Merge pull request #2 from timwahoo/post_processing

minor changes to recon
BrkRaw · Feb 1, 2024 · 1352b90 · 1352b90
2 parents 2b6a194 + 0bca426
commit 1352b90
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diff --git a/brkraw/scripts/brkrecon.py b/brkraw/scripts/brkrecon.py
@@ -60,7 +60,7 @@ def main():
                 if len(data.shape) > 3:
                     output_fname =f"{acqp._parameters['ACQ_scan_name'].strip().replace(' ','_')}"
                     for c in range(data.shape[4]):
-                        ni_img  = nib.Nifti1Image(np.abs(np.squeeze(data)), affine=np.eye(4))
+                        ni_img  = nib.Nifti1Image(np.abs(np.squeeze(data[:,:,:,:,c,:,:])), affine=np.eye(4))
                         nib.save(ni_img, os.path.join(output,f"{acqp._parameters['ACQ_scan_name'].strip().replace(' ','_')}_C{c}.nii.gz"))
                     print('NifTi file is generated... [{}]'.format(output_fname))
         else:

diff --git a/tests/recon_testing.py b/tests/recon_testing.py
@@ -50,9 +50,11 @@
 
     # Reconstructed Image Matrix is always 7-dimensional
     if len(data.shape) == 7:
+        print(data.shape)
         output_fname =f"{acqp._parameters['ACQ_scan_name'].strip().replace(' ','_')}"
+
         for c in range(data.shape[4]):
-            ni_img  = nib.Nifti1Image(np.abs(np.squeeze(data)), affine=np.eye(4))
+            ni_img  = nib.Nifti1Image(np.abs(np.squeeze(data[:,:,:,:,c,:,:])), affine=np.eye(4))
             nib.save(ni_img, os.path.join(output,f"{acqp._parameters['ACQ_scan_name'].strip().replace(' ','_')}_C{c}.nii.gz"))
         print('NifTi file is generated... [{}]'.format(output_fname))