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
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
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*
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