...@nmr.mgh.harvard.edu wrote:
what is your mri_convert command line?
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
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.harvard.edu
From: fis
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 norm.mgz file the .gca atlas is needed first. If I create the
seg_edited.mgz file from my manually labelled file can I use
the
inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our
compute cluster queueing system which is what the pbsubmit script is.
You'll need to modify it to use whatever cluster you are using or to run
them in series
cheers
Bruce
On Tue, 28 Aug 2012, Jeff Thompson wrote
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_mask_LUTComplete_float.nii.gz -odt float
I will try some other methods
you want to train on that contains the labels, and an accompanying
intensity volume (we usually use the norm.mgz for this purpose). Then we
extract statistics to create the .gca across these subjects using
mri_ca_train
cheers
Bruce
On Thu, 23
Aug 2012, Jeff Thompson wrote:
From
or is there 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
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
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.nmr.mgh.harvard.edu/mailman/listinfo
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's.
Thank you for any help,
Jeff Thompson
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 input.nii.gz
--atlas avgeragetemplate --xfm talairach_avitest.xfmI had put the
averagetemplate.nii.gz file in the average folder in freesurfer for this to
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 input.nii.gz
--atlas avgeragetemplate --xfm talairach_avitest.xfmI had put the
averagetemplate.nii.gz file in the average folder in freesurfer for this to
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 WIrwin at memory.ucsf.edu wrote:
Hi-
I’m at a bit of a loss as to how to address
13 matches
Mail list logo
