Hi Mike
yes, I remember that and it is fixed in the upcoming 6.0. Not sure if
that handles crossing the midline though. Were you having that issue, or
just white/pial crossing?
cheers
Bruce
On Fri, 24 Apr 2015, Harms, Michael wrote:
Is this perhaps the same issue that I reported in this thread?:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38258.html
If so, it is due to a "bug" of sort in the recon-all in v5.3
It appears that some of our followup conversation occurred off list, so
for others benefit, I'm pasting in the key exchange below (and to remind
Bruce):
--- from Bruce ---
ok, I see what's going on. Here is the sequence of calls:
1. mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs
L408_base lh
Makes the white surface *without* using the aparc. Because there are a
string of "hypointensity" labels in the aseg, the white surface is frozen
in these locations.
2. mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs L408_base
lh
internally recreates the white surface but doesn't save it. The frozen
vertices are allowed to move since the aparc *is* used in this call, and
the vertices are deemed to be in real cortical regions.
The pial surface then starts from the (inwards deformed but not written to
disk) white surface, and then settles inside the white surface that is on
disk.
I'm not sure how we settled on this logic. Why recreate the white surface?
Why not run with -nowhite -orig_pial white? That way the algorithm uses the
white surface that the user can see and things should be consistent
Bruce
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
On 4/24/15 7:42 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
no, I don't think it would. If you upload a case with crossing surfaces
I'll take a look
cheers
Bruce
On Fri, 24 Apr 2015, Clara Kuehn wrote:
Dear Bruce,
thanks for the reply. I often have the case that the aseg.mgz is already
correct, however the surfaces cross because the aparc+aseg.mgz
incorrectly classified the hemispheres. If running autorecon2-cp uses the
aseg.mgz, which is already correct, would that make any changes to the
aparc+aseg.mgz?
Cheers, Clara
----- Ursprüngliche Mail -----
Von: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Freitag, 24. April 2015 03:12:55
Betreff: Re: [Freesurfer] crossing medial surfaces
I don't think you want noaseg. Why not try autorecon2-cp so it starts
after the aseg but uses it?
cheers
Bruce
On Thu, 23 Apr 2015, Clara Kuehn wrote:
Hi Paul,
thanks for your reply. I think the problem is that after editing the
aseg.mgz and rerunning -autorecon2-noaseg it doesn't update the
aparc+aseg.mgz, so the surfaces still cross.
Cheers, Clara
----- Ursprüngliche Mail -----
Von: silve...@gmx.com
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 23. April 2015 03:24:51
Betreff: Re: [Freesurfer] crossing medial surfaces
Hi Clara,
The method for dealing with the crossing medial surfaces that works for
me is decribed in the email below. Though, I'm not sure if there are any
issues or concerns with this approach particularly in regard to
thickness or the segmentations.
Paul
Sent: Tuesday, October 22, 2013 at 9:49 AM
From: "silve...@gmx.com" <silve...@gmx.com>
To: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] medial wall crossing the surface: repost
Thanks Bruce for your response, I'll fix aseg where it is incorrect,
but what about the instances where the aseg is correct and the pial
surfaces cross? Other than needing to update aseg.stats, are there any
other concerns with the 'hemisphere' approach I described below?
Thanks again,
Paul
----- Original Message -----
From: Bruce Fischl
Sent: 10/22/13 09:46 AM
To: silve...@gmx.com
Subject: Re: [Freesurfer] medial wall crossing the surface: repost
Try fixing the aseg and rerunning
Cheers
Bruce
On Oct 21, 2013, at 6:23 PM, "silve...@gmx.com" <silve...@gmx.com>
wrote:
Not always, but yes, in some instances the aseg crosses.
----- Original Message -----
From: Bruce Fischl
Sent: 10/18/13 01:22 PM
To: silve...@gmx.com
Subject: Re: [Freesurfer] medial wall crossing the surface
Does the aseg cross as well?
On Oct 17, 2013, at 10:07 PM, "silve...@gmx.com" <silve...@gmx.com>
wrote:
Dear All,
I too am seeing the medial pial surfaces crossing hemispheres in
some subjects.
The approach that appears to be working for me involves making
copies of brainmask.mgz and aseg.mgz
For the left hemisphere crossing into the right, edit brainmask.mgz
and aseg.mgz to delete voxels at the crossing belonging to the right
hemisphere.
I then run recon-all -autorecon-pial -hemi lh -subjid subject
followed by returning the brainmask.mgz and aseg.mgz back to their
original copy.
This is similarly repeated for the right hemisphere crossing into
the left.
Are there any issues or concerns with this approach particularly in
regard to thickness or the segmentations?
Thanks,
Paul
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