Sorry I have one last quesiton, is it possible to uncompress an image with FSL through the command line? Because I changed a little bit the script for generating the matrix and I need to introduce the images in .nii, because I got a problem when I tried to use .nii.gz

Thanks,

On Mon, Mar 28, 2011 at 4:29 PM, Jose Angel Pineda Pardo <[log in to unmask]> wrote:

Hi Monica,

it seems you are just using two seed regions. So in that case it will be correct.

Cheers

Jose

On Mon, Mar 28, 2011 at 4:10 PM, Monica Giraldo <[log in to unmask]> wrote:

Hi Saad, thanks for your help. Well, my seeds are already in the DTI space. I did all the pre processing of the images with SPM before running anything in FSL and all the images used are in the same space as the DTI. That's why im not using the --xfm option in probtrackx.

I tried anyway running your script and I did got a result but I don't know it it's correct. I got the following matrix:

ConMat = 

62470809    321160

461766        46066148

but why the waytotal file shows the number 1.5015e+07? If it is not the sum of the numbers of the matrix?

It may be something else wrong?

Thankx,

On Mon, Mar 28, 2011 at 2:15 PM, Saad Jbabdi <[log in to unmask]> wrote:

sorry, I forgot another thing. and MATLAB doesn't recognize the command read_avw, is there any chance that you wrote it wrong? Do I have to install somehting in matlab to run that command?

that is why I've added the line "addpath([getenv('FSLDIR') '/etc/matlab']);" in the script that I suggested to you. This tells matlab to look for the appropriate directory where read_avw is coded.

Saad.

On Mon, Mar 28, 2011 at 12:46 PM, Monica Giraldo <[log in to unmask]> wrote:

Hello Saad, I just tryed doing what you told Jose. I executed first the following command for adding all the seed masks: 

fslmaths -dt double "mask1_path" -add "mask2_path" "resultImage_path"

I put the type of the images as double because when I open them in MATLAB it says that they are double type.

Then, I executed the probtrackx command with the following options:

probtrackx --mode=seedmask -x "resultImage_path" -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir --opd -s "bedpostDirectory+/merged" -m "nodif_brain_mask_path"  --dir="output directory" --omatrix1

Well, it did created the files it should have created: the coords_for_fdt_matrix1, fdt_matrix1, fdt_paths and waytotal. But there is something strange, although it does find tracks because in the waytotal file it appears the number 1.5015e+07 when I open the fdt_paths there is nothing! The other images dimensions are correct. And when I open the images I can visualize something.

Other quesiton I have is, in your code when you write seeds = {'seed1','seed2',...}; 'seed1' and 'seed2' are the paths of the seed images or what?

Thanks,

--
Monica Giraldo
Master student in Biomedical Engineering
Universidad de Barcelona - Universidad Politécnica de Cataluña

--
Monica Giraldo
Master student in Biomedical Engineering
Universidad de Barcelona - Universidad Politécnica de Cataluña

--

Saad Jbabdi

University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK

(+44)1865-222466  (fax 717)

www.fmrib.ox.ac.uk/~saad

--
Monica Giraldo
Master student in Biomedical Engineering
Universidad de Barcelona - Universidad Politécnica de Cataluña

--
Monica Giraldo
Master student in Biomedical Engineering
Universidad de Barcelona - Universidad Politécnica de Cataluña