Hi
You need an "=" sign whenever an option has two "-" instead of one.
For example: " -m mask" but " --xfm=transform.mat"
Saad
On 14 Sep 2012, at 23:35, Alistair Perry wrote:
> Thanks, however I am having issues actually running the tractography.
>
> This is my command line:
>
> -s ./bedpostx/2393_20090210.bedpostX/ -m
> ./bedpostx/2393_20090210/nodif_brain_mask.nii.gz -x
> ./subjects/2393_20090210/convertedsurfaces/rois.ascii --xfm
> ./subjects/fs2dti.mat --meshspace freesurfer --targetmasks
> ./subjects/2393_20090210/convertedsurfaces/rois.ascii --dir
> ./subjects/2393_20090210/probtrackresults/ --forcedir --os2t
> --s2tastext
>
> I get the following error:
>
> --xfm: Missing non-optional argument!
>
> I tried to rearrange the command line:
>
> probtrackx2 -s ./bedpostx/2393_20090210.bedpostX/ -m
> ./bedpostx/2393_20090210/nodif_brain_mask.nii.gz -x
> ./subjects/2393_20090210/convertedsurfaces/rois.ascii --seedref
> ./subjects/2393_20090210/mri/T1.nii --xfm ./subjects/fs2dti.mat
> --meshspace freesurfer --targetmasks
> ./subjects/2393_20090210/convertedsurfaces/rois.ascii --dir
> ./subjects/2393_20090210/probtrackresults/ --forcedir --os2t
> --s2tastext
>
> and get another error:
>
> --seedref: Missing non-optional argument!
>
>
> Do you have any idea what is going on here? I have looked through the
> forums and it is pretty much carbon copy to what other people have
> been doing. It doesnt matter whether I rearrange the command line it
> will still get stuck on either --xfm or --seedref. Is there another
> option I must include if i choose to use either --xfm or --seedref?
>
> When I
> On Thu, Sep 13, 2012 at 9:15 PM, Saad Jbabdi <[log in to unmask]> wrote:
>> Hi
>> You need to transform your label files to surface files as explained here: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Label_files
>>
>> Cheers
>> Saad
>>
>>
>> On 13 Sep 2012, at 00:26, Alistair Perry wrote:
>>
>>> I have all the working parts:
>>>
>>> - DTI image registered to freesurfer image using bbregister and flirt.
>>> From here I have created a transformation and inverse matrix
>>> - I have used mri_annotation2label to generate a label for each
>>> cortical ROI of the aparc parcellation (so I have 68)..
>>>
>>> Now, the part I do not understand is the ascii text file list of the
>>> volumes and/or surfaces. Is this merely just a list of the labels?
>>>
>>> For example:
>>>
>>> lh.bankssts.label
>>> lh.caudalanteriorcingulate.label
>>>
>>> Thanks,
>>>
>>> Alistair
>>>
>>> On Fri, Sep 7, 2012 at 11:59 PM, Saad Jbabdi <[log in to unmask]> wrote:
>>>> Hi Alistair
>>>>
>>>> This should now be explained better in the new FSL5 doc (released yesterday). Please have a look at the freesurfer section and let me know if you have issues.
>>>>
>>>> saad
>>>>
>>>> On 5 Sep 2012, at 04:23, Alistair Perry wrote:
>>>>
>>>>> Hello FSL experts,
>>>>>
>>>>> I know this has been posted elsewhere with the original probtrackx.
>>>>>
>>>>> I am basically trying to create a surface file from the aseg+aparc.mgz cortical parcellation created when running recon-all. I wish to use this surface file as the seed reference file when performing probtrackx2.
>>>>>
>>>>> I have succeeded sucessfully in transforming the cortical parcellation into diffusion space, and have created a label file for it.
>>>>>
>>>>> However, I am having difficulty understanding converting the label file into ascii format, as required for probtrackx2. I am aware that you can convert a label file into ascii format using mri_convert, but you have to specify the lh.white surface file created when performing recon-all. This does not make sense to me for one this label file is not in diffusion space. Plus, why would I only specify one surface hemisphere when I have a label file that lists vertices across both hemispheres?
>>>>>
>>>>> In the end I am asking whether it is possible/and the best method in creating an ascii surface file of the whole cortical parcellation in diffusion space?
>>>>>
>>>>> Regards,
>>>>>
>>>>> Alistair
>>>>>
>>>>
>>>> --
>>>> 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
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