> Hi Saad. Ok, the label2surface now works, but:
>
> 1) Now I need to have my LGN in .gii (I guess), so I type:
> surf2surf -i L_LGN2freesurfer.nii.gz -o L_LGN2freesurfer.gii
your LGM is a volume mask (i.e. voxels) - you can use it as is in probtrackx, no need to transform it into a surface.
>
> and I receive the following error: terminate called after throwing an
> instance of 'NEWMAT::ProgramException' Abort trap
>
> 2) When creating the lh_V1.gii I do see the file but the command line
> prints this while running label2surf: It ends with null.... is
Don't worry about this.
Saad
> normal??
>
> numda2 3
> write vertcies 147396
> write traingles 294788
> 294788 147396
> resize trinagle array
> write faces 884364
> scalar 0 2
> set scalar names 1 MyScalars
> do memcpy
> scalar int 0
> done scalar
> null
>
> Thank you very much,
>
>
> 2012/10/12, Saad Jbabdi <[log in to unmask]>:
>> Hi
>>
>> There are two problems here.
>>
>> 1) FSL does not read .mgz files. You need to first convert the brain.mgz
>> into brain.nii.gz with the following freesurfer command:
>>
>> mri_convert brain.mgz brain.nii.gz
>>
>> 2) the label2surf command takes as input a text file with a bunch of labels
>> in it. So in your case, you need to do:
>>
>> echo lh.V1.label > label_list.txt
>> label2surf -l label_list.txt -s lh.white.asc -o lh_V1.gii
>>
>>
>> You don't need to work with the Caret conventions, just stick to freesurfer
>> so that everything else is easier for you.
>>
>> cheers
>> Saad
>>
>> On 12 Oct 2012, at 20:29, Monica G. Chica wrote:
>>
>>> Hi Saad, sorry so many questions. I am following the wiki and it says
>>> that I must have all my surfaces using the same convention and that
>>> prefer format is GIFTI. I want to use the L_LGN.nii.gz or L_LGN.mgh
>>> (both are in conformed space - left LGN) as seed and lh.V1.label and
>>> lh.V2.label as targets. I want all in caret convention and gifti
>>> format at it is said is the prefered.
>>>
>>> So, I first try to transform my label files to a surface, as the
>>> manual indicates, using label2surf. This way:
>>> label2surf -s brain.mgz -o lh_V1 -l lh.V1.label
>>> It tells me that brain.mgz is unknown format. so I try typing this
>>> command:
>>> label2surf -s brain.nii.gz -o lh_V1 -l lh.V1.label
>>> Still, unknown format.
>>> So, I try this:
>>> label2surf -s lh.white.asc -o lh_V1 -l lh.V1.label
>>> Then, it says: Could not open label file #!ascii
>>>
>>> So, I really don't know what to put as input surface. Sorry, Im new
>>> with this files formats and conventions.
>>>
>>> Then I try to switch conventions for my LGN using surf2surf:
>>>
>>> surf2surf -i L_LGN2freesurfer.mgh -o median2freesurfer.gii
>>> --convin=freesurfer --convout=caret --volin=brain.mgz
>>> and I get the following error:
>>> Image Exception : #22 :: ERROR: Could not open image
>>> /Volumes/FreeAgentGoFlexDrive/dyslexia/p2/freesurfer/mri/brain.mgz
>>> So again I try using the brain.nii.gz and neither work, I get the same
>>> error.
>>>
>>> Please, help.... thanks.
>>>
>>> 2012/10/12, Saad Jbabdi <[log in to unmask]>:
>>>> Hi Monica
>>>>
>>>> The new documentation is a wiki :
>>>> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Using_surfaces
>>>>
>>>> And note that you need to download FSL5 in order to use these new
>>>> features.
>>>>
>>>> I am not entirely sure how mri_label2vol works, but my guess is that the
>>>> reference volume is simply the brain in conformed space (e.g.
>>>> $SUBJECTS_DIR/subject/mri/brain.mgz)
>>>>
>>>> But note that you don't need to convert your labels to volumes if you
>>>> follow
>>>> the instructions on the wiki page.
>>>>
>>>> Cheers
>>>> Saad
>>>>
>>>>
>>>> On 12 Oct 2012, at 06:31, Monica G. Chica wrote:
>>>>
>>>>> Hello Saad, ok I realize that labels were only available in probtrackx
>>>>> older version. So now I try to convert my labels to a volume using
>>>>> mri_label2vol:
>>>>>
>>>>> 1. I'm using as input to --reg a file that is created like this:
>>>>> printf "p2\n1 \n1 \n1 \n1 0 0 0\n0 1 0 0 .... Etc, creating an identity
>>>>> matrix.
>>>>> Is that correct?
>>>>>
>>>>> 2. but now it asks me for a template volume. What should be that
>>>>> volume?
>>>>>
>>>>> Thank you very much.
>>>>>
>>>>> Le jeudi 11 octobre 2012, Monica G. Chica a écrit :
>>>>> Hello, in FSL web page, in the documentation "Running probtrackx from
>>>>> free
>>>>> surfer cortical surfaces" (fsl.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html)
>>>>> it
>>>>> says just one paragraph before point 3 "this will create a file called
>>>>> myroilabel.label that you can use directly in probtrackx ....etc"
>>>>>
>>>>> And in section 3 the command that is given as example on how to run
>>>>> probtrackx with surfaces says "probtrackx -x myroilabel.label ....etc"
>>>>>
>>>>> So it means there is an error in documentation and .label files can't
>>>>> be
>>>>> really used directly in probtrackx? Or is that they can only be used
>>>>> with
>>>>> probtrackx and not with probtrackx2? Because in probtrackx it says in
>>>>> section 3 the surface information is in the parameter --mesh.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Le jeudi 11 octobre 2012, Saad Jbabdi a écrit :
>>>>> Hi
>>>>>
>>>>>
>>>>>> Hello, thanks for the response. You mean with probtrackx2 I don't have
>>>>>> to
>>>>>> enter the --mesh parameter?
