oh, that must of been it. I did not keep edits in brainmask
On 5/1/17 4:39 PM, Antonin Skoch wrote:
Doug,
did you process from scratch or did you retain edits to brainmask.mgz
and wm.mgz?
The -cubic should not be necessary, since recon-all (which I primarily
obtained from
https://surfer.n
Doug,
I tried to replicate again v5.3 results of subject 1.
I checked wm.mgz, orig.mgz, ?h.orig, ?h.pial, ?h.white and found everything
identical (by using mri_diff and mris_diff) except FLAIR.mgz and ?h.pial (after
FLAIRpial refinement).
The difference was small, I have traced it to the level
Doug,
did you process from scratch or did you retain edits to brainmask.mgz and
wm.mgz?
The -cubic should not be necessary, since recon-all (which I primarily obtained
from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ has
UseCubic=1 ).
I could try to replicate v5.3 agai
It is subject #1, trying to replicate in our version of 5.3 using the
scripts/recon-all.local-copy
./recon-all.local-copy -all -FLAIRpial -s 1.dng.v53.local-cubic -cubic
The results were close, but they were not exact
On 5/1/17 4:13 PM, Antonin Skoch wrote:
Dear Doug,
that is strange. What
Dear Doug,
that is strange. What precisely you cannot replicate? The results with v5.3 or
with v6.0? What subject from the group I uploaded you have tried?
I could try to run the comparison again but I have seen the results already in
many subjects and the difference between -cubic and no cubic
I can't seem to replicate your results locally, even with the recon-all
you used. The one thing I'm missing is the expert options file. Can you
send that to me?
On 04/24/2017 12:49 PM, Antonin Skoch wrote:
> Dear Doug,
>
> the subject with leak of white surface outside brain (my first post with
Dear Doug,
the subject with leak of white surface outside brain (my first post with
screenshots) is subject 1. Slice number (coronal) around 100.
The subject in second post (with text below) is subject 2, slice number
(coronal) also 100.
I have processed the subjects with v 6.0 (in fact dev ver
And what slice number?
On 04/24/2017 11:16 AM, Douglas N Greve wrote:
> Anonin, of the three subjects you sent, which one is shown in these
> pictures?
>
>
> On 04/19/2017 05:23 PM, Antonin Skoch wrote:
>> Dear experts,
>>
>> I am sending just one more example to illustrate issue with white
>>
ffect !
I will try your suggestions and let you know.
Antonin
From: Bruce Fischl
To: Antonin Skoch
Cc:
Sent: 4/21/2017 1:00 AM
Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in
comparison to v5.3 - worse GM/WM contrast
Hi Antonin
Doug points out to me tha
.c I did not comprehend where the
> basis of the issue lies, but in any case there are big differences in
> mri_normalize.c code between versions.
>
> Antonin
>
> From: David Semanek
> To: Antonin Skoch , "freesurfer@nmr.mgh.harvard.edu"
>
> Sent: 4/20/2017 3:4
RROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM
YOUR SYSTEM. Thank you for your cooperation.
From: Antonin Skoch
Date: Wednesday, April 19, 2017 at 5:23 PM
To:
Subject: [Freesurfer] Worse determination of ?h.white with v6.0 in
comparison to v5.3 - worse GM/WM contrast
Dear experts,
I
ended filtration which affects GM/WM contrast.
>
> Looking at the source code of mri_normalize.c I did not comprehend where
the
> basis of the issue lies, but in any case there are big differences in
> mri_normalize.c code between versions.
>
> Antonin
>
t: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in
comparison to v5.3 - worse GM/WM contrast
Agreed. A validated protocol run on a very large group of
subjects in 5.3 was attempted with similar data in 6.0 and not
only was the longitudinal edit stream nearly non-function
at 10:25 AM
To: David Semanek ,
"freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in
comparison to v5.3 - worse GM/WM contrast
Dear David,
thank you for the feedback; I saw your posts concerning edits and responded
to them, see
e-mail. PLEASE NOTIFY US
IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM
YOUR SYSTEM. Thank you for your cooperation.
From: Antonin Skoch
Date: Wednesday, April 19, 2017 at 5:23 PM
To:
Subject: [Freesurfer] Worse determination of ?h.white with v6.0 in
comparison to v5
case there are big differences in
mri_normalize.c code between versions.
Antonin
From: David Semanek
To: Antonin Skoch , "freesurfer@nmr.mgh.harvard.edu"
Sent: 4/20/2017 3:41 PM
Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in
comparison to v5.3 - worse GM/WM
Hi Antonin
if you upload this subject and give me the voxel coords of that location
I'll take a look
cheers
Bruce
On Wed, 19 Apr 2017, Antonin Skoch wrote:
> Dear experts,
>
> I am sending just one more example to illustrate issue with white surface
> estimation in v6.0. See the attached scree
5:23 PM
To:
Subject: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison
to v5.3 - worse GM/WM contrast
Dear experts,
I am sending just one more example to illustrate issue with white surface
estimation in v6.0. See the attached screenshots: In v6.0 there seems to be
Hi,
I've also come across similar situations in my FS 6.0 dataset.
I have tried tweaking the seg-wlo and seg-ghi values and these steps have led
to marked improvements in some cases.
Curious to hear from the FS team too.
Thanks.
Best Wishes,
Elijah
Elijah Mak, Research Associate Depar
19 matches
Mail list logo
