This document too specific, you need to understand what you're doing, not follow it blindly.

1) Motion QC

• Same thing than for motion QC T1

2) Preprocessing

First, do :

module load minc-toolkit-extras

module load ANTs/20191007

The preprocessing script is :

/data/chamal/projects/gabriel/src/minc-toolkit-extras/t2-slab-preprocess.sh

This script contains the following steps:

• Registration of T1.mnc and T2.mnc and creation of the transform.xfm
• Application of the transform.xfm on T1-mask.mnc to create T2-mask.mnc
• N4 correction
• Resampling of T2-mask.mnc (if needed)
• Application of T2-mask.mnc on T2.mnc to extract the T2-extracted.mnc brain

Apply the script this way :

/data/chamal/projects/gabriel/src/minc-toolkit-extras/t2-slab-preprocess.sh T2.mnc T1.n4correct.cutneckapplyautocrop.mnc T1.n4correct.cutneckapplyautocrop.beastmask.mnc T2-corrected.mnc

• For that you can do a loop :

Example : if you have 2 subjects, SUBJECT1.mnc and SUBJECT2.mnc, you can create different folders such as :

1- A folder raw-T2/ contains :

SUBJECT1.mnc
SUBJECT2.mnc

2- A folder T1-n4correct-cutneck/ contains :

SUBJECT1.n4correct.cutneckapplyautocrop.mnc 
SUBJECT2.n4correct.cutneckapplyautocrop.mnc 

3- A folder Beastmask/ contains :

SUBJECT1.n4correct.cutneckapplyautocrop.beastmask.mnc
SUBJECT2.n4correct.cutneckapplyautocrop.beastmask.mnc

4- A folder T2-corrected/ contains :

Nothing yet.

• Here is the loop corresponding to this example :

for files in raw-T2/*.mnc ; do echo /data/chamal/projects/gabriel/src/minc-toolkit-extras/t2-slab-preprocess.sh $files T1-n4correct-cutneck/"${files:7:8}".n4correct.cutneckapplyautocrop.mnc Beastmask/"${files:7:8}".n4correct.cutneckapplyautocrop.beastmask.mnc T2-corrected/"${files:7:8}"-T2-corrected.mnc ; done

• "${files:7:8}" means : take the characters of your files (defined as raw-T2/*.mnc) from character 7, and for a length of 8 characters, so for us : SUBJECT1 or SUBJECT2.

• echo : will allow you to see the code that you created with the loop and to check if there is no mistakes.

• When you are sure of your code, you can remove echo, the script will run.

• Then you check your T2-corrected/ and if everything went well you will obtain :

  • SUBJECT1-T2-corrected.mnc
  • SUBJECT2-T2-corrected.mnc