Hi Chia-Shu
The matrices are stored in a 3-column format. Buried somewhere in the doc, it says that you can load them in matlab using:
x=load('fdt_matrix3.dot');
M=spconvert(x);
Cheers
Saad
On 2 Jul 2012, at 05:32, Chia-shu Lin wrote:
> Hi Saad
>
> Just a quick question about the NxN connectivity matrix of probtrackx2. I have tried omatrix3, and it seems that I also have to put target3 in the command line.
>
> So my command is something like this
>
> probtrackx2
> -x ....../${roi}.nii.gz -l -c 0.2 -S 2000 --steplength=0.5 -P 50
> --xfm=....../$1/bedpostX/xfms/standard2ptx.mat --forcedir --opd
> -s ....../$1/bedpostX/merged
> -m ....../$1/bedpostX/nodif_brain_mask
> --dir=....../$1/pt2/track_${roi}
> --targetmasks=....../clf_masks/all_GM2.txt --os2t
> --omatrix3 --target3=....../clf_masks/all_GM2.txt;
>
> (my ROIs are '01', '02', etc. )
>
> And it returned the file 'fdt_matrix3.odt' in each result folder (e.g., 'track_01', track_02' etc.). This fdt_matrix3 however did not look like a NxN matrix that I expected.
>
> Did I miss anything here? Thanks in advance -Chiashu
>
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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