Hi Lance,

I forgot to mention that you may have to adjust the first two parameter values to the mask dimensions you are using - the values I indicated work for 2mm masks.

Best
Udo

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From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Lance Stevens [[log in to unmask]]
Sent: Monday, August 15, 2016 3:42 PM
To: [log in to unmask]
Subject: Re: [FSL] fslmaths combining two masks

Thanks Udo,

I will try this later today.

Again thank you very much.

Best,

Lance

On Sun, Aug 14, 2016 at 6:02 PM, Will, Udo <[log in to unmask]> wrote:

Hi Lance,

you can use -roi option in fslmaths.

For example:

fslmaths ROI_1 -roi 45 90 1 -1 1 -1 0 1 lH_ROI_1

would give you the left hemisphere part of ROI_1; if you change the first two parameter to 1 and 45 you'll get the right hemisphere part.
HTH

Best
Udo
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Lance Stevens [[log in to unmask]]
Sent: Sunday, August 14, 2016 11:17 AM
To: [log in to unmask]
Subject: [FSL] fslmaths combining two masks

FSL experts,

I need to isolate the right and left hemisphere parts of a mask.

The mask, ROI_1, includes both hemispheres but I would like it to be divided into the right and left hemispheres. This is not simply adding masks (fslmaths mask_a -add mask_b -bin combinedMasks_a_b).

I have created a masks to isolate each hemisphere the MNI152_T1_1mm_brain
fslmaths $FSLDIR/data/standard/MNI152_T1_1mm_brain -bin  -91 -1 -1 -1 -1 -1 -1 -1 Right_MNI_mask
fslmaths $FSLDIR/data/standard/MNI152_T1_1mm_brain -bin  91 -1 -1 -1 -1 -1 -1 -1 Left_MNI_mask

But I think I need to combine the RO1_1 mask in logical operations filtered by the Right_MNI_mask and Left_MNI_mask.

So I assume this would involve an AND function in fslmaths to create a single hemisphere mask, where ROI_1 mask is split by the Right_MNI_mask and Left_MNI_mask

In theory, and using isolating the right hemiphere of ROI_1 as an exmple, this might look like:  fslmaths ROI_1 AND Right_MNI_mask -bin output_Right_ROI_1
Of, course, I this syntax is incorrect and merely conveys the objective.

Admittedly, this shows my lack of shell script and fslmaths insight. Any guidance would be much appreciated

Thanks,
Lance