I think noaseg is a bit different as it will not use the aseg in
downstream processing. From the help:
-noaseg
Skips subcortical segmentation steps (same as -nosubcortseg), and does
not use aseg.presurf.mgz for inorm2, wm segmentation, or filling.
Use this flag for brains that do not support usage of Freesurfers
subcortical
segmentation, such as baby brains, or non-human primates.
On Fri, 24 Apr 2015, silve...@gmx.com wrote:
For the approach below you need to edit both the aseg.mgz and brainmask.mgz
and run -autorecon-pial for each hemishphere individually.
Just make sure you keep a copy of the unedited brainmask.mgz and aseg.mgz so
you can do both hemispheres.
Also, I think -autorecon2-noaseg and autorecon2-cp ponit to the same command
set. Is that right? From recon-all it lists:
case "-autorecon2-cp":
case "-autorecon2-noaseg": case "-autorecon2-wm": set
DoNormalization2 = 1; set DoSegmentation = 1; set DoFill
= 1;
etc..
>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
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> The information in this e-mail is intended only for the person to whom
it is
>>>> addressed. If you believe this e-mail was sent to you in error and the
e-mail
>>>> contains patient information, please contact the Partners Compliance
HelpLine at
>>>> http://www.partners.org/complianceline . If the e-mail was sent to you
in error
>>>> but does not contain patient information, please contact the sender and
properly
>>>> dispose of the e-mail.
>>>
>>>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
is
> addressed. If you believe this e-mail was sent to you in error and the
e-mail
> contains patient information, please contact the Partners Compliance
HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
error
> but does not contain patient information, please contact the sender and
properly
> dispose of the e-mail.
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it
is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
