Hi -
Was there ever a solution found for this? I am currently having the same
problem.
Thanks,
Jeff Thompson
Can you send us e recon-all.log file?
On Aug 8, 2011, at 4:30 AM, "Irwin, William" wrote:
> Hi-
>
>
>
> I’m at a bit of a loss as to how to addres
standard atlas and template files to be able to run recon-all?
Any help is much appreciated,
Jeff Thompson
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailma
Hi,I have run talairach_avi with the template I have made, and an input file
that is manually skull stripped. I ran: talairach_avi --i .nii.gz
--atlas --xfm talairach_avitest.xfmI had put the
.nii.gz file in the average folder in freesurfer for this to
work. I also have .4dfp.hdr , .4dfp
Hi,I have run talairach_avi with the template I have made, and an input file
that is manually skull stripped. I ran: talairach_avi --i .nii.gz
--atlas --xfm talairach_avitest.xfmI had put the
.nii.gz file in the average folder in freesurfer for this to
work. I also have .4dfp.hdr , .4dfp
avoid needing the .gca file if cortical thickness
measurements is the only goal?Or could there be a limited number of labels
needed incorporated into the .gca file for this goal. Ex. Just Cerebral cortex
ROI'
another way?
Thank you,
Jeff Thompson
___
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
I found this info on the tksurfer webpage.
The label file format is interchangable with TkMedit. You can create a label in
TkSurfer, save it, and load it in TkMedit, or vice versa.
Jeff Thompson
From: jeff_rthomp...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: creating labels
the labels.mgz file and
the others manually, and turn that into the .gca file with mri_convert.
Can this be done?
Thank you,
Jeff Thompson
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail
of the most likely label at each voxel (indices refer
> > to '#No.' column of $FREESURFER_HOME/FreeSurferColorLUT.txt)
> >
> > *
> >
> > priors --> the probability that that label occurs at that voxel
> >
> >
t build the gca from a handful
> of brains instead of the dozens we need for humans
>
> cheers
> Bruce
>
>
> On Mon, 27 Aug 2012, Jeff
> Thompson wrote:
>
> > Hello,
> > Okay, but from looking at the recon-all pipeline it looks like to generate
> > the no
gt; CC: freesurfer@nmr.mgh.harvard.edu
> > > Subject: RE: [Freesurfer] creating a gca file from .mgz files
> > >
> > > Hi Jefff
> > > you can give mri_ca_normalize a flag to tell it to use a manual
> > > segmentation instead of the gca. Try -seg . T
t sounds like things don't fail
> after you changed to float until you get the pbsubmit problem, correct?
>
> On Tue, 28 Aug 2012, Jeff Thompson wrote:
>
> > To change to type Float I used:
> > fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0
> > Alloybrain
me to .mgz
with mri_convert without throwing all of the label values off.
This resulted in a lot of errors when running rebuild_gca_atlas.csh and gave an
error stating
"ERROR: mri_ca_train check found 1 subjects with bad labels!"
Thanks,
Jeff Thompson
CC: freesurfer@nmr.mgh.h
I have has dimensions of : ~0.6 , 0.6 , 1.0 mm and 256x256x90.
Any recommendations to solve this problem?
Thank you,
Jeff Thompson
> Subject: Re: [Freesurfer] creating a gca file from .mgz files
> From: ni...@nmr.mgh.harvard.edu
> To: jeff_rthomp...@hotmail.com
> CC: fis...@nmr.mgh
> On Wed, 5 Sep 2012, Jeff Thompson wrote:
>
>> Hello,
>> I got mri_ca_train to complete and to produce a .gca file, which looks to be
>> what is expected after splitting it up into means/labels/priors files.
>> The problem was the norm.mgz file. I ended up copyin
15 matches
Mail list logo
