Hi,

You should not be using the mask for registration in either case.  The second option is really not a good idea at all.

All you need to do is:
 - register your FA to your T1 image (where both look like brains) using FLIRT
 - invert the transformation matrix
 - take the inverted matrix and apply this transformation to your mask image (e.g. with flirt and -applyxfm, or with applywarp, or with the ApplyXFM GUI)
 - this will move your mask into the FA space

In general you should always derive transformations from brain-like images, but then *apply* these transformations to mask images.  You should never try and derive a transformation (matrix or warp) using a mask image.

All the best,
Mark


On 6 Aug 2014, at 16:01, "Alshikho, Mohamad J." <[log in to unmask]> wrote:

Hi Mark and Steve,
The purpose of my FLIRT between the mask (generated from T1 segmentation in Free surfer) and the FA map is two things: first of all to calculate the mean FA using the following command line: fslstats dti_FA.nii –k <my FLIRT ed mask > -M , secondly to  unify the dimensions between the mask and the FA map so I can view both of them in FSLview to check the effectiveness of FLIRT.
 
Kindly, I have two points here :
1.       In FLIRT GUI if I used my dti_FA.nii as reference image and my T1.nii (AFTER BET) as input image then at that point can I include the output of FLIRT in fslstats as the following fslstats <OUTPUT OF FLIRT> -k <my mask generated from the T1 segmentation> -M
2.       In FLIRT GUI if I used the mode  (low res image -> High res image -> Reference image) then can I use my FA map as reference image , my T1 as High red image and my mask as low res image AND I will include the output of this process in fslstats as the following : fslstats dti_FA.nii –k <the output of this process_myflirted mask>-M
 
 
Looking forward to learn from you
Many Thanks
Mohamad
 
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Mark Jenkinson
Sent: Tuesday, August 05, 2014 4:03 AM
To: [log in to unmask]
Subject: Re: [FSL] FLIRT
 
Hi,
 
In addition to what Steve wrote, you should not use your mask image as the input.  You should use your original T1w image (the one that is already aligned with your mask) as the input/reference and the FA or nodif (b=0) image as the reference/input.
 
All the best,
Mark
 
 
 
On 4 Aug 2014, at 08:15, Stephen Smith <[log in to unmask]>
 wrote:


Hi - DOF=3 is for 2D images - you will need DOF=6 or more.
Steve.
 
 
 
On 3 Aug 2014, at 18:50, M. alshikho <[log in to unmask]> wrote:


Hi FSL Experts,
In order to register a white matter mask from the T1 structural space into diffusion space (FA_map). I used FLIRT gui ( refference image is my dti map, input image is my mask ) and I did regid translation 3DOF. The resultant output image is pretty good but it needs a little bit warp to right.and a little bit moving up right. Kindly what is your advice to make my registeration more effective.
Many thanks,
Mohamad
 

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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
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