The command line to get the aseg was:
Mri_convert -rt nearest -c <file containing all valued label masks>.nii.gz aseg.mgz
Fslmaths was used to match label values to the colour lut and combine them all into one file.
Thanks,
Jeff
On 2012-09-05, at 1:05 PM, Bruce Fischl fischl@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 ended up copying and renaming the T1.mgz file to replace the norm.mgz file, and it seemed to work in mri_ca_train. I am now having trouble with the aseg.mgz file in mri_normalize. It states that the aseg.mgz file needs to be conformed. When I conform the image the label values are way off. I tried the mri_convert conform with the rt nearest , but the label values seemed to still be off. The file 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: nicks@nmr.mgh.harvard.edu To: jeff_rthompson@hotmail.com CC: fischl@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Date: Wed, 29 Aug 2012 19:56:09 -0400
i think there should be an error log that outputs the errors that mri_ca_train found. or you can run mri_ca_train with the -check flag. it performs checks looking for voxels that are in the wrong hemisphere, based on the talairach registration.
for mri_convert, be sure to include the flag
-rt nearest
which overrides the default resample type of 'interpolate', which is not appropriate for labeled volumes.
n.
On Wed, 2012-08-29 at 18:20 -0300, Jeff Thompson wrote:
Hello,
Still getting the bus error when running mri_ca_train. I tried running it after I conformed the manually labelled volume as well.
I've been working on getting rebuild_gca_atlas.csh to work. I don't know how to get the labelled volume to conform when converting the labelled volume 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.harvard.edu From: fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Date: Tue, 28 Aug 2012 20:12:45 -0400 To: jeff_rthompson@hotmail.com
Oh, so you still got a bus error? I didn't realize that. Make sure the seg volumes are ok
On Aug 28, 2012, at 6:10 PM, Jeff Thompson jeff_rthompson@hotmail.com wrote:
Hopefully that doesn't scale the values I will make sure it doesn't.
When running mri_ca_train by itself after changing to float the next error was the Bus error.
When running rebuild_gca_atlas.csh I was having problems with pbsubmit, but after avoiding that it seems to be stuck with mri_ca_train.
Date: Tue, 28 Aug 2012 17:02:51 -0400 From: fischl@nmr.mgh.harvard.edu To: jeff_rthompson@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz
files
does that scale the values? Hopefully not. It 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_mask_LUTComplete_float.nii.gz -odt float
I will try some other methods for changing the data type,
but if that isn't
the issue are there other cases of getting similar errors
from mri_ca_train?
thanks,
Jeff
> Date: Tue, 28 Aug 2012 16:37:19 -0400 > From: fischl@nmr.mgh.harvard.edu > To: jeff_rthompson@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] creating a gca file from .mgz
files
> > how did you change the type to float? Make sure it
doesn't scale 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: > > > > > Hello, > > When running the mri_ca_train I am getting a Bus error
near the
beginning of > > it. > > > > 'bash-3.2$ mri_ca_train -parc_dir
Alloybrain_mask_LUTComplete_float.mgz
-T1 > > norm.mgz Alloy single_oneAlloy.gcareading segmentation
from subject's
> > mri/Alloybrain_mask_LUTComplete_float.mgz directory > > reading T1 data from subject's mri/norm.mgz directory > > training on 1 subject and writing results to
single_oneAlloy.gca
> > gcaAllocMax: node dims 64 64 64 > > gcaAllocMax: prior dims 128 128 128 > > gcaAllocMax: max_labels 4 >
> > processing subject Alloy, 1 of 1... > > reading input 0:
Desktop/freesurfer/subjects/Alloy/mri/norm.mgz
> > Bus error > > ' > > Previously it was giving an error saying
that :"mri_ca_train:
segmentation > > file > >
Desktop/freesurfer/subjects/Buddha/mri/Alloybrain_mask_LUTComplete.nii.gz is
> > not type UCHAR or FLOAT" > > > > So I changed the file type to float to get rid of
that.
> > Any ideas? > > > > When I run rebuild_gca_atlas.csh it gives a pbsubmit
command not found
> > error. If I have a cluster to use, but am able to just
load everything
onto > > it and then run it, can I comment out all of the
pbsubmit lines?
> > > > Thank you for all the help, > > > > Jeff > > > > > Date: Mon, 27 Aug 2012 12:00:13 -0400 > > > From: fischl@nmr.mgh.harvard.edu > > > To: jeff_rthompson@hotmail.com > > > 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 <manual
seg volume>. Then
the > > > gca name won't matter - it should ignore it. > > > > > > You could use label2label I guess, although if it's
accurate across
brains > > > then you probably don't need it and can just 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 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 that in
> > > > rebuild_gca_atlas.csh to generate the .gca atlas?
This would
incorporate > > the > > > > mri_ca_train, is that correct? > > > > > > > > The other question I have is regarding
mri_label2label. If I have
> > manually > > > > labelled one brain from my set, can I use
mri_label2label to convert
> > these > > > > labels to other dog brains in my set if they have
been registered to
the > > > > first brain used? > > > > > > > > Thank you, > > > > > > > > > > > > > > > > Jeff Thompson > > > > > > > > > > > > > > > > > Date: Sat, 25 Aug 2012 11:11:46 -0400 > > > > > From: fischl@nmr.mgh.harvard.edu > > > > > To: jeff_rthompson@hotmail.com > > > > > CC: freesurfer@nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] creating a gca file
from .mgz files
> > > > > > > > > > Hi Jeff > > > > > > > > > > it's more complicated than that. You need a .mgz
volume for every
> > subject > > > > > 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 the gcaFormat freesurfer wiki page I
know that: The .gca
file > > is > > > > > > composed of three volumes, which can be
extracted like this:
> > > > > > > > > > > > mri_convert atlas.gca -nth 0 means.mgz > > > > > > mri_convert atlas.gca -nth 1 labels.mgz > > > > > > mri_convert atlas.gca -nth 2 priors.mgz > > > > > > > > > > > > where: > > > > > > > > > > > > * > > > > > > > > > > > > means --> the mean intensity of the most
likely label
> > > > > > > > > > > > * > > > > > > > > > > > > labels --> indices 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
> > > > > > > > > > > > > > > > > > Is it possible to go the other way? I want to
create 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 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 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
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