Correct oblique

Dockerfile

@@ -18,7 +18,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
 # Install a few minimal AFNI components
 RUN curl -L -O https://afni.nimh.nih.gov/pub/dist/tgz/linux_ubuntu_16_64.tgz && \
     mkdir -p /opt/afni && \
-    tar xzvf linux_ubuntu_16_64.tgz -C /opt/afni linux_ubuntu_16_64/{libmri.so,libf2c.so,3dDespike,3dTshift,3dAutobox} --strip-components=1 && \
+    tar xzvf linux_ubuntu_16_64.tgz -C /opt/afni linux_ubuntu_16_64/{libmri.so,libf2c.so,3dDespike,3dTshift,3dWarp,3dAutobox} --strip-components=1 && \
     rm -f linux_ubuntu_16_64.tgz
 ENV PATH=/opt/afni${PATH:+:$PATH}
 

rabies/parser.py

@@ -215,6 +215,15 @@ def get_parser():
             "(default: %(default)s)\n"
             "\n"
         )
+    preprocess.add_argument(
+        '--oblique2card', dest='oblique2card', action='store_true',
+        help=
+            "Applies AFNI's 3dWarp -oblique2card on all structural and functional data to \n"
+            "convert oblique data to cartesian (see https://github.com/CoBrALab/RABIES/issues/160). \n"
+            "WARNING: this is modifying the original data by resampling on a new grid, only apply if necessary. \n"
+            "(default: %(default)s)\n"
+            "\n"
+        )    
     preprocess.add_argument(
         '--apply_despiking', dest='apply_despiking', action='store_true',
         help=
@@ -457,7 +466,8 @@ def get_parser():
     g_stc.add_argument(
         '--TR', type=str, default='auto',
         help=
-            "Specify repetition time (TR) in seconds. (e.g. --TR 1.2)\n"
+            "Specify repetition time (TR) in seconds. (e.g. --TR 1.2). 'auto' will read the TR from \n"
+            "the nifti header. \n"
             "(default: %(default)s)\n"
             "\n"
         )
@@ -659,7 +669,8 @@ def get_parser():
     confound_correction.add_argument(
         '--TR', type=str, default='auto',
         help=
-            "Specify repetition time (TR) in seconds. (e.g. --TR 1.2)\n"
+            "Specify repetition time (TR) in seconds. (e.g. --TR 1.2). 'auto' will read the TR from \n"
+            "the nifti header. \n"
             "(default: %(default)s)\n"
             "\n"
         )

rabies/preprocess_pkg/main_wf.py

@@ -7,7 +7,7 @@
 from .inho_correction import init_inho_correction_wf
 from .commonspace_reg import init_commonspace_reg_wf
 from .bold_main_wf import init_bold_main_wf
-from .utils import BIDSDataGraber, prep_bids_iter, convert_to_RAS, resample_template, apply_autobox
+from .utils import BIDSDataGraber, prep_bids_iter, convert_to_RAS, convert_oblique2card, apply_autobox, resample_template
 from . import preprocess_visual_QC
 
 def init_main_wf(data_dir_path, output_folder, opts, name='main_wf'):
@@ -170,6 +170,26 @@ def init_main_wf(data_dir_path, output_folder, opts, name='main_wf'):
                                                 function=convert_to_RAS),
                                        name='bold_convert_to_RAS')
 
+    if opts.oblique2card:
+        bold_oblique2card_node = pe.Node(Function(input_names=['input'],
+                                                    output_names=['output'],
+                                                    function=convert_oblique2card),
+                                        name='bold_oblique2card')
+        workflow.connect([
+            (bold_selectfiles, bold_oblique2card_node, [
+                ('out_file', 'input'),
+                ]),
+            (bold_oblique2card_node, bold_convert_to_RAS_node, [
+                ('output', 'img_file'),
+                ]),
+            ])
+    else:
+        workflow.connect([
+            (bold_selectfiles, bold_convert_to_RAS_node, [
+                ('out_file', 'img_file'),
+                ]),
+            ])
+
     format_bold_buffer = pe.Node(niu.IdentityInterface(fields=['formatted_bold']),
                                         name="format_bold_buffer")
 
