Merge pull request #1127 from 36000/expose_fa_thresh_csd

[ENH] expose FA thresh param for autoresponse ssst for csd
yeatmanlab · Apr 16, 2024 · f79b3a7 · f79b3a7
2 parents 39ecef2 + 4022552
commit f79b3a7
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Showing 2 changed files with 15 additions and 7 deletions.
diff --git a/AFQ/models/csd.py b/AFQ/models/csd.py
@@ -23,7 +23,7 @@ class CsdNanResponseError(Exception):
     pass
 
 
-def _model(gtab, data, response=None, sh_order=None):
+def _model(gtab, data, response=None, sh_order=None, csd_fa_thr=0.7):
     """
     Helper function that defines a CSD model.
     """
@@ -50,7 +50,7 @@ def _model(gtab, data, response=None, sh_order=None):
         response, _ = csd.auto_response_ssst(response_gtab,
                                              data,
                                              roi_radii=10,
-                                             fa_thr=0.7)
+                                             fa_thr=csd_fa_thr)
     # Catch conditions where an auto-response could not be calculated:
     if np.all(np.isnan(response[0])):
         raise CsdNanResponseError
@@ -59,11 +59,13 @@ def _model(gtab, data, response=None, sh_order=None):
     return csdmodel
 
 
-def _fit(gtab, data, mask, response=None, sh_order=None, lambda_=1, tau=0.1):
+def _fit(gtab, data, mask, response=None, sh_order=None,
+         lambda_=1, tau=0.1, csd_fa_thr=0.7):
     """
     Helper function that does the core of fitting a model to data.
     """
-    return _model(gtab, data, response, sh_order).fit(data, mask=mask)
+    return _model(gtab, data, response, sh_order, csd_fa_thr).fit(
+        data, mask=mask)
 
 
 def fit_csd(data_files, bval_files, bvec_files, mask=None, response=None,

diff --git a/AFQ/tasks/data.py b/AFQ/tasks/data.py
@@ -281,7 +281,8 @@ def msdki_msk(msdki_tf):
 @as_img
 def csd_params(dwi, brain_mask, gtab, data,
                csd_response=None, csd_sh_order=None,
-               csd_lambda_=1, csd_tau=0.1):
+               csd_lambda_=1, csd_tau=0.1,
+               csd_fa_thr=0.7):
     """
     full path to a nifti file containing
     parameters for the CSD fit
@@ -309,6 +310,9 @@ def csd_params(dwi, brain_mask, gtab, data,
         set to tau*100 percent of the mean fODF amplitude (here, 10 percent
         by default)
         (see [1]_). Default: 0.1
+    csd_fa_thr : float, optional.
+        The threshold on the FA used to calculate the single shell auto
+        response. Can be useful to reduce for baby subjects. Default: 0.7
 
     References
     ----------
@@ -324,7 +328,8 @@ def csd_params(dwi, brain_mask, gtab, data,
             gtab, data,
             mask=mask,
             response=csd_response, sh_order=csd_sh_order,
-            lambda_=csd_lambda_, tau=csd_tau)
+            lambda_=csd_lambda_, tau=csd_tau,
+            csd_fa_thr=csd_fa_thr)
     except CsdNanResponseError as e:
         raise CsdNanResponseError(
             'Could not compute CSD response function for file: '
@@ -334,7 +339,8 @@ def csd_params(dwi, brain_mask, gtab, data,
         SphericalHarmonicDegree=csd_sh_order,
         ResponseFunctionTensor=csd_response,
         lambda_=csd_lambda_,
-        tau=csd_tau)
+        tau=csd_tau,
+        csd_fa_thr=csd_fa_thr)
     meta["SphericalHarmonicBasis"] = "DESCOTEAUX"
     meta["ModelURL"] = f"{DIPY_GH}reconst/csdeconv.py"
     return csdf.shm_coeff, meta