Merge pull request #8 from zugmana/main

changed functions for fmriprep

contarg/normgrid.py

@@ -40,6 +40,7 @@
 from mixedvines.copula import GaussianCopula
 from scipy.stats import norm
 from scipy import stats
+import bids
 
 
 GII_PATTERN = ['sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_hemi-{hemi}][_space-{space}][_den-{density}][_desc-{desc}][_part-{part}]_{suffix<T1w|T2w|T2star|T2starw|FLAIR|FLASH|PD|PDw|PDT2|inplaneT[12]|angio|curv|inflated|midthickness|pial|sulc|thickness|white|mask>}{extension<.nii|.nii.gz|.surf.gii|.shape.gii>}']
@@ -452,6 +453,8 @@ def load_surfaces(subject, layout, anat_dir, overwrite=False):
     anat_dir = Path(anat_dir)
     anat_out_dir = anat_dir / f'sub-{subject}/anat'
     anat_out_dir.mkdir(exist_ok=True, parents=True)
+    if isinstance(layout,str):
+        layout = bids.BIDSLayout( database_path=layout)
     # transform surface to fsLR
     tmpsurfaces = {}
     for H in ['L', 'R']:
@@ -463,13 +466,14 @@ def load_surfaces(subject, layout, anat_dir, overwrite=False):
                     datatype='anat',
                     hemi=H,
                     suffix=surface,
+                    space=None,
                     extension='.surf.gii'
                 )[0].path
                 current_sphere = layout.get(
                     subject=subject,
                     datatype='anat',
                     space='fsLR',
-                    desc='reg',
+                    desc='msmsulc',
                     hemi=H,
                     suffix='sphere',
                     extension='.surf.gii'
@@ -678,7 +682,7 @@ def calc_stimgrid(subject, src_surf_dir, surf_info_dir,
             raise ValueError("Must pass a layout if fmriprep is True")
         if anat_dir is None:
             raise ValueError("Must pass an anat_dir if ")
-        surfaces = load_surfaces(subject=subject, layout=layout, anat_dir=anat_dir)
+        surfaces = load_surfaces(subject=subject, layout=layout, overwrite=overwrite, anat_dir=anat_dir)
     else:
         surfaces = load_liston_surfs(subject, src_surf_dir)
 
@@ -1225,6 +1229,8 @@ def run_clusters(subject, concat_nii, clust_outdir, src_surf_dir,
                  refroi='bilateralfullSGCsphere',
                  stimroi='expandedcoleBA46',
                  out_prefix='',
+                 layout=None,
+                 anat_dir=None,
                  overwrite=False):
     """
     subject : str
@@ -1247,6 +1253,10 @@ def run_clusters(subject, concat_nii, clust_outdir, src_surf_dir,
         name of the roi where stimulation will be delivered
     out_prefix : str
         string preprended to output files
+    layout : bids.layout.layout.BIDSLayout | str
+        The layout object or a path to a saved bids layout
+    anat_dir : Pathlib path | str
+        Upper level directory under which new surfaces will be saved if needed. Files will be saved to anat_dir / f'sub-{subject}/anat'
     overwrite : bool
         Should files be overwritten
     """
@@ -1273,7 +1283,13 @@ def run_clusters(subject, concat_nii, clust_outdir, src_surf_dir,
     if not outputs_present or overwrite:
 
         # load surfaces
-        if surf_source == 'liston':
+        if surf_source == 'fmriprep':
+            if layout is None:
+                raise ValueError("Must pass a layout if fmriprep is True")
+            if anat_dir is None:
+                raise ValueError("Must pass an anat_dir if ")
+            surfaces = load_surfaces(subject=subject, layout=layout, anat_dir=anat_dir, overwrite=overwrite)
+        elif surf_source == 'liston':
             surfaces = load_liston_surfs(subject, src_surf_dir)
         else:
             raise NotImplementedError
@@ -1508,4 +1524,4 @@ def make_uncert_surfaces(subject, src_surf_dir, uncert_dir, overwrite=False, fmr
             ]
             subprocess.run(create_cifti_cmd, check=True)
         cifti_outs.append(cifti_out)
-    return cifti_outs
+    return cifti_outs