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
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