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 1 as of 2019-06-20 14:18:26 → 
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+   ← Revision 12 as of 2021-02-17 19:14:04 → ⇥
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  Editor: MeenaMakary
  Comment:
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'''Index'''
<<TableOfContents(2)>>

= 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
}}}

= Development Version =