Sorry - if anyone's looking at this in the future, you also need
--regheader <subID> in the command:
mri_vol2surf --mov <input_volume> \
--o $<output_name> \
--projdist -2 \
--interp nearest \
--surf pial \
--hemi lh \
--regheader <subid>
Kx
On 4 December 2014 at 20:41, Kirstie Whitaker <kw...@cam.ac.uk> wrote:
> Thank you, Doug.
>
> Can I just check that projdist is the same as projabs but with a different
> name?
>
> Just in case I'm using an old/wrong version, here's the last line from the
> mri_vol2surf help output:
> $Id: mri_vol2surf.c,v 1.63 2011/03/05 01:11:14 jonp Exp $
>
> From that help and your email I'm looking to run:
>
> mri_vol2surf --mov <input_volume> \
> --o $<output_name> \
> --projdist -2 \
> --interp nearest \
> --surf pial \
> --hemi lh
>
> Which will give me values that are 2mm toward white matter from the pial
> surface.
>
> Thanks again for all the help!
> Kx
>
>
> On 3 December 2014 at 04:48, Douglas Greve <gr...@nmr.mgh.harvard.edu>
> wrote:
>
>>
>> You can spec the surface to be pial (instead of the default white). Then
>> spec --projabs to specify the distance into cortex (using negative numbers).
>> doug
>>
>>
>> On 11/27/14 1:24 PM, Kirstie Whitaker wrote:
>>
>> Hi,
>>
>> I was wondering if it's possible to sample x mm from the pial surface
>> using mri_vol2surf (or another tool!). The point is that I'd like to be
>> agnostic about exactly where the grey/white matter boundary lies.
>>
>> I've had a look through the help for mri_vol2surf and nothing's jumping
>> out at me, is there an obvious option I'm missing?!
>>
>> Thank you!
>> Kx
>>
>>
>> --
>> Kirstie Whitaker, PhD
>> Research Associate
>>
>> Department of Psychiatry
>> University of Cambridge
>>
>> *Mailing Address*
>> Brain Mapping Unit
>> Department of Psychiatry
>> Sir William Hardy Building
>> Downing Street
>> Cambridge CB2 3EB
>>
>> *Phone: *+44 7583 535 307
>> *Website:* www.kirstiewhitaker.com
>>
>>
>> _______________________________________________
>> Freesurfer mailing
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
> --
> Kirstie Whitaker, PhD
> Research Associate
>
> Department of Psychiatry
> University of Cambridge
>
> *Mailing Address*
> Brain Mapping Unit
> Department of Psychiatry
> Sir William Hardy Building
> Downing Street
> Cambridge CB2 3EB
>
> *Phone: *+44 7583 535 307
> *Website:* www.kirstiewhitaker.com
>
--
Kirstie Whitaker, PhD
Research Associate
Department of Psychiatry
University of Cambridge
*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB
*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
