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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