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yes that looks ok. 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 > > > > > > > > > > > -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.fmrib.ox.ac.uk/~saad