Hi Saad
The coordinates are saved correctly with the latest FSL, but now there is a problem with the fdt_matrix1.dot. I get the following error when I try to load it in Matlab:
>> load('fdt_matrix1.dot')
??? Error using ==> load
Number of columns on line 11247647 of ASCII file
/nobackup/s072040-s072291/MLSP2013/data/ms_dwi/HC06/probtrackx_aal_mask1/from_aal_mask/fdt_matrix1.dot
must be the same as previous lines.
Do you know if there also is a cap on volume size in the fdt_matrix1.dot? Do you know how to solve the problem?
Thanks
Karen
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Fra: FSL - FMRIB's Software Library [[log in to unmask]] på vegne af Saad Jbabdi [[log in to unmask]]
Sendt: 13. maj 2013 18:35
Til: [log in to unmask]
Emne: Re: [FSL] Whole brain tractography
Hi Karen
That's a problem that has been spotted and solved (you need the latest FSL). The problem was that the coords file was saved as NIFTI, which has a cap on volume size.
If you don't want to re-run your tractography, you can still get the coord information by loading your seed mask in matlab (using the i/o tools in $FSLDIR/etc/matlab) like this:
mask=read_avw('seed_mask');
[x,y,z]=ind2sub(size(mask),find(mask));
Cheers
Saad
On 13 May 2013, at 17:20, Karen Ambrosen <[log in to unmask]> wrote:
> Hello,
>
> I have a question about whole brain tractography performed with probtrackx2 in FSL.
>
> I have a seed mask in standard space containing about 185,000 voxels of interest. To obtain a seed x seed matrix I use the matrix1 option in probtrackx2. The result of the tractography looks fine when considering the outputs fdt_paths.nii.gz and fdt_matrix1.dot. The problem is that the coords_for_fdt_matrix1.nii is not saved correctly (gives a 1x5 matrix, but I expected a 185,000x5 matrix). Is there any way to solve this problem?
>
> I tried to run my script with a smaller seed mask and it looks fine.
>
> I need the coordinates to partition the connectivity matrix in smaller regions. The reason not to partition the brain before the tractography is that I want to make different partitions later on and it will be nice if I don’t have to run the tractography again for each partition.
>
> Thanks,
>
> Karen
>
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