Are you trying to run this from outside of recon-all? If not, can you
send the recon-all log file? Also, have you looked at the talairach
registration?
On 8/15/2022 7:50 AM, 丁晴 wrote:
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Hello FreeSurfer Developers,
I'm attempting to generate filled.mgz us
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Hello FreeSurfer Developers,
I'm attempting to generate filled.mgz using the mri_fill -a */ponscc.cut.log
-xform */talairach.lta -segementation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
Error : *** Error in `mri_fill': double free or corruption (!p
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Hello,
I am trying to generate an inflated surface for a macaque brain, but mri_fill
has stopped working for this subject. Below is my command line and output. I
specify the corpus callosum and pons as well. Any suggestions?
mri_fill -CV 101 100 66
Dear FreeSurfer experts,
I'm attempting to make cortical surfaces for a macaque brain, and am having
trouble getting mri_fill to work. The command has worked without any errors
for a different macaque dataset in the past, and I can't seem to figure out
why it isn't working this time.
I am using v
Hi Bruce,
Yes. I am using voxel coordinates.
The command line is:
mri_fill /space/data/shayo/cooked/test2/mri/wm.nii
/space/data/shayo/cooked/test2/mri/filled.nii -CV 122 116 91
(I also gave the pons values, but it didn't seem to change anything).
-- Shay
Tsao lab
Caltech
On Thu, Jun 7, 2012 a
What's your command line? Are you using voxel coords?
On Jun 7, 2012, at 9:52 PM, Shay Ohayon wrote:
> Hi,
>
> I am having problem getting mri_fill to run on one of my volumes (it did work
> with another monkey, so I assume I am running things right).
> I am using v5.0 (but it also happens o
Hi,
I am having problem getting mri_fill to run on one of my volumes (it did
work with another monkey, so I assume I am running things right).
I am using v5.0 (but it also happens on 5.1).
The input is a monkey wm file with specified coordinates for the corpus
callosum.
The error I get is: "could
ly erasing
some voxels, so I think I will stick with it.
Thanks in advance,
Regards,
Falk
-Original Message-
From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu]
Sent: Tuesday, May 19, 2009 5:38 PM
To: Nick Schmansky
Cc: Falk Lüsebrink
Subject: RE: [Freesurfer] mri_fill
Falk,
I c
me voxels, so I think I will stick with it.
Thanks in advance,
Regards,
Falk
-Original Message-
From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu]
Sent: Tuesday, May 19, 2009 5:38 PM
To: Nick Schmansky
Cc: Falk Lüsebrink
Subject: RE: [Freesurfer] mri_fill
Falk,
I can help you g
mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Falk Lüsebrink
> Sent: Monday, May 18, 2009 2:36 PM
> To: 'Bruce Fischl'
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] mri_fill
>
> Hi Bruce,
>
> Actually I need to skip the whole
PM
To: 'Bruce Fischl'
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] mri_fill
Hi Bruce,
Actually I need to skip the whole aseg process as this is incompatible to
the high resolution volumes I'm using. I read that prior to the aseg files
the talairach transform was used to
urfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_fill
p.s. you can pick seed points in the callosum and pons in tkmedit and see if
that fixes your problem, but if there is something else going on then it may
not (e.g. if the aseg is badly wrong) On Mon, 18 May 2009, Falk Lüsebrink
wrote:
p.s. you can pick seed points in the callosum and pons in tkmedit and see
if that fixes your problem, but if there is something else going on then
it may not (e.g. if the aseg is badly wrong)
On Mon, 18 May 2009, Falk
Lüsebrink wrote:
Hi FreeSurfers,
At the end of mri_fill Im told to chec
hmm, this almost never fails anymore. What does the aseg look like? Did
it label things correctly? Is the skull stripping ok?
Bruce
On Mon, 18 May 2009,
Falk Lüsebrink wrote:
Hi FreeSurfers,
At the end of mri_fill Im told to check the filled volume as the cerebellum
may be included. It i
Hi FreeSurfers,
At the end of mri_fill Im told to check the filled volume as the cerebellum
may be included. It is and also the brainstem. But actually I dont know
how to fix this. Do I need to include the seed points for cc and pons for
better cutting planes? Do I need to manually edit the
you can set those points in recon-all
run:
recon-all -cc-xyz -stage2 -subjid
On Mon, 22 Nov 2004, Calabrese Massimiliano wrote:
Hi everybody,
I'm trying to fix a problem and I would be very happy if someone has an
advice for me :)
In some case I get an error about finding Corpus Callosum.
So I ha
Hi everybody,
I'm trying to fix a problem and I would be very happy if someone has an
advice for me :)
In some case I get an error about finding Corpus Callosum.
So I have tried mri_fill -cc-xyz X Y Z and it seem to work.
Now can I use recon-all to go ahead?
(I really don't know if I'm able to
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