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 ?
Other question... what do you mean with " You might be comparing dewarped vs not dewarped"
Sincerely,
Gonzalo Rojas Costa
Message: 6 Date: Thu, 10 Sep 2020 12:42:41 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] big difference between ICV same patient.... To: freesurfer@nmr.mgh.harvard.edu Message-ID: 0112a2be-2c41-a100-6ac7-e8d054e970eb@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
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" <dgreve@mgh.harvard.edu
mailto:dgreve@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-e8d054e970eb@mgh.harvard.edu
mailto:0112a2be-2c41-a100-6ac7-e8d054e970eb@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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Gonzalo Rojas Costa