rotate nifti files

init_preprocessing.py

@@ -15,7 +15,7 @@
 algs = [("tens", "dtidet", "lmax2"), ("detr", "csddet", "lmax8"), ("prob", "csdprob", "lmax8")]
 
 def getSublong(num_str):
-    sublong = {"001": "pestilli_test", "002": "takemura", "003": "knk", "004": "lmperry"}
+    sublong = {"0001": "pestilli_test", "0002": "takemura", "0003": "knk", "0004": "lmperry"}
     if num_str in sublong:
         return sublong[num_str]
     else:
@@ -85,11 +85,23 @@ def getSublong(num_str):
 outputs = mapping[dataset]["output"]
 copier.copy(inputs[0].format(params[0]), outputs[0].format(subject, subject), dummy = False)
 action = "copy"
-if inputs[1][:-3] == "mgz":
+if inputs[1][-3:] == "mgz":
     action = "mri_convert"
-copier.copy(inputs[1].format(params[1]), outputs[1].format(subject, subject), action = action, dummy = False)
-copier.copy(inputs[2].format(params[2]), outputs[2].format(subject, subject), dummy = False)
-copier.copy(inputs[3].format(params[3]), outputs[3].format(subject, subject), dummy = False)
+
+out_str = outputs[1].format(subject, subject)
+copier.copy(inputs[1].format(params[1]), out_str, action = action, dummy = False)
+if dataset != "hcp7t":
+    copier.copy(out_str, out_str, action = "rotate", dummy = False)
+
+out_str = outputs[2].format(subject, subject)
+copier.copy(inputs[2].format(params[2]), out_str, dummy = False)
+if dataset != "hcp7t":
+    copier.copy(out_str, out_str, action = "rotate", dummy = False)
+
+out_str = outputs[3].format(subject, subject)
+copier.copy(inputs[3].format(params[3]), out_str, dummy = False)
+if dataset != "hcp7t":
+    copier.copy(out_str, out_str, action = "rotate", dummy = False)
 
 bvec_in = mapping[dataset]["bval_in"].format(name) + ".bvecs"
 bval_in = mapping[dataset]["bval_in"].format(name) + ".bvals"

init_recon_models.py

@@ -72,7 +72,10 @@
 
     copier.copy(in_str, out_str, action = action, dummy = False)
 
-    if (dataset == "hcp7t" and files[i][:-10] in masks):
+    if (dataset != "hcp7t" and files[i][-7:] == ".nii.gz"):
+        copier.rotate(out_str, out_str, dummy = False)
+
+    if (dataset == "hcp7t" and files[i][-10:] in masks):
         mask = mapping[dataset]["mask"].format(name)
         # for ease, I am overloading the meaning of "anatomy" in the copy function
         copier.copy(out_str, out_str, anatomy = mask, action = "mask", dummy = False)

utils/copy_template.py

@@ -94,6 +94,12 @@ def mrconvert(infile, outfile, dummy = True):
         # call(['module', 'load', 'mrtrix'])
         call(['mrconvert', '-force', infile, outfile])
 
+def rotate(infile, outfile, dummy = True):
+    if dummy:
+        print 'rotate command print not implemented'
+    else:
+        call(['mri_convert', '-iid', '1', '0', '0', infile, outfile])
+
 def mask(infile, outfile, mask, dummy = True):
     if dummy:
         print ""
@@ -169,6 +175,8 @@ def copy(in_inter, out_inter, action = "copy", dummy = True, anatomy = ""):
             tck2trk(all_in[i], all_out[i], dummy = dummy, anatomy = anatomy)
         elif (action == "mask"):
             mask(all_in[i], all_out[i], dummy = dummy, mask = anatomy)
+        elif (action == "rotate"):
+            rotate(all_in[i], all_out[i], dummy = dummy)
         elif (action == "copy"):
             if dummy:
                 print "cp " + all_in[i] + " >> " + all_out[i]