@@ -244,9 +264,6 @@ def init_main_wf(data_dir_path, output_folder, opts, name='main_wf'):
         (main_split, bold_selectfiles, [
             ("scan_info", "scan_info"),
             ]),
-        (bold_selectfiles, bold_convert_to_RAS_node, [
-            ('out_file', 'img_file'),
-            ]),
         (bold_selectfiles, outputnode, [
             ('out_file', 'input_bold'),
             ]),
@@ -334,6 +351,26 @@ def init_main_wf(data_dir_path, output_folder, opts, name='main_wf'):
                                                     function=convert_to_RAS),
                                            name='anat_convert_to_RAS')
 
+        if opts.oblique2card:
+            anat_oblique2card_node = pe.Node(Function(input_names=['input'],
+                                                        output_names=['output'],
+                                                        function=convert_oblique2card),
+                                            name='anat_oblique2card')
+            workflow.connect([
+                (anat_selectfiles, anat_oblique2card_node, [
+                    ('out_file', 'input'),
+                    ]),
+                (anat_oblique2card_node, anat_convert_to_RAS_node, [
+                    ('output', 'img_file'),
+                    ]),
+                ])
+        else:
+            workflow.connect([
+                (anat_selectfiles, anat_convert_to_RAS_node, [
+                    ('out_file', 'img_file'),
+                    ]),
+                ])
+
         format_anat_buffer = pe.Node(niu.IdentityInterface(fields=['formatted_anat']),
                                             name="format_anat_buffer")
 
@@ -369,8 +406,6 @@ def init_main_wf(data_dir_path, output_folder, opts, name='main_wf'):
             (run_split, bold_selectfiles, [
                 ("run", "run"),
                 ]),
-            (anat_selectfiles, anat_convert_to_RAS_node,
-             [("out_file", "img_file")]),
             (format_anat_buffer, anat_inho_cor_wf, [
                 ("formatted_anat", "inputnode.target_img"),
                 ("formatted_anat", "inputnode.name_source"),

rabies/preprocess_pkg/utils.py

@@ -215,6 +215,18 @@ def convert_to_RAS(img_file, out_dir=None):
         return out_file
 
 
+def convert_oblique2card(input):
+    import pathlib
+    import os
+    from rabies.utils import run_command
+    # apply AFNI's 3dWarp to convert from oblique to cartesian
+    split = pathlib.Path(input).name.rsplit(".nii")[0]
+    output = os.path.abspath(f"{split}_2card.nii.gz")
+    command = f'3dWarp -oblique2card -prefix {output} {input}'
+    rc = run_command(command)
+    return output
+
+
 def resample_template(template_file, mask_file, file_list, spacing='inputs_defined', rabies_data_type=8):
     import os
     import SimpleITK as sitk

scripts/error_check_rabies.py

@@ -126,7 +126,7 @@ def get_parser():
 command = f"rabies --inclusion_ids {tmppath}/inputs/sub-token1_bold.nii.gz --verbose 1 --force preprocess {tmppath}/inputs {tmppath}/outputs --anat_inho_cor method=disable,otsu_thresh=2,multiotsu=false --bold_inho_cor method=disable,otsu_thresh=2,multiotsu=false \
     --anat_template {tmppath}/inputs/sub-token1_T1w.nii.gz --brain_mask {tmppath}/inputs/token_mask.nii.gz --WM_mask {tmppath}/inputs/token_mask.nii.gz --CSF_mask {tmppath}/inputs/token_mask.nii.gz --vascular_mask {tmppath}/inputs/token_mask.nii.gz --labels {tmppath}/inputs/token_mask.nii.gz \
     --bold2anat_coreg registration=no_reg,masking=true,brain_extraction=true --commonspace_reg masking=true,brain_extraction=true,fast_commonspace=true,template_registration=no_reg --data_type int16  \
-    --HMC_option 0 --apply_despiking --anat_autobox --bold_autobox"
+    --HMC_option 0 --oblique2card --apply_despiking --anat_autobox --bold_autobox"
 process = subprocess.run(
     command,
     check=True,