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 > >
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