FSL commands to modify atlas

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1

Hi there,

I’m doing diffusion analysis and I need to use a specific atlas (eg. atlas.nii.gz) - it’s in FSL’s MNI space, 2mm, but it doesn’t split the left and right hemisphere. I will need to separate the left and right, and reorganize the integer values (to make it double). I assume I could use fslmaths commads but I’m not sure how to do it. Does anyone have any ideas?

Many thanks in advance!

2

To select specific rois where for which you know the label number, you can use:

fslmaths atlas.nii.gz -thr $roi_number -uthr $roi_number atlas_roi${roi_number}.nii.gz -odt double

-odt sets the output datatype (default as original image)
Possible datatypes are: char short int float double

3

Hi Jsein,

I want to modify the atlas (let’s say, separate it to left and right hemisphere and rearrange it to new label numbers), instead of extracting a certain region from the atlas. Thanks for replying though!

4

Hi,

Please allow me to complete my answer, it is one way to create a new atlas by selecting a number of rois and give them other numbers before putting them together, but there must be more clever ways:

This is a bash script using FSL functions.

Let’s say the labels for your right hemisphere are ranging from 1 to 10:

mkdir my_new_rois/
#extract the roi from a specific range
for roi_number in {1..10}
do fslmaths atlas.nii.gz -thr $roi_number -uthr $roi_number atlas_roi${roi_number}.nii.gz -odt double
done

#change the label number for a specific roi
for roi_number in {1..10}
do new_roi_number=$(expr 500 + $roi_number)
echo "new roi number is: $new_roi_number"
fslmaths atlas_roi${roi_number}.nii.gz -div $roi_number -mul $new_roi_number my_new_rois/atlas_roi${new_roi_number}.nii.gz -odt double
done

#merge all the rois with new numbers
list_add= 
i= 
for roi in $list_rois
  do i=$(expr $i + 1 )
  if [ $i = 1 ]
    then list_add=$roi
  else  list_add="$list_add -add $roi"
  fi
done

fslmaths $list_add my_new_atlas.nii.gz
5

Hi Jsein,

The atlas I use doesn’t separate the left and right hemisphere. The values are the same. However, replace your step one to my script can perfectly solve my problem.

fslmaths atlas.nii.gz -roi 0 45 0 -1 0 -1 0 -1 right_mask.nii.gz

Many thanks!

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