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On 20 Sep 2012, at 07:56, Alistair Perry wrote:

> Thanks, still having issues...
> 
> I have sucessfully initiated probtrackx2, with the same command as above.
> 
> However, after a minute or so after calling at the command line, it
> abruptly terminates. Here is a log:
> 
> "Running in seedmask mode
> load seeds
> read gifti
> read scalar data that is float32
> nz=116523
> nnz=1601
> read gifti
> read scalar data that is float32
> nz=117080
> nnz=1044
> read gifti
> read scalar data that is float32
> nz=115083
> nnz=3041
> read gifti
> read scalar data that is float32
> nz=115740
> nnz=2384
> read gifti
> read scalar data that is float32
> nz=117844
> nnz=280
> read gifti
> read scalar data that is float32
> nz=117842
> nnz=282
> read gifti
> read scalar data that is float32
> nz=114311
> nnz=3813
> read gifti
> read scalar data that is float32
> nz=112058
> nnz=6066
> read gifti
> read scalar data that is float32
> nz=113721
> nnz=4403
> Killed""
> 
> Do you think this is an issue with the data quality of the surface
> labels. If so, is there anyway in which I can check?
> 
> In addition, I thought that I could get around this issue by
> converting the initial label files (before running label2surf) by
> converting them individually to asc files. However, I am unable to do
> so.
> 
> I ran the command: # mris_convert --label lh.bankssts.label
> lh.bankssts lh.white lh.bankssts.asc
> ERROR: unknown file annot file type specified for output: lh.bankssts.asc
> 
> It is not specified in the documentation how to do so.
> 
> Thanks,
> 
> Alistair
> 
> 
> On Sat, Sep 15, 2012 at 8:32 PM, Saad Jbabdi <[log in to unmask]> wrote:
>> 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
> 

--
Saad Jbabdi
University of Oxford, FMRIB Centre

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