type>Standalone Application</param.target.type>
     <param.appname>fix_3_clean_no_vol</param.appname>
@@ -443,7 +443,7 @@
       <vista>false</vista>
       <linux>true</linux>
       <solaris>false</solaris>
-      <osver>2.6.32-504.23.4.el6.x86_64</osver>
+      <osver>2.6.32-573.7.1.el6.x86_64</osver>
       <os32>false</os32>
       <os64>true</os64>
       <arch>glnxa64</arch>

ReApplyFix/scripts/functionmotionconfounds.m

@@ -8,6 +8,11 @@
         TR = str2num(TR)
     end
 end
+
+func_name='functionmotionconfounds';
+fprintf('%s - TR: %d\n', func_name, TR);
+fprintf('%s - hp: %d\n', func_name, hp);
+
 %%%% must have "hp" and "TR" already set before calling this
 
 [grota,grotb]=call_fsl('imtest mc/prefiltered_func_data_mcf_conf_hp');
@@ -30,7 +35,12 @@
   end
   if hp>0
     save_avw(reshape(confounds',size(confounds,2),1,1,size(confounds,1)),'mc/prefiltered_func_data_mcf_conf','f',[1 1 1 TR]);
-    call_fsl(sprintf('fslmaths mc/prefiltered_func_data_mcf_conf -bptf %f -1 mc/prefiltered_func_data_mcf_conf_hp',0.5*hp/TR));
+
+    %call_fsl(sprintf('fslmaths mc/prefiltered_func_data_mcf_conf -bptf %f -1 mc/prefiltered_func_data_mcf_conf_hp',0.5*hp/TR));
+    cmd_str=sprintf('fslmaths mc/prefiltered_func_data_mcf_conf -bptf %f -1 mc/prefiltered_func_data_mcf_conf_hp',0.5*hp/TR);
+    fprintf('%s - About to execute: %s\n',func_name,cmd_str);
+    system(cmd_str);	
+
     confounds=functionnormalise(reshape(read_avw('mc/prefiltered_func_data_mcf_conf_hp'),size(confounds,2),size(confounds,1))');
   end
 end

version.txt

@@ -1 +1 @@
-v3.13.1
+v3.13.2