Sorry, I've found that!

You mean lecture slides and practical data right?

Thanks again,

Ikko

2014-05-16 23:05 GMT+09:00 木村一皓 <[log in to unmask]>:

Thanks!

I didn't know that, and I'm always just struggling with documents about FDT!

But, I'm so sorry, I can't find "online tutorial."

Could you show me the URL?

Thanks a lot!

Ikko

2014-05-16 22:21 GMT+09:00 Saad Jbabdi <[log in to unmask]>:

HI - If you are not familiar with probtrackx, I would recommend that you go through the online tutorial on our wikipage and use our tutorial data, before jumping onto using it on the HCP data.

Cheers

Saad

On 16 May 2014, at 13:39, 木村一皓 <[log in to unmask]> wrote:

Thanks Saad,

However I've got another problem.

As you advised, I used a seed mask and came nothing but eroors in opening the files of seed.(e.g. CSV::load_rois:Unknown file type: /home/fsl/Desktop/...) I've tried several files but nothing seemed to make progress.

From "WU-Minn HCP", I've got structural data and used "MNINOnLiner/fsavearge_LR32k," following HCP manual saying that this is useful for analysis of dMRI.

Could you tell me what I am wrong?

Should I change the file?

Thanks,

Ikko

 

 

2014-05-16 19:09 GMT+09:00 Saad Jbabdi <[log in to unmask]>:

Hi - simple mode means you are only tracking from one voxel.

You need to use a seed mask if you want to use matrix1 or 3

Saad

On 15 May 2014, at 23:58, 木村一皓 <[log in to unmask]> wrote:

Hi Saad,

I've done BEDPOSTX for probtrackx2, and set BEDPOSTX directory to

"Diffusion.bedpostX" in probtrackx.

But when I set Matrix options to see Matrix 1and started, there comes an error, saying

"Error: cannot use matrix1 and matrix3 in simple mode"

Could you tell me what does "simple mode" mean?

And what should I do to see matrix1?

Thanks,

Ikko

Ikko Kimura

Department of Medicine

Osaka University

2014-05-16 7:16 GMT+09:00 木村一皓 <[log in to unmask]>:

Thanks, then I'll do that.

Ikko

2014-05-16 0:38 GMT+09:00 Saad Jbabdi <[log in to unmask]>:

Hi - No, sorry. If you want to run probtrackx2 you need to run bedpostX first.

Cheers

Saad

On 15 May 2014, at 16:25, 木村一皓 <[log in to unmask]> wrote:

Dear all,

I'm thinking about making matrix(seed*seed) by probtrackx2 from the data of "WU-Minn Human Connectome Project"

When I launch fsl by typing fsl in terminal and launch probtrackx2, it says that BEDPOSTX data is needed.

I've got the following data and am wondering if I can do without BEDPOSTX.(because it takes a lot of time)

 T1w_acpc_dc_restore_1.25.nii

data.nii

grad_dev.nii

nodif_brain_mask.nii

bvals

bvecs

Does someone have any idea?

Thanks,

Ikko

--

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

--

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

--

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