Hi Gabriel
remove the -check from your command line
cheers Bruce On Fri, 21 Dec 2012, Gabriel Gonzalez Escamilla wrote:
Thanks for your reply Anastasia,
You totally got it, I must say that actually have the Mori tract atlas, in nii format. But the thing I'm looking for, is to use this WM parcellation to parcellate WM of my subjects in FS.
I have tried to use recon-all tools for successfully reconstruct the MNI152_1mm subject supplied by FSL (as is the same used in the Mori atlas), I have transformed my mori_labels_atlas into mgz and change to the subject space by a resampling and adding the talairach.xfm to the header of the seg_atlas.mgz. This method sets everything onto the FS_MNI_305 space. All these steps worked as you can see in the attached image.
Then, I have tried to use mri_ca train to get the gca file as: mri_ca train -prior_spacing2 -node_spacing 8 -mask $FSreconned_MNI152/brain.mgz -parc_dir JHU.ICBMtracts.1mm.mgz -zform talairach.xfm -T1 norm.mgz -check FSreconned_MNI152 JHU.ICBMtracts.1mm.2012-12-20.gca
It always try to check the left_pallidum label and right_putamen and fails in many coordenates and outputs.
ERROR: mri_ca_tain check found 1 subjects with bad labels!
I checked and all the mgz files are in uchar format, I don't know if the problem is that I already have all labels into a single mgz file, In that case, how can I compute the gca file?
Do you have any advice for me?
Bests, Gabriel.
PD. If you are agree I will repost this to the FS-list, beacuse may be helpuful for someone else. And may be get some more tips from the others.
El 20/12/12, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu escribió:
Hi Gabriel - If you just need volumetric labels of the Mori tracts, you can get that directly by downloading their atlas. The tracula atlas doesn't have an average volume (it doesn't represent the tracts as volumes at all) and in any case you'd still have the problem of registering your individuals to a common space (it sounds like you want to use fsaverage as your common space, which tracula is independent of). Am I misunderstanding what you're asking? a.y On Wed, 19 Dec 2012, Gabriel Gonzalez Escamilla wrote: >Dear Anastasia Yendiki, > > >My name is Gabriel, I'm a student on a Spanish university, working with MRI and FS, I?m >looking for a new way to parcellate the WM on a group of subjects (without DTI data) >processed with FS v5.1. I know there exist some WM fiber atlas, but I saw that you have >develop something that could match more precisely the FS space on my subjects, and as you >have as background the Mori atlas, that to my knowledge, is the most complete WM atlas (Mori >et al., 1999; Wakana et al., 2007). > >I have found in your 2011 tracula paper, the next phrase: > >?We have developed TRACULA (TRActs Constrained by UnderLying Anatomy), a method for automated >reconstruction of major white-matter pathways that is based on the global probabilistic >approach of Jbabdi et al. (2007) and utilizes prior information on the anatomy of the >pathways from a set of training subjects. Once the pathways have been labeled manually in the >training set, their trajectories are combined with an automatic anatomical segmentation of >the same subject (Dale et al., 1999; Fischl et al., 1999a,b, 2002, 2004a,b; Fischl and Dale, >2000) to derive a description of the pathways in terms of the structures that they intersect >and neighbour. The knowledge on path anatomy that is extracted from the training set is then >used to initialize a global probabilistic tractography algorithm and also to constrain its >search space by penalizing connections that do not match our prior anatomical knowledge. This >allows the algorithm to reconstruct the pathways reliably in a novel subject with no manual >intervention, facilitating the analysis of large data sets.? > >I?m wondering if the manually labeled pathways (trajectories) combined in an anatomical >segmentation of the same subject are available? or if this subject is distributed somehow >with FS v5.1? > >Or if can you give me an advice of how to proceed to make my own from a stardard atlas (i.e. >JHU_atlas in MNI space). > > >Many thanks in advanced, > >Gabriel. > > > > 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.