On 11 Nov 2010, at 20:52, Shugao Xia wrote:

Hi, Saad, thank you very much for your prompt respond

If I only want to track the fibre between this two ROIs, Is the right way as

probtrackx -x lh_orbital.label --mesh=lh.white.asc --xfm=fs2fa_warp --invxfm=fa2fs_warp

--seedref=brain.ni.gz -s ../merged -m=../nodif_brain_mask --dir=fibretrack -l -c 0.2 -S 2000

--steplength=0.5 -P 5000 --forcedir --opd  --waypoints=lh_suptem.nii.gz --stop=non_wm_mask.nii.gz

Best

Shugao

On Thu, Nov 11, 2010 at 3:34 PM, Saad Jbabdi <[log in to unmask]> wrote:

Hi Shugao,

On 11 Nov 2010, at 20:29, Shugao Xia wrote:

Hi, Saad

I update the fsl version to fsl 4.1.6. But I ran probtrackx as:

probtrackx -x lh_orbital.label --mesh=lh.white.asc --xfm=fs2fa_warp --invxfm=fa2fs_warp

--seedref=brain.ni.gz -s ../merged -m=../nodif_brain_mask --dir=fibretrack -l -c 0.2 -S 2000

--steplength=0.5 -P 5000 --forcedir --opd  --waypoints=lh_suptem.nii.gz

the error messages still appeared:

load mesh files

Read othererror opening file

this error means probtrackx couldn't read you label file (the -x option).

either the path is wrong, or the file is not in the right format.

What am I doing wrong about the above command?

I try to track the fibre form the orbitalfrontal to the superior temporary. ROIs lh_orbital and lh_suptem is generated from freesurfer.

1) I am not sure which mask option as target mask, --waypoints or --stop?   are they same or what is different?

yes they are very different. the doc explains how they are different. you can use either one or both or none depending on your experiment.

2) can we use this two lables as seed mask in multiple masks?

sorry, this is not (yet) available. you can only use a label file in "single mask" mode.

cheers,

saad.

Thank you very much

Shugao

On Wed, Nov 10, 2010 at 10:29 AM, Saad Jbabdi <[log in to unmask]> wrote:

Hi

You cannot use FNIRT warpfields in probtrackx (even from the GUI) if you are using an older version.

Please install a newer version and try again.

Or use a FLIRT transform matrix for seed->diffusion.

Saad.

On 10 Nov 2010, at 15:23, Shugao Xia wrote:

Thank you very much.

I tried to run probtrackx on GUI, but there was a error message:

../bin/probtrack --mode=seedmask -x ../lh_orbital.nii.gz -l -c 0.2 -S 2000

-steplength=0.5 -P 5000 --xfm=../fs2fa_warp.nii.gz --stop=../non_wm_mask.nii.gz

--forcedir --opd -s ../bedpostX/merged -m ../nodif_brain_mask --dir=probtrack

--targetmasks=../lh_suptem.nii.gz --os2t

Log directory is : ../probtrack

1_1

1_2

1_3

2_1

2_2

2_3

7

Error: terminate called after throwing an instance of 'NEWMAT:IndexException'

Do you have any idea what I was doing wrong? Thank you again.

BTW: lh_orbital.nii.gz lh_suptem.nii.gz non_wm_mask.nii.gz are generated from Freesurfer

Shugao

On Wed, Nov 10, 2010 at 9:24 AM, Saad Jbabdi <[log in to unmask]> wrote:

You need a more recent version (>=4.1.5).

Note: the doc on the web is only valid for the current release.

The doc installed with your FSL version (e.g. $FSLDIR/src/fdt/doc/index.html ) is valid for your version.

Cheers,

Saad.

On 10 Nov 2010, at 14:20, Shugao Xia wrote:

I checked and I ran the probtrackx in the directory in which the file  lh_orbital.label lies. And if I input option

-invxfm, there was a message:

--invxfm: option doesn't exist

is fsl v4.10 version too old?

On Tue, Nov 9, 2010 at 3:38 PM, Saad Jbabdi <[log in to unmask]> wrote:

Looks like it couldn't locate your input in -x.

Make sure you provide the full path to the file lh_orbital.label (unless it is in the directory you run probtrackx from)

saad

On 9 Nov 2010, at 20:08, Shugao Xia wrote:

Thank you very much.

When I ran probtrackx,

probtrackx -x lh_oribital.label --mesh=lh.white.asc --xfm=fs2fa_warp --seedref=brain.nii.gz

-s ../bedpostX/merged -m ../bedpostX/nodif_brain_mask --dir=probtrackx

-l --pd -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir --opd

some errors happened:

Log directory is : probtrackx

Loading mesh files

Read othererror openning file

but I ran as

probtrackx -x lh_oribital.nii.gz --xfm=fs2fa_warp --seedref=brain.nii.gz

-s ../bedpostX/merged -m ../bedpostX/nodif_brain_mask --dir=probtrackx

-l --pd -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir --opd



The errors were following :

Log directory is : probtrackx

exit without doing anything

Could you please tell me where I was doing wrong? There is no option -invxfm,

I use fsl v4.10 version, is it old such that there is no option -invxfm in probtrackx?

Thank you

Best

Shugao

On Tue, Nov 9, 2010 at 12:31 PM, Saad Jbabdi <[log in to unmask]> wrote:

Hi
No you need your seedref to be in the "freesurfer space".
Follow the instructions on the website! www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html

Saad.

On 9 Nov 2010, at 17:22, Shugao Xia wrote:

> Dear FSL Experts,
> I am working on running probtrackx from freesurfer. The label file and GM/WM boundary surfuce are generated from freesurfer.
> when running probtracks:
>
> probtrackx -x mylabel.label --mesh=lh.white.asc --seedref=brain.nii.gz --xfm=fs2fa_warp.nii.gz --invxfm=fa2fs_warp ...
>
> I know there are different directions in Freesurfer and FSL. I am not sure whether I need convert barin.nii.gz same as DTI image using fslswapdim? If I need, do I need to change mylabel.label or lh.white.asc too?
>
> Thank you in advance
>
> All the best
>
> Shugao

--
Saad Jbabdi
University of Oxford, FMRIB Centre

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

--

Saad Jbabdi

University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK

(+44)1865-222466  (fax 717)

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

--

Saad Jbabdi

University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK

(+44)1865-222466  (fax 717)

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

--

Saad Jbabdi

University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK

(+44)1865-222466  (fax 717)

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

--

Saad Jbabdi

University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK

(+44)1865-222466  (fax 717)

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