Table of Contents
How to make a composite ROI (and use it!)
So you read that paper when they choose some regions of interest and put all together to make a single compostie ROI and determine the mean value of FDG activity there. And you really want to make the same shit.
Ok, let's see how. First you need to know what regions you want. Take, for example the HO Atlas. If the desired composite ROI includes:
right and left angular gyri, bilateral posterior cingulate gyrus, left middle/inferior temporal gyrus and right middle/inferior temporal gyrus
then the following ROIs:
- Angular_Gyrus
- Cingulate_Gyrus_posterior_division
- Middle_Temporal_Gyrus_anterior_division
- Middle_Temporal_Gyrus_posterior_division
- Middle_Temporal_Gyrus_temporooccipital_part
- Inferior_Temporal_Gyrus_anterior_division
- Inferior_Temporal_Gyrus_posterior_division
- Inferior_Temporal_Gyrus_temporooccipital_part
must be extracted from HO atlas and joined into a composite single ROI.
Put your ROIs toghether into the same mask
Luckily the HO Atlas (see Pipeline HO Altas individual ROI files for MNI standard space) is already separated into every single ROI at pipeline lib directory. Just make,
$ cd /opt/neuro.dev/lib/ $ fslmaths oxford/Cortical_21.nii.gz -add oxford/Cortical_30.nii.gz -add oxford/Cortical_11.nii.gz -add oxford/Cortical_12.nii.gz -add oxford/Cortical_13.nii.gz -add oxford/Cortical_14.nii.gz -add oxford/Cortical_15.nii.gz -add oxford/Cortical_16.nii.gz wroi.nii.gz
in order to get you composite ROI.
Use it
At this point you need to have all your PET images corregistered into the MNI space (aquí hay una pista). Then get into working directory and make something like this:
$ for x in *_pet_inMNI*; do a=`echo $x | awk -F"_" '{print $1}' | sed 's/mci//;s/hc//'`; b=`fslstats $x -k /opt/neuro.dev/lib/mni_cerebellum.nii.gz -M`; c=`fslstats $x -k /opt/neuro.dev/lib/wroi.nii.gz -M`; echo $a, `echo $c/$b | bc -l` ; done > ../wroi.csv
Voilá! You got it. 
What about batches?
$ for y in /opt/neuro.dev/lib/composites/*.nii.gz; do z=`basename $y .nii.gz`;for x in *_pet_inMNI*; do a=`echo $x | awk -F"_" '{print $1}' | sed 's/mci//;s/hc//'`; b=`fslstats $x -k /opt/neuro.dev/lib/mni_cerebellum.nii.gz -M`; c=`fslstats $x -k $y -M`; echo $a, `echo $c/$b | bc -l` ; done > ../${z}.csv; done
good luck
Imaging problems huh
There are some images with incomplete scans. In particular some of those images have incomplete around cerebellum. What happen then if there is an image with half cerebellum? To avoid those problem I will assume that the mean value of the signal in the scanned portion of cerebellum is equal to the mean value in the whole cerebellum.
This way:
for y in /opt/neuro.dev/lib/composites/*.nii.gz; do z=`basename $y .nii.gz`; for x in *_pet_inMNI*; do a=`echo $x | awk -F"_" '{print $1}' | sed 's/mci//;s/hc//'`; fslmaths $x -thr 0 ${x%.nii.gz}_tmp; b=`fslstats ${x%.nii.gz}_tmp -k /opt/neuro.dev/lib/mni_cerebellum.nii.gz -M`; c=`fslstats ${x%.nii.gz}_tmp -k /opt/neuro.dev/lib/composites/$z -M`; echo $a,`echo $c/$b | bc -l`;done > ../${z}.csv; rm *_tmp*; done;
What about FS?
mmmm, se puede implementar pero hay que mirar esto:
Primeramente hay que mirar como aplicar los labels en FS.
The ADNI way (thanks to S. Landau)
Esto es muy parecido pero usando las zonas correctas. Ahi vamos:
for x in *_pet_inMNI*; do a=`echo $x | awk -F"_" '{print $1}' | sed 's/mci//;s/hc//'`; b=`fslstats $x -k /opt/neuro.dev/lib/bin_rpons_vermis.nii.gz -M`; c=`fslstats $x -k /opt/neuro.dev/lib/ADNI_Composite.nii.gz -M`; echo $a, `echo $c/$b | bc -l` ; done > ../slandau.csv
