On Mon, Feb 29, 2016 at 7:52 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

try this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize

On 02/23/2016 10:17 AM, Maheen Siddiqui wrote:
> I changed the directory and it ran, but with errors. I had to change
> the last part --surf lh.seghead --surf-smooth 10 because it does not
> recognise --surf. When I change this to --o, it runs but with errors.
>
> On Tue, Feb 23, 2016 at 2:42 PM, Douglas Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>
>
> On 2/23/16 9:39 AM, Maheen Siddiqui wrote:
>> It seems to be giving me an error and saying it cannot read the
>> seghead.mgz file.
> Is it in the same directory where you are running the command? If
> so, what is the terminal output?
>>
>> From my earlier question; do you know how to check if lh.seghead
>> is corrupted?
> If you can view it in tksurfer/freeview, then it is probably not
> corrupted. I vaguely remember that there was some problem reading
> this file in matlab, but I don't remember every coming up with a fix
>
>>
>> On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve
>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>>
>> you can try
>>
>> mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead
>> --surf-smooth 10
>>
>>
>>
>>
>> On 2/23/16 9:22 AM, Maheen Siddiqui wrote:
>>> Is it possible to use a different function? Can I use
>>> mri_vol2surf on the seghead.mgz file? Or do you think that
>>> mkheadsurf is the right one to be using?
>>>
>>> Thanks!!
>>>
>>> On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve
>>> <greve@nmr.mgh.harvard.edu
>>> <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>>>
>>> Can you load it in tksurfer or freeview?
>>>
>>>
>>> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
>>>> Hi FreeSurfer users,
>>>>
>>>> I have used the "mkheadsurf" command to create a head
>>>> surface for my subject. However when I try to use
>>>> "read_surf" to read the "lh.seghead" file that is
>>>> created, the magic number is not one that is recognised.
>>>>
>>>> Having read some previous posts/questions with similar
>>>> problem/error, I think the problem is probably within
>>>> the "lh.seghead" file. I think someone wrote that
>>>> incompatibility of the magic number means that the
>>>> surface is corrupted. Is there a way to check errors of
>>>> mkheadsurf? Or whether something is wrong? It looked
>>>> fine in freeview.
>>>>
>>>> Does anybody have any advice?
>>>>
>>>> Thanks,
>>>>
>>>> Maheen
>>>>
>>>>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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