FSL commands to modify atlas

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!

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

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!


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

#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

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

fslmaths $list_add my_new_atlas.nii.gz

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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