Hi, Saad,
I couldn't get the right ROI label from Freesurfer.
I did it as following:
1) tkmedit 001 brain.mgz
2) File ---> load segmentation ---> select aparc+aseg.mgz and for color table, choose FreesurferColorLUT.txt
3) click on the label needed (lh_...)
4) Tools ---> segmentation ---> select main segmentation lable at cursor
5) File ---> label---> save lable as...
and mris_convert $SUBJECT_DIR/001/surf/lh_white lh_white_asc
when I ran the probtrackx with this label
the error messaged appeared:
load mesh files
Segmentation fault
I tried several different labels, but still didn't work.
what should I get the right label? Thank you very much for your help
Best
Shugao
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)
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)