UPDATE: fromnifti uncompress data into aa rather than into the raw di…

…rectory

aa_modules/aamod_diffusionfromnifti.m

@@ -38,10 +38,10 @@
             end
         end
         comp = false;
-        if strcmp(spm_file(niftifile,'Ext'),'gz'),
+        if strcmp(spm_file(niftifile,'Ext'),'gz')
             comp = true;
-            gunzip(niftifile);
-            niftifile = niftifile(1:end-3);
+            gunzip(niftifile,fullfile(sesspth,'temp'));
+            niftifile = spm_file(niftifile(1:end-3),'path',fullfile(sesspth,'temp'));
         end
 
         % BVals/BVecs
@@ -59,7 +59,7 @@
         for ln=1:3
             fprintf(fid,'%.14f ',bvecs(:,ln));
             fprintf(fid,'\n');
-        end;
+        end
         fclose(fid);
 
         % Image
@@ -73,7 +73,7 @@
             V(fileind).n=[1 1];
             spm_write_vol(V(fileind),Y);
             finalepis=[finalepis fn];
-        end;
+        end
 
         % Write out the files        
         % Now move dummy scans to dummy_scans directory
@@ -84,7 +84,7 @@
             for d=1:numdummies
                 cmd=['mv ' finalepis{d} ' ' dummypath];
                 dummylist=strvcat(dummylist,spm_file(finalepis{d},'path','dummy_scans'));
-                [s w]=aas_shell(cmd);
+                s=aas_shell(cmd);
                 if (s)
                     aas_log(aap,1,sprintf('ERROR:Problem moving dummy scan\nERROR:    %s to\nERROR:    %s\n',finalepis{d},dummypath));
                 end
@@ -98,7 +98,7 @@
             finalepis = finalepis{1};
             ind = find(finalepis=='-');
             sfx = '';
-            if isempty(ind),
+            if isempty(ind)
                 ind = find(finalepis=='.');
                 sfx = '_4D';
             end
@@ -109,7 +109,7 @@
         end
 
         %% Describe outputs
-        if comp, delete(niftifile); end
+        if comp, rmdir(fullfile(sesspth,'temp'),'s'); end
         aap=aas_desc_outputs(aap,domain,indices,'dummyscans',dummylist);
         aap=aas_desc_outputs(aap,domain,indices,'diffusion_data',finalepis);
         aap=aas_desc_outputs(aap,domain,indices,'bvals',bvals_fn);
@@ -119,5 +119,5 @@
 
     otherwise
         aas_log(aap,1,sprintf('Unknown task %s',task));
-end;
+end
 end

aa_modules/aamod_epifromnifti.m

@@ -25,6 +25,9 @@
         series = series{sess};
 
         %% Process
+        sesspth=aas_getsesspath(aap,subj,sess);
+        aas_makedir(aap,sesspth);
+
         % Files
         headerFn ='';
         imageFn = series;
@@ -47,8 +50,8 @@
         comp = false;
         if any(strcmp(spm_file(niftifile,'Ext'),'gz'))
             comp = true;
-            gunzip(niftifile{1});
-            niftifile{1} = niftifile{1}(1:end-3);
+            gunzip(niftifile{1},fullfile(sesspth,'temp'));
+            niftifile{1} = spm_file(niftifile{1}(1:end-3),'path',fullfile(sesspth,'temp'));
         end
 
         % Header
@@ -73,8 +76,6 @@
         finalepis={};
         V = spm_vol(niftifile); 
         if iscell(V), V = cell2mat(V); end
-        sesspth=aas_getsesspath(aap,subj,sess);
-        aas_makedir(aap,sesspth);
         fle = spm_file(niftifile,'basename');
         ext = spm_file(niftifile,'Ext');
         for fileind=1:numel(V)
@@ -139,7 +140,7 @@
             spm_file_merge(char({V(numdummies+1:end).fname}),finalepis,0,DICOMHEADERS{1}.volumeTR);
         end
         % And describe outputs
-        if comp, delete(niftifile{1}); end
+        if comp, rmdir(fullfile(sesspth,'temp'),'s'); end
         aap=aas_desc_outputs(aap,subj,sess,'epi',finalepis);
         aap = aas_desc_outputs(aap,subj,sess,'dummyscans',dummylist);
         dcmhdrfn = fullfile(sesspth,'dicom_headers.mat');

aa_modules/aamod_fieldmapfromnifti.m

@@ -37,8 +37,8 @@
         for f = 1:numel(niftifile)
             comp = strcmp(spm_file(niftifile{f},'Ext'),'gz');
             if comp
-                gunzip(niftifile{f});
-                niftifile{f} = niftifile{f}(1:end-3);
+                gunzip(niftifile{f},fullfile(sesspth,'temp'));
+                niftifile{1} = spm_file(niftifile{f}(1:end-3),'path',fullfile(sesspth,'temp'));
             end
 
             aas_makedir(aap,fullfile(sesspth,sprintf('serie%02d',f)));
@@ -48,7 +48,7 @@
             spm_write_vol(V,Y);
             fn{f} = V.fname;
 
-            if comp, delete(niftifile{f}); end
+            if comp, rmdir(fullfile(sesspth,'temp'),'s'); end
         end
         aap=aas_desc_outputs(aap,'session',[subj sess],'fieldmap',char(fn));
 

aa_modules/aamod_structuralfromnifti.m

@@ -38,6 +38,8 @@
                     end
             end
 
+            sesspth=fullfile(aas_getsubjpath(aap,subj),aap.directory_conventions.structdirname);
+            aas_makedir(aap,sesspth);
             Ys = 0;
             for s = 1:numel(series)
                 niftifile = series(s).fname;
@@ -51,20 +53,18 @@
                     end
                 end
                 comp = false;
-                if strcmp(spm_file(niftifile,'Ext'),'gz'),
+                if strcmp(spm_file(niftifile,'Ext'),'gz')
                     comp = true;
-                    gunzip(niftifile);
-                    niftifile = niftifile(1:end-3);
+                    gunzip(niftifile,fullfile(sesspth,'temp'));
+                    niftifile = spm_file(niftifile(1:end-3),'path',fullfile(sesspth,'temp'));
                 end
-                sesspth=fullfile(aas_getsubjpath(aap,subj),aap.directory_conventions.structdirname);
-                aas_makedir(aap,sesspth);
 
                 fn(s,:)=spm_file(niftifile,'path',sesspth,'suffix','_0001');
                 V(s)=spm_vol(niftifile);
                 Y=spm_read_vols(V(s));  
                 V(s).fname=deblank(fn(s,:));
                 V(s).n=[1 1];
-                if comp, delete(niftifile); end                
+                if comp, rmdir(fullfile(sesspth,'temp'),'s'); end                
 
                 if aap.options.(['autoidentify' stream '_average'])
                     Ys = Ys + Y/numel(series);