Re: [Freesurfer] Which pial surface to trust, with or without -FLAIR option

[Douglas N. Greve]

We get a lot of variable results with FLAIR. Sometimes it helps, 
sometimes it hurts. FLAIR scans themselves can be very variable across 
sites. If it is looking like it is hurting your results, then just run 
without it.


On 3/12/2021 11:07 AM, Xiaojiang Yang wrote:


External Email - Use Caution

Dear FS developers,

I have run FS’s recon-all on many cases, with and without -FLAIR 
options. I found the pial  surface results (?h.pial) I obtained 
without -FLAIR option fit to the original image 
(subjected/mri/orig.mgz) much better than those with -FLAIR option, at 
least from my visual judgment. See *MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
https://imgur.com/a/wrY0HTY 
 for 
one example.


I know -FLAIR option was introduced to improve the quality of pial 
surface segmentation. Now for many cases, my intuition is that -FLAIR 
option decreases the pial quality. My questions are:


  * Is this intuition correct?
  * Should I trust the pial surface that’s obtained with or without
-FLAIR option in general?

In addition, when I use the -FLAIR option, I sometimes get failed when 
running recon-all. After I did some manual edits to the brainmask 
image, and re-run the recon-all:


recon-all -autorecon-pial -subjid 

I can get recon-all successful. But if I run recon-all without -FLAIR 
option, I can get successful results without needing to manually edit 
the brainmask image.


So my last question is:

  * Should I just run recon-all without -FLAIR option, or, with -FLAIR
option + manual edit + re-run with -autorecon-pial? Which is better?

Thank you very much!

John


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[Freesurfer] Which pial surface to trust, with or without -FLAIR option

[Xiaojiang Yang]

External Email - Use Caution

Dear FS developers,



I have run FS’s recon-all on many cases, with and without -FLAIR options. I
found the pial  surface results (?h.pial) I obtained without -FLAIR option
fit to the original image (subjected/mri/orig.mgz) much better than those
with -FLAIR option, at least from my visual judgment. See
https://secure-web.cisco.com/1jL9MUfd9oLXR_SVyZl8-wPztrX70T9SJxxJaJElRv5e-Dj4sp4RQ3M4KUFAgUKpZxTsy39_ZpJl8bnnPbnvx2YzJvRH_uTKNfjANjJd-5gjcRF6xLXUfsXjqCmSKGe2yz1c7u_wmpF_bHrEno5pHCvh7SC8bm74VtmPYYNj-YuJSnlcZ85bx_0q82bTlL56VDSPkTK1ifobJsYiFQf7k5pSOsiAvHKbOmRIQvzx-ezp9lvzhHLbD0MIodNOc9hyrNxaG0ZWxK49VfLdGXKCgmg/https%3A%2F%2Fimgur.com%2Fa%2FwrY0HTY
 for one example.



I know -FLAIR option was introduced to improve the quality of pial surface
segmentation. Now for many cases, my intuition is that -FLAIR option
decreases the pial quality. My questions are:

   - Is this intuition correct?
   - Should I trust the pial surface that’s obtained with or without -FLAIR
   option in general?



In addition, when I use the -FLAIR option, I sometimes get failed when
running recon-all. After I did some manual edits to the brainmask image,
and re-run the recon-all:

recon-all -autorecon-pial -subjid 

I can get recon-all successful. But if I run recon-all without -FLAIR
option, I can get successful results without needing to manually edit the
brainmask image.



So my last question is:

   - Should I just run recon-all without -FLAIR option, or, with -FLAIR
   option + manual edit + re-run with -autorecon-pial? Which is better?



Thank you very much!

John
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