Hi - Are you sure you intended to use --omatrix3? This option requires you to set a --target3 file.
Cheers
Saad
On 25 Oct 2012, at 05:34, Alistair Perry wrote:
> Sorry, still having issues.
>
> To rehash what I am wanting to achieve, I am trying to perform
> whole-brain tractography analysis.
>
> I have preprocessed DTI and T1 scan using combination of
> freesurfer/fsl, so I have sucessfully created bedpostx and all
> recon-all files.
>
> I have obtained 68 cortical label labels from performing
> mri_annotation2label, and then label2surf. Obviously these are all in
> conformed space.
> I have used the instructions as per your wiki page in obtaining
> freesurfer<>structural<>dti(S0 image) transformation files
>
> I have all the working parts and here is the command: N.B all of the
> working files have been placed in the same directory
>
> probtrackx2 -s ./merged -m ./nodif_brain_mask.nii -x ./rois.ascii --seedref=./or
> ig.nii --xfm=./fs2dti.mat --targetmasks=./rois.ascii --dir=../probtrackresults/
> --forcedir --s2tastext --omatrix1 --omatrix3
>
> This is the following error message I receive after initally going
> through loading all of the seeds:
>
> Load bedpostx samples
> 1_1
> 1_2
> 1_3
> 2_1
> 2_2
> 2_3
>
> nfibres : 2
> nsamples : 50
>
> Done loading samples.
> does not exist
>
> It is interesting that another time (where the command would of been
> identical, although I can't exactly remember) probtrackx2 went past
> this stage and halted at a specific label file and exited with the
> error message again "does not exist"
>
> Is there anything wrong you can see with my working parts, more
> specifically, my label files? I have eliminated errors occuring due to
> different version of fsl used in pre-processing, or the program not
> finding the files in the directory folder.
>
>
>
>
> On Thu, Sep 20, 2012 at 7:28 PM, Saad Jbabdi <[log in to unmask]> wrote:
>> Looks like you're running out of RAM.
>>
>> 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
>
--
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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