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 <fis...@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: ni...@nmr.mgh.harvard.edu >> > To: jeff_rthomp...@hotmail.com >> > CC: fis...@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: fis...@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_rthomp...@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_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. >> > > > > > > > > >> > > > > > > > > >> > > > > > > >> > > > > > > >> > > > > >> > > > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
