[RTM] RF: Assume phase-encoding direction is A-P unless specified L-R

fmriprep/interfaces/reports.py

@@ -33,6 +33,7 @@
 
 FUNCTIONAL_TEMPLATE = """\t\t<h3 class="elem-title">Summary</h3>
 \t\t<ul class="elem-desc">
+\t\t\t<li>Phase-encoding (PE) direction: {pedir}</li>
 \t\t\t<li>Slice timing correction: {stc}</li>
 \t\t\t<li>Susceptibility distortion correction: {sdc}</li>
 \t\t\t<li>Registration: {registration}</li>
@@ -141,6 +142,8 @@ class FunctionalSummaryInputSpec(BaseInterfaceInputSpec):
     distortion_correction = traits.Enum('epi', 'fieldmap', 'phasediff', 'SyN', 'None',
                                         desc='Susceptibility distortion correction method',
                                         mandatory=True)
+    pe_direction = traits.Enum(None, 'i', 'i-', 'j', 'j-', mandatory=True,
+                               desc='Phase-encoding direction detected')
     registration = traits.Enum('FLIRT', 'bbregister', mandatory=True,
                                desc='Functional/anatomical registration method')
     output_spaces = traits.List(desc='Target spaces')
@@ -163,7 +166,11 @@ def _generate_segment(self):
         reg = {'FLIRT': 'FLIRT with boundary-based registration (BBR) metric',
                'bbregister': 'FreeSurfer boundary-based registration (bbregister)'
                }[self.inputs.registration]
-        return FUNCTIONAL_TEMPLATE.format(stc=stc, sdc=sdc, registration=reg,
+        if self.inputs.pe_direction is None:
+            pedir = 'MISSING - Assuming Anterior-Posterior'
+        else:
+            pedir = {'i': 'Left-Right', 'j': 'Anterior-Posterior'}[self.inputs.pe_direction[0]]
+        return FUNCTIONAL_TEMPLATE.format(pedir=pedir, stc=stc, sdc=sdc, registration=reg,
                                           output_spaces=', '.join(self.inputs.output_spaces),
                                           confounds=', '.join(self.inputs.confounds))
 

fmriprep/workflows/anatomical.py

@@ -153,7 +153,7 @@ def init_anat_preproc_wf(skull_strip_ants, output_spaces, template, debug, frees
             FreeSurfer SUBJECTS_DIR
         subject_id
             FreeSurfer subject ID
-        fs_2_t1_transform
+        t1_2_fsnative_reverse_transform
             Affine transform from FreeSurfer subject space to T1w space
         surfaces
             GIFTI surfaces (gray/white boundary, midthickness, pial, inflated)
@@ -174,7 +174,7 @@ def init_anat_preproc_wf(skull_strip_ants, output_spaces, template, debug, frees
         fields=['t1_preproc', 't1_brain', 't1_mask', 't1_seg', 't1_tpms',
                 't1_2_mni', 't1_2_mni_forward_transform', 't1_2_mni_reverse_transform',
                 'mni_mask', 'mni_seg', 'mni_tpms',
-                'subjects_dir', 'subject_id', 'fs_2_t1_transform', 'surfaces']),
+                'subjects_dir', 'subject_id', 't1_2_fsnative_reverse_transform', 'surfaces']),
         name='outputnode')
 
     # 0. Reorient T1w image(s) to RAS and resample to common voxel space
@@ -314,7 +314,7 @@ def len_above_thresh(in_list, threshold, longitudinal):
             (surface_recon_wf, outputnode, [
                 ('outputnode.subjects_dir', 'subjects_dir'),
                 ('outputnode.subject_id', 'subject_id'),
-                ('outputnode.fs_2_t1_transform', 'fs_2_t1_transform'),
+                ('outputnode.t1_2_fsnative_reverse_transform', 't1_2_fsnative_reverse_transform'),
                 ('outputnode.surfaces', 'surfaces')]),
         ])
 
@@ -499,7 +499,7 @@ def init_surface_recon_wf(omp_nthreads, hires, name='surface_recon_wf'):
             FreeSurfer SUBJECTS_DIR
         subject_id
             FreeSurfer subject ID
-        fs_2_t1_transform
+        t1_2_fsnative_reverse_transform
             FSL-style affine matrix translating from FreeSurfer T1.mgz to T1w
         surfaces
             GIFTI surfaces for gray/white matter boundary, pial surface,
@@ -521,7 +521,8 @@ def init_surface_recon_wf(omp_nthreads, hires, name='surface_recon_wf'):
         name='inputnode')
     outputnode = pe.Node(
         niu.IdentityInterface(
-            fields=['subjects_dir', 'subject_id', 'fs_2_t1_transform', 'surfaces', 'out_report']),
+            fields=['subjects_dir', 'subject_id', 't1_2_fsnative_reverse_transform', 'surfaces',
+                    'out_report']),
         name='outputnode')
 
     recon_config = pe.Node(FSDetectInputs(hires_enabled=hires), name='recon_config',
@@ -542,6 +543,7 @@ def init_surface_recon_wf(omp_nthreads, hires, name='surface_recon_wf'):
     fs_transform = pe.Node(
         fs.Tkregister2(fsl_out='freesurfer2subT1.mat', reg_header=True),
         name='fs_transform')
+    fsl2lta = pe.Node(fs.utils.LTAConvert(out_lta=True), name='fsl2lta')
 
     autorecon_resume_wf = init_autorecon_resume_wf(omp_nthreads=omp_nthreads)
     gifti_surface_wf = init_gifti_surface_wf()
@@ -572,12 +574,15 @@ def init_surface_recon_wf(omp_nthreads, hires, name='surface_recon_wf'):
         # reoriented image
         (inputnode, fs_transform, [('t1w', 'target_image')]),
         (autorecon1, fs_transform, [('T1', 'moving_image')]),
+        (inputnode, fsl2lta, [('t1w', 'target_file')]),
+        (autorecon1, fsl2lta, [('T1', 'source_file')]),
+        (fs_transform, fsl2lta, [('fsl_file', 'in_fsl')]),
         # Output
         (autorecon_resume_wf, outputnode, [('outputnode.subjects_dir', 'subjects_dir'),
                                            ('outputnode.subject_id', 'subject_id'),
                                            ('outputnode.out_report', 'out_report')]),
         (gifti_surface_wf, outputnode, [('outputnode.surfaces', 'surfaces')]),
-        (fs_transform, outputnode, [('fsl_file', 'fs_2_t1_transform')]),
+        (fsl2lta, outputnode, [('out_lta', 't1_2_fsnative_reverse_transform')]),
     ])
 
     return workflow

fmriprep/workflows/base.py

@@ -437,7 +437,8 @@ def init_single_subject_wf(subject_id, task_id, name,
                 (anat_preproc_wf, func_preproc_wf,
                  [('outputnode.subjects_dir', 'inputnode.subjects_dir'),
                   ('outputnode.subject_id', 'inputnode.subject_id'),
-                  ('outputnode.fs_2_t1_transform', 'inputnode.fs_2_t1_transform')]),
+                  ('outputnode.t1_2_fsnative_reverse_transform',
+                   'inputnode.t1_2_fsnative_reverse_transform')]),
             ])
 
     return workflow