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_rthomp...@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: fis...@nmr.mgh.harvard.edu > > To: jeff_rthomp...@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: fis...@nmr.mgh.harvard.edu > > > > To: jeff_rthomp...@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: fis...@nmr.mgh.harvard.edu > > > > > > To: jeff_rthomp...@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: fis...@nmr.mgh.harvard.edu > > > > > > > > To: jeff_rthomp...@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 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
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