>>>>>
>>>>> Yes that's right.
>>>>>
>>>>>>
>>>>>> I want to use as seed a ROI in the left heliosphere and as
>>>>>> classification
>>>>>> targets one ROI of the left and one of the right. As I understand to
>>>>>> include the targets I write their paths in a file and give it as
>>>>>> --targetmasks parameter. Do I need to include that file with my
>>>>>> targets
>>>>>> also in the parameter --waypoints?? or I don't need to pass it twice?
>>>>>
>>>>> Use waypoint if you want to use an inclusion mask. the --targetmasks
>>>>> option will only do the counting, it will not exclude streamlines that
>>>>> do
>>>>> not pass through the targets.
>>>>>
>>>>>> Oh, I thought I could enter for the paremeter -x a .label file. So it
>>>>>> needs to be a .mgh file?
>>>>>
>>>>> You can't use the label file, as these do not contain surface
>>>>> information.
>>>>> You can't use .mgh either. Please have a look at the doc to see which
>>>>> file
>>>>> formats are available.
>>>>>
>>>>> Cheers
>>>>> Saad
>>>>>
>>>>>>
>>>>>> Thank you,
>>>>>>
>>>>>> Le lundi 8 octobre 2012, Saad Jbabdi a écrit :
>>>>>> Hi
>>>>>>
>>>>>> I would recommend using probtrackx2 for this, as unlike probtrackx,
>>>>>> you
>>>>>> don't need a surface description: probtrackx2 does not assume that you
>>>>>> are using just one surface, but instead each ROI mask defines its own
>>>>>> surface.
>>>>>>
>>>>>> If you need both hemispheres (e.g. one where the seed is and one where
>>>>>> the waypoint mask is) then you should use both surfaces.
>>>>>>
>>>>>> I am assuming your seed/target masks are freesurfer label files? In
>>>>>> this
>>>>>> case, you will need to transform these into surface files using
>>>>>> label2surf (seed the doc)
>>>>>>
>>>>>> Cheers
>>>>>> Saad
>>>>>>
>>>>>>
>>>>>> On 8 Oct 2012, at 05:38, Monica Giraldo wrote:
>>>>>>
>>>>>>> Dear FSL experts, I'm trying to run tracktography between a region in
>>>>>>> left hemisphere to a region in the right one using freesurfer
>>>>>>> surfaces.
>>>>>>> I don't know what file to put as a description of the whole cortical
>>>>>>> surface. In FSL page you recommend lh.white.asc if Left hemisphere
>>>>>>> and
>>>>>>> rh...etc if right hemisphere .... But if I'm tracking in both
>>>>>>> hemispheres then what file I put? I see in the folder mri (from the
>>>>>>> output of freesurfer) a wm.mgz file but is not a label file.
>>>>>>> Sorry, I'm new with freesurfer. I was thinking on passing that .mgz
>>>>>>> to
>>>>>>> nifti as you tell to do with the brain.mgz in tutorial and use that
>>>>>>> but
>>>>>>> I'm not sure.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> Saad Jbabdi
>>>>>> University of Oxford, FMRIB Centre
>>>>>>
>>>>>> JR Hospital, Headington, OX3 9DU, UK
>>>>>> (+44)1865-222466 (fax 717)
>>>>>> www.fmrib.ox.ac.uk/~saad
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Mónica Giraldo Chica
>>>>>> PhD student in Biomedicine
>>>>>> University of Barcelona (Spain) - York University (Canada)
>>>>>> Neuroimaging Laboratory
>>>>>> 1008 Sherman Health Science Research Center. Toronto, Canada
>>>>>> www.monicagiraldochica.com
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Mónica Giraldo Chica
>>>>> PhD student in Biomedicine
>>>>> University of Barcelona (Spain) - York University (Canada)
>>>>> Neuroimaging Laboratory
>>>>> 1008 Sherman Health Science Research Center. Toronto, Canada
>>>>> www.monicagiraldochica.com
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Mónica Giraldo Chica
>>>>> PhD student in Biomedicine
>>>>> University of Barcelona (Spain) - York University (Canada)
>>>>> Neuroimaging Laboratory
>>>>> 1008 Sherman Health Science Research Center. Toronto, Canada
>>>>> www.monicagiraldochica.com
>>>>>
>>>>
>>>> --
>>>> Saad Jbabdi
>>>> University of Oxford, FMRIB Centre
>>>>
>>>> JR Hospital, Headington, OX3 9DU, UK
>>>> (+44)1865-222466 (fax 717)
>>>> www.fmrib.ox.ac.uk/~saad
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> *Mónica Giraldo Chica
>>> PhD student in Biomedicine
>>> University of Barcelona (Spain) - York University (Canada)
>>> Neuroimaging Laboratory
>>> 1008 Sherman Health Science Research Center. Toronto, Canada*
>>> *www.monicagiraldochica.com*
>>>
>>
>> --
>> Saad Jbabdi
>> University of Oxford, FMRIB Centre
>>
>> JR Hospital, Headington, OX3 9DU, UK
>> (+44)1865-222466 (fax 717)
>> www.fmrib.ox.ac.uk/~saad
>>
>
>
> --
> *Mónica Giraldo Chica
> PhD student in Biomedicine
> University of Barcelona (Spain) - York University (Canada)
> Neuroimaging Laboratory
> 1008 Sherman Health Science Research Center. Toronto, Canada*
> *www.monicagiraldochica.com*
>
--
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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