Hi Gari - The authors of probtrackx would be able to give you more
information on how to normalize probtrackx outputs, but I'd suggest taking
a look at the methods section of this paper as an example:
S. B. Eickhoff, S. Jbabdi, S. Caspers, A. R. Laird, P. T. Fox, K.
Zilles, and T. E. J. Beh
Hi Gari - You're talking about thresholding the probtrackx maps, right? If
so the 20% at which the tracula maps are thresholded by default is
probably too high for probtrackx, I'd try something like 2%. (Tracula is
global and probtrackx is local tractography, so their outputs are
different be
Hi Anastasia,
it worked perfectly and I could run probtrack between my anatomical seed
and using waypoints from Tracula tracts.
I have another doubt right now. The probabilities in each new tract are
very different. I divided every value with waytotal using fslmaths -div in
order to normalize them
Hi Gari - Yes, fslmaths should be able to do it, with -thrp 20.
a.y
On Mon, 13 Jan 2014, Garikoitz Lerma-Usabiaga wrote:
Thanks Anastasia, I finally got it, I had to do mri_vol2vol twice to have it
in the diffusion space.
I have an additional question:
I want to create waypoint masks for pr
Thanks Anastasia, I finally got it, I had to do mri_vol2vol twice to have
it in the diffusion space.
I have an additional question:
I want to create waypoint masks for probtracx from Tracula tracts (for
example, uncinate).
Should I use mri_binarize on path.pd.nii to create the mask?
Should I use
Has mri/hippo_subfield_in_diffusion_space.nii been actually transformed to
diffusion space by applying the anatorig2diff transformation? I'm assuming
that your diffusion data is not 0.5mm resolution? You can search for the
name of the transformation in trac-all.log to see examples of how it is
Hi Anastasia,
the problem is with mri/hippo_subfield_in_diffusion_space.nii, which
originally is mri/hippo_subfield.mgz, the output of running recon-all
-hippo-subfields. So as far as I understand it is not in anatomical space,
according to MRI info, it is (one example):
- LIA
- 85x97x141
- 0.5x0.5
Hi Gari - So if I understand correctly, your inputs to probtrackx are:
mri/hippo_subfield_in_diffusion_space.nii
dmri.bedpostX/merged
dmri.bedpostX/nodif_brain_mask
If these all come from the output of tracula, aren't these all in LAS
orientation?
a.y
On Thu, 9 Jan 20
Thanks Doug!
just editing to correct a minor error in the last question:
> 3.- Afterwards I want to run probtracx with the following command (my
> doubt is mainly about the files to use, since FSL files are RAS,
> freesurfer anatomicals are LIA and freesurfer diffusion are LAS, are
> all the files
On 01/09/2014 12:45 PM, Garikoitz Lerma-Usabiaga wrote:
> Hi Anastasia,
> I want to use a hippocampal subfield as a seed in FSL. I am having
> problems understanding how to change spaces around...
>
> 1.- Is this command ok?
> mri_vol2vol --mov dmri/dtifit_FA.nii.gz --targ
> mri/hippo_subfield_i
Hi Anastasia,
I want to use a hippocampal subfield as a seed in FSL. I am having problems
understanding how to change spaces around...
1.- Is this command ok?
mri_vol2vol --mov dmri/dtifit_FA.nii.gz --targ
mri/hippo_subfield_in_anatomical_space.mgz --inv --interp nearest --o
mri/hippo_subfield_in_
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