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