Hi Jeff,
I'm still not sure what format you want.
Do you want a NIFTI image that contains voxels with different label values (e.g. 1 is region A, 2 for region B, etc.)?
If so then just change the "value" that the pen in FSLView writes with and you can do exactly this.
Make sure that you change the display range (to have the maximum set to the maximum label value) and colourmap too, so that you can see the different colours as you draw them on.
If this isn't what you want then please let us know.
You are right that FSL does not calculate cortical thickness and that you should use FreeSurfer for that.
All the best,
Mark
On 23 Aug 2012, at 14:58, Jeff Thompson <[log in to unmask]> wrote:
> Hey,
> Okay thanks, has the process of combining these masks to create one
> file been described anywhere. I'm assuming that fslmaths would be
> used.
> I want to use freesurfer, because I need cortical thickness
> measurements. I was told that FSL wouldn't be able to do these, is
> that correct?
>
> -Jeff
>
> On Thu, Aug 23, 2012 at 7:32 AM, Mark Jenkinson <[log in to unmask]> wrote:
>> Dear Jeff,
>>
>> I'm not quite sure what you are asking here.
>> In FSLView you can create manual masks or labels.
>> Just use the "Create Mask" option in the File menu and then select the drawing tool and set voxels to whatever value you specify.
>> It saves this as a NIFTI image where each voxel contains the label value as set by you in FSLView.
>> I'm not really sure how easy this is to import into FreeSurfer or what you want to use it for.
>>
>> I hope this answers your question - if not, please explain what you want in more detail.
>>
>> All the best,
>> Mark
>>
>>
>>
>> On 22 Aug 2012, at 16:54, Jeff Thompson <[log in to unmask]> wrote:
>>
>>> Hello,
>>>
>>> I need to manually parcellate a canine brain to be able to create a
>>> gca file for the freesurfer recon-all pipeline. In FSLview am I able
>>> to create '.label' files from manual drawing the ROI's? Could someone
>>> please explain a method of manual parcellation in FSL?
>>>
>>> Thank you,
>>>
>>> --
>>> Jeff Thompson
>>>
>
>
>
> --
> Jeff Thompson
> (905) 746-9794
> Electrical and Biomedical Engineering IV
> McMaster University
>
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