and when you say it is "way off" what do you mean? Is the intensity volume conformed in the same way?
On Thu, 6 Sep 2012, Jeff Thompson wrote: > > 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 <[email protected]> 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: [email protected] >>>> To: [email protected] >>>> CC: [email protected]; [email protected] >>>> 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: [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
