BrainPET

HI

Aether-Mirror Version

PseudoCT mu-map generation

This function generates pseudoCT mu-map using SPM8 atlas-based method (David Izquierdo-Garcia et al.)

$/!\$ Warning

For DICOM input:

perl brainPET_pCT_AeMir.pl -i /<DIR>/<SUJID>/MR/MPRAGE -f 107000-000005-000001.dcm -c 0

For NIFTI input

perl brainPET_pCT_AeMir.pl -i /<DIR>/<SUJID>/MR_PET -f cp_iso_mprage.nii -c 0

IMP1: The r-l flip is applied only to .dcm input but not to .nii input (see Imp2) IMP2: If you input a nifti file, it should be named as cp_iso_mprage.nii and it should be r-l flipped (i.e., it is the output of a previously ran pesudo CT).

Supporting Functions

Denoise MPRAGE

perl brainPET_denoise_mprage.pl -i /<DIR>/<SUBJID>/MR_PET/cp_iso_mprage.nii -t 25 -s 0

ifile2nifti

perl brainPET_ifile2nifti.pl -i /<DIR>/file.i

-  ⇤ ← Revision 10 as of 2021-02-17 19:06:16 → 
  Size: 1692
  Editor: MeenaMakary
  Comment:
+   ← Revision 12 as of 2021-02-17 19:14:04 → ⇥
  Size: 1725
  Editor: MeenaMakary
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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----- /!\ '''Edit conflict - other version:''' ----
+---- /!\ '''Warning''' ----
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-= Bullet list =
 * item 1

 * item 2, with gap
 * item 3
   * item 3.1
+ * For DICOM input:
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----- /!\ '''Edit conflict - your version:''' ----

= Bullet list =
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+ * For NIFTI input
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-perl brainPET_pCT_AeMir.pl -i /<DIR>/<SUJID>/MR/MPRAGE -f 107000-000005-000001.dcm -c 0
+perl brainPET_pCT_AeMir.pl -i /<DIR>/<SUJID>/MR_PET -f cp_iso_mprage.nii -c 0
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+Line 39:
- * item 2

---- /!\ '''End of edit conflict''' ----
+IMP1: The r-l flip is applied only to .dcm input but not to .nii input (see Imp2)
IMP2: If you input a nifti file, it should be named as cp_iso_mprage.nii and it should be r-l flipped (i.e., it is the output of a previously ran pesudo CT).