sorry, don't use the mri.2mm/aseg.mgz use the one from mri/
The --inv take the inverse so it maps in the right direction
On 6/16/14 6:16 PM, Yang, Daniel wrote:
Hi Doug,
The way you are referring is to convert from MNI152 to MNI305? But I
wanted to do the opposite. You can see that the right_amygdala.mgz I
have as the input is already in the MNI305 space?
mri_binarize --i
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o
right_amygdala.mgz --match 54
If I use $FREESURFER_HOME/average/mni152.register.dat instead of
reg.2mm.mni152.dat, the product does not look right.
Thanks,
Daniel
From: Douglas Greve <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, June 16, 2014 at 11:43 AM
To: "freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>"
<freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] subcortical segment NIFTI files
That is not the right registration. Use
$FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat
specify right_amyg as the --targ and MNI152 as --mov and add --inv and
spec --interp nearest
doug
On 6/16/14 3:13 PM, Yang, Daniel wrote:
Hi Doug,
I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152
2mm space. The code posted below, for example, generate the right
amygdala in the MNI152 2mm space.
I am a little bit confused why my code is viewed as not doing
sensible things. In that mri_vol2vol command, the right_amygdala.mgz
is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to
transform to MNI152 2mm space.
Could you tell me which part is wrong?
Thanks,
Daniel
From: Douglas Greve <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, June 16, 2014 at 8:16 AM
To: "freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>"
<freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] subcortical segment NIFTI files
Sorry, I was trying to find out what it is you are trying to do, not
what your command line is. The command may run, it is not doing
anything intelligible, ie, it appears to be using the 2mm reg from
fsaverage/mni305 with the 2mm mni152, which does not make sense
doug
On 6/16/14 1:38 PM, Yang, Daniel wrote:
It appears that Email in Plaint Text makes the command line look
ugly. Here is a cleaner view. These two should provide the right
amygdala as the anatomical ROI in MNI152 2mm space.
mri_binarize --i
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o
right_amygdala.mgz --match 54
mri_vol2vol --mov right_amygdala.mgz --targ
${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz ---reg
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o
right_amygdala.nii.gz
If you run them, you will see what they do. They work for me.
Again, my next question is, where can I find reg.1mm.mni152.dat? Or
how can I generate one?
Thanks!
On 6/16/14, 3:51 AM, "Douglas Greve" <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>> wrote:
Sorry, what are you trying to do with that vol2vol command? The
command
line is surely wrong ...
On 6/16/14 5:57 AM, Yang, Daniel wrote:
Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.
I am able to obtain, for example, the right amygdala, using
the following
commands:
mri_binarize --i
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz
--o right_amygdala.mgz --match 54
mri_vol2vol --mov right_amygdala.mgz --targ
${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat
--o
right_amygdala.nii.gz
rm right_amygdala.mgz
One question: I don't see a file like reg.1mm.mni152.dat.
How do I obtain
a similar file in MNI152 1mm space, based on
${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <-- I
think this is a
1mm file?
Best,
Daniel
On 6/15/14, 10:58 PM, "Bruce Fischl"
<fis...@nmr.mgh.harvard.edu
<mailto:fis...@nmr.mgh.harvard.edu>> wrote:
mri_vol2vol with the transforms/talairach.xfm as the
transform should do
the trick. Make sure that the resample type is nearest
neighbor
Cheers
Bruce
On Jun 15, 2014, at 10:28 PM, "Yang, Daniel"
<yung-jui.y...@yale.edu <mailto:yung-jui.y...@yale.edu>>
wrote:
Hi Bruce,
Sorry, I wasn¹t clear. It¹s great to know that the
FreeSurfer is very
flexible. I meant to obtain the aseg individual
label files in MNI152
space as NIfTI files, for example, the different
parts of the CC.
Could you please point me to the right direction, as
to what tool I
should
use for this purpose (preferably a command line
tool, rather than a
visualization tool)?
Best,
Daniel
On 6/15/14, 10:16 PM, "Bruce Fischl"
<fis...@nmr.mgh.harvard.edu
<mailto:fis...@nmr.mgh.harvard.edu>>
wrote:
Hi Daniel
Any of our tools can write nifti if you give the
output volume the
extension .nii or .nii.gz
Cheers
Bruce
On Jun 15, 2014, at 5:54 PM, "Yang, Daniel"
<yung-jui.y...@yale.edu
<mailto:yung-jui.y...@yale.edu>>
wrote:
Dear all,
While it is possible to obtain NIfTI files
for cortical parcellation
using mri_annotation2label, I am running if
it is possible to obtain
NIfTI files associated with aseg parts?
Thanks!
Daniel
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