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Awesome, thank you Paul!
Best,
Panos
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Wighton, Paul
Date: Wednesday, September 21, 2022 at 5:24 PM
To: Freesurfer support list
Subject: [External] Re: [Freesurfer] Voxel to mm coordinates
Hi Panos,
Yes that is correct. Taking a voxel value and multiplying it by the vox2ras
matrix will give you a coordinate in the "patient coordinate system" which is
in mm. RAS denotes that the directions (R)ight, (A)nterior and (S)uperior are
positive.
-Paul
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Hello,
I was wondering what the best way would be to extract the coordinates of each
voxel in my nifti volume in mm. I have used MRIread to load the nifti volume
into Matlab (=mri) and wanted to essentially create a new variable that takes
each
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On other thought: You may want to do Doug's suggestion of calculating the
paired-diff in the longitudinal stream's subject-specific unbiased template
space of each participant instead of doing it all in fsaverage. Then take
the resultant file, the
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Thank you Doug, I will follow your suggestion.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve
Sent: Wednesday, September 21, 2022 9:58 AM
To: freesurfer@nmr.mgh.harvard.edu
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Good afternoon,
I am having trouble unzipping the freesurfer folder downloaded from your
website as a password is required and I could not find it. I have done my
registration and got the licence.txt file, but I don't know if the password is
in it.
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Dear Freesurfer experts,
In order to normalize white matter intensity of T1 images and correct for
bias field. We do the following steps:
mri_convert T1.nii.gz T1.mgz
mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
mri_normalize -g 1
by template I'm assuming you mean the atlas. There is not an easy way to
create a new atlas or modify the existing one (though we are developing
methods to do both). For the eyes, you could probably just write
something to look at the column index in the eyes. If it is less than
128, then set
You may be able to use one of the paired diff options in mris_preproc.
Run it with --help. I also put some info on it below. QDEC has been
deprecated
--paired-diff
After concatenating all the inputs together, create a new output file by
computing paired differences, ie, Input1-Input2,
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Dear Freesurfers,
I have been using samseg for a while and like it a lot. Thank you for this
tool. How do you modify the template for this tool? Is there a guideline
for this?
I would like to divide Fluid_Inside_Eyes label to left and right and
improve
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