fsl normalization/template

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sdika
Posts: 3
Joined: Fri Dec 21, 2007 10:47 am

fsl normalization/template

Post by sdika »

Hi,

I am new using brainvisa and I'd like to use the cortical fold recognition module.

I understood that before, I have to run the 2004 T1 pipeline and before that, I have prepare the subject.

I want to normalize it automatically and I wonder if I can use FSL to do that (because I don't need matlab and FSL is already installed here).

A priori, only the template matters for the normalization, so I can use any rigid (or affine ?) registration procedure. Am I right ?

Do I have to "steal" the template from SPM or can I use one of the FSL template, here is the list:
$FSLDIR/data/standard/avg152T1_brain.nii.gz
$FSLDIR/data/standard/MNI152_T1_0.5mm.nii.gz
$FSLDIR/data/standard/MNI152_T1_1mm.nii.gz
$FSLDIR/data/standard/MNI152_T1_2mm.nii.gz
$FSLDIR/data/standard/MNI152lin_T1_1mm.nii.gz
$FSLDIR/data/standard/MNI152lin_T1_2mm.nii.gz

thank you,

Michaël Sdika
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Jean-Francois Mangin
Posts: 337
Joined: Mon Mar 01, 2004 10:24 am
Location: Neurospin, CEA, France
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Post by Jean-Francois Mangin »

You can do what you want for normalizing outside BrainVISA I think, except if you apply non linear normalization, I do not know the consequence. The tricky thing is also that I do not know if the default coordinates of AC/PC will be correct for you in the prepare subject.

Afterward, the most usual use of the current release is:
0)Prepare
1)Bias correction with 2005 module,
2)Lock bias correction with the validation module
3)Pipeline 2004
4)Sulcus recognition

In fact when I process data myself, I am much less optimistic,
and I control everything step by step. It depends on your goal and schedule...
sdika
Posts: 3
Joined: Fri Dec 21, 2007 10:47 am

Post by sdika »

So if I use for example the MNI template with any affine registration procedure, I choose "MNI form Mritotal" and the AC/PC coordinates should be set correctly ? (if nothing failed...)

If yes, where can I find any of the three template you support ?
( it seems fsl provide two 1x1x1 MNI template)

thanks

Michaël
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Jean-Francois Mangin
Posts: 337
Joined: Mon Mar 01, 2004 10:24 am
Location: Neurospin, CEA, France
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Post by Jean-Francois Mangin »

Well, I am not quite sure, because I added this option when I was in the MNI in 2001. And there are numerous format pb that could disturb the process.
If you have some problem and you really want to use this approach to specify AC and PC coordinate, maybe the easiest way for you would be to create the *.APC file once and copy it for all your subject in the anatomy directory. Here is an example of the file content:

AC: 79 112 114
PC: 79 139 112
IH: 79 128 53
The previous coordinates, used by the system, are defined in voxels
They stem from the following coordinates in millimeters:
ACmm: 79.2645 112.441 114.0
PCmm: 79.2645 139.265 112.0
IHmm: 79.2645 127.971 53.0

The only mandatory lines are the three first lines I think.
The last point is anywhere in the interhemispheric plane far
above the commissures.
the file name is toto.APC
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