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
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