Hi Bruce, Thanks for the reply. Would 'bbregister' work to register the files to eachother or would there be a more useful way to do that?
Also I noticed that across many of the subjects there is a slight difference in the TR, TE, TI, and flip angle values. For instance, one of the subjects has a TR: 9.39 and another might have a TR: 9.44. This clearly prevents me from using them to create an atlas. I am not really sure why these values are slightly off, they should be the same. Is there anyway to change those values manually? Is it because I am using the T1.mgz files? Thank you! - MP On Tue, Jul 23, 2013 at 3:15 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Mark > > have you tried using a transform? Usually with more than one subject we > require that they be registered. I haven't looked at that code in a long > time, so I am not positive that it would fix this problem, but it might. In > any case if they aren't registered it won't generate a useful atlas, even > if it does run to completion > Bruce > > > On Tue, 23 Jul 2013, Mark Plantz wrote: > > Hello freesurfers, >> I recently ran into a problem with mri_ca_train, a function that >> creates >> a .gca atlas from a manually segmented volume and input volume(s). >> >> My command line is: >> >> mri_ca_train -T1 T1.mgz CMH-11460 CMH-11461 ~/Desktop/atlas.gca >> >> The results: >> >> processing subject CMH-11461, 1 of 1... >> reading input 0: >> /Volumes/Wong_Lab/LabMRIData/**FreeSurfer/CMH-11461/mri/norm.**mgz >> filling holes in the GCA... >> 404261 classifiers: 1.5 per node, 7.59 in brain (0 holes filled) >> computing covariances for subject CMH-11461, 1 of 1... >> average std = 6.1 using min determinant for regularization = 3.7 >> 298584 singular and 4268 ill-conditioned covariance matrices regularized >> writing trained GCA to /Users/IngvalsonLab/Desktop/**atlas1.gca... >> classifier array training took 0 minutes and 27 seconds. >> dhcp-165-124-23-230:LabMRIData IngvalsonLab$ >> dhcp-165-124-23-230:LabMRIData IngvalsonLab$ >> dhcp-165-124-23-230:LabMRIData IngvalsonLab$ mri_ca_train -T1 T1.mgz >> CMH-11460 CMH-11461 ~/Desktop/atlas1.gca >> reading T1 data from subject's mri/T1.mgz directory >> training on 2 subject and writing results to >> /Users/IngvalsonLab/Desktop/**atlas1.gca >> **************************************************************** >> *************** >> processing subject CMH-11460, 1 of 2... >> reading input 0: >> /Volumes/Wong_Lab/LabMRIData/**FreeSurfer/CMH-11460/mri/T1.**mgz >> **************************************************************** >> *************** >> processing subject CMH-11461, 2 of 2... >> reading input 0: >> /Volumes/Wong_Lab/LabMRIData/**FreeSurfer/CMH-11461/mri/T1.**mgz >> filling holes in the GCA... >> 468392 classifiers: 1.8 per node, 10.41 in brain (0 holes filled) >> computing covariances for subject CMH-11460, 1 of 2... >> GCAupdateNodeCovariance(17, 35, 28, 4): could not find label >> dhcp-165-124-23-230:LabMRIData IngvalsonLab$ >> >> >> According to the fswiki, the same bug was eliminated in the 2009 >> version. >> For some odd reason, this command works with one subject, but not with >> multiple subjects. >> >> Any ideas? >> >> Thanks in advance, >> >> MP >> >> >> > > 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<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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