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.
Diffusion MRI Slice Alignment
- Jean-Francois Mangin
- Posts: 337
- Joined: Mon Mar 01, 2004 10:24 am
- Location: Neurospin, CEA, France
- Contact:
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...)
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
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.
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.