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Hi Karen
I am not sure what this is. Can you zip your probtrackx output folder and send it to me?

Saad


On 22 May 2013, at 17:36, Karen Marie Sandø Ambrosen <[log in to unmask]> wrote:

> 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
> 
> ________________________________________
> Fra: FSL - FMRIB's Software Library [[log in to unmask]] p&#229; 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
>> 
> 

--
Saad Jbabdi
University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466  (fax 717)
www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi