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: [email protected] > From: [email protected] > Subject: Re: [Freesurfer] creating a gca file from .mgz files > Date: Tue, 28 Aug 2012 20:12:45 -0400 > To: [email protected] > > 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 > <[email protected]> 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: [email protected] > > To: [email protected] > > CC: [email protected] > > 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: [email protected] > > > > To: [email protected] > > > > CC: [email protected] > > > > 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: [email protected] > > > > > > To: [email protected] > > > > > > CC: [email protected] > > > > > > 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: [email protected] > > > > > > > > To: [email protected] > > > > > > > > CC: [email protected] > > > > > > > > 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 > e-mail was sent to > > > you > > > > > in > > > > > > > error > > > > > > > > but does not contain patient information, please > contact the > > > sender > > > > > and > > > > > > > properly > > > > > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
