On 9/11/2020 6:48 PM, Gonzalo Rojas Costa wrote:
External Email - Use Caution
Hi:
I modified the coregistration using "tkregister2 --s subj1 --fstal
--surfs". Then, I used "recon-all -make all -s subj1", but I got
"Nothing to be done"... why ?... Which command must I run after
tkregister2 to reprocess ?
In theory, you have to re-run everything (so use -all instead of -make all)
Other question... what do you mean with " You might be comparing
dewarped vs not dewarped"
On some scanners, there is an option to remove the gradient distortion
from the scan ("dewarping"). if you did that for one time point and not
the other, then you could get a big diff in ICV
Sincerely,
Gonzalo Rojas Costa
>Message: 6
>Date: Thu, 10 Sep 2020 12:42:41 -0400
>From: "Douglas N. Greve" <dgr...@mgh.harvard.edu
<mailto:dgr...@mgh.harvard.edu>>
>Subject: Re: [Freesurfer] big difference between ICV same patient....
>To: <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
>Message-ID: <0112a2be-2c41-a100-6ac7-e8d054e97...@mgh.harvard.edu
<mailto:0112a2be-2c41-a100-6ac7-e8d054e97...@mgh.harvard.edu>>
>Content-Type: text/plain; charset="utf-8"
>
>It all comes down to the registration. See
>https://surfer.nmr.mgh.harvard.edu/fswiki/eTIV
>The image may have more-or-less neck and that can change the
>registration and ICV. The contrast may be different. The scanner may
>have had software updates. You might be comparing dewarped vs not
dewarped.
>
>On 9/10/2020 2:16 PM, Gonzalo Rojas Costa wrote:
>>
>> ????????External Email - Use Caution
>>
>> Hi:
>>
>> ? Why I got a big ICV difference between MPRAGE of the same patient
>> (2019: 1775887.317631, 2020: 1566398.53576 mm3), one-year difference
>> acquisition, and the same MRI Skyra 3T equipment? I used freesurfer
>> 5.1.0 on the same computer, and operating system in both cases...
>>
>> ? I reviewed the coregistration to MNI305 and it is reasonably good in
>> both cases...
>>
>> ? The case was reviewed by an expert neuroradiologist, and she does
>> not consider that there is a significant visual difference between
>> both sizes.
>>
>> ? Sincerely
>>
>>
>>
>> Gonzalo Rojas Costa
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