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_suppress 0 -min_dist 1 \
-aseg $mdir/aseg.presurf.mgz \
-surface $sdir/rh.white identity.nofile \
-surface $sdir/lh.white identity.nofile \
$mdir/${t2flair}.prenorm.mgz \
$mdir/${t2flair}.norm.mgz
On 02/27/2017 01:28 PM, ali reza mohammadi nejad wrote:
> 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, 2017, at 12:53 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
>> wrote:
>>
>> 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 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 <analysisID>.FSspace.mgz (in mri
>>> folder) and T1_to_<analysisID>.v10.Ita (in transform folder) files in
>>> mri_segstats command?
>>>
>>> Thank you in advance for any help.
>>> Best regards,
>>> Alireza
>>>
>>>
>>>> On Feb 24, 2017, at 10:51 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
>>>> wrote:
>>>>
>>>> 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 res one)
>>>>
>>>>
>>>>> On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote:
>>>>> 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 any help.
>>>>> Alireza
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
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>>>> --
>>>> Douglas N. Greve, Ph.D.
>>>> MGH-NMR Center
>>>> gr...@nmr.mgh.harvard.edu
>>>> Phone Number: 617-724-2358
>>>> Fax: 617-726-7422
>>>>
>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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>>>>
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>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
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>
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>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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