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.
> >
> >
> >
> >
>
>
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