Diffusion MRI Slice Alignment

Questions about BrainVisa usage and installation

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Zahir Momin
Posts: 13
Joined: Sun Jul 18, 2004 8:35 am

Diffusion MRI Slice Alignment

Post by Zahir Momin »

Dear BrainVisa users and developers,

Again, I am analyzing patient MRI data collected on day 0 and day 5. These are diabetic patients presenting with ketoacidosis(DKA). I need a way to align their MRI slices with each other. Is there any feature in BrainVisa or Anatomist that will allow me to do that. I want to preferebly align them right so that I can put a region of interest in exact location on slices obtained on two different days.

Thank you for your time and help.
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Jean-Francois Mangin
Posts: 337
Joined: Mon Mar 01, 2004 10:24 am
Location: Neurospin, CEA, France

Post by Jean-Francois Mangin »

The registration toolbox of brainVISA is not developped yet. Various people are thinking about it. Therefore, there are some registration tools behind but not with a clear interface.
The most general way to align images is the AimsMIRegister commandline, which should yield a transformation file. This file should then be used to resample the image to be aligned,
for instance using VipSplineResample. This is something people do on a regular basis here, I will try to find somebody to give you more precise information.

Otherwise you may use other packages (AIR, FSL, SPM...)
Posts: 4
Joined: Mon Aug 16, 2004 3:19 pm
Location: CEA, Orsay, France

Post by delzescaux »

AimsMIRegister was developed to register TEP and MRI exams using rigid spatial transformation and mutual information as optimization criterion.

Commandline to register mri1.ima with mri2.ima:

AimsMIRegister -r mri1 -t mri2 --seuilref 0.05 --seuiltest 0.05

Two transformations are estimated: mri1_TO_mri2 and mri2_TO_mri1
The registration can be evaluated visually using anatomist in fusion mode.

Commandline to resample mri2:

VipSplineResamp -i mri2 -t mri1 -d mri2_TO_mri1 -o rsp_mri2 -r t -w t

If you need help, you can contact me.
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