Is there a T2.prenorm.mgz in the mri folder? If not, you can run
bbregister --mov T2.nativespace.mgz --t2 --s subject --reg t2.reg.lta
mri_vol2vol --mov T2.nativespace.mgz --reg t2.reg.lta --targ orig.mgz
--o T2.prenorm.mgz
Then run something like
mri_normalize \
-sigma 0.5 -nonmax_su
I processed the T1-weighted data without T2. Therefore, we do not have
T2.norm.mgz in the mri folder of each subject.
Only for the HP-subfields segmentation, we added additional high-resolution
T2-weighted data to increase the accuracy of HP-subfields segmentation.
Thanks!
Alireza
> On Feb 27,
There is usually a T2.norm.mgz file in the mri folder. If that is there,
then you should use that rather than the raw data that is not bias field
corrected
On 02/27/2017 12:30 PM, ali reza mohammadi nejad wrote:
> Thank you so much Dr. Doug! I just have one more question:
>
> Now I want to comp
Thank you so much Dr. Doug! I just have one more question:
Now I want to compute the same information for our second modality (i.e., mean
and std intensity of different HP_subfields for our additional scan, e,g., T2
or FLAIR).
My question is that how could I use .FSspace.mgz (in mri folder)
and
Thank you so much Dr. Doug! I just have one more question:
Now I want to compute the same information for our second modality (i.e., mean
and std intensity of different HP_subfields for our additional scan, e,g., T2
or FLAIR).My question is that how could I use .FSspace.mgz (in mri
folder) and T
The basic command is
mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz
where seg is the hippo sub field seg and input is the input where you
want to get the intensities from (probably norm.mgz). Note that you need
to use the hipp sub field output that is 1mm (not the high re
Dear FreeSurfer Experts,
I want to compute some intensity information (e.g., mean and std) of each
Hippocampal subfields (similar to aseg.stats file).
I think one option could be mri_segstats command, but I am not sure.
If it works, what are the inputs of this command?
Thank you in advance for a
