$ mris_expand -thickness surf/lh.white 0.35 surf/lh.white_outer0.35GM
using distance as a % of thickness
expanding surface surf/lh.white by 35.0% of thickness and writing it to surf/lh.white_outer0.35GM
$ mris_expand surf/lh.white -1 surf/lh.white_inner1mmWM
expanding surface surf/lh.white by -1.0 mm and writing it to surf/lh.white_inner1mmWM
Hi Markus
use mris_expand.
cheers
Bruce
On Thu, 27 Mar 2014, Markus Gschwind wrote:
Thank you, Doug!
One last question:
- Using which command would one construct the "?h.white -1mm surface" and
the "?h.white+30%GM surface" for visualisation purposes as in Salat Figure
1(http://www.sciencedirect.com/science/article/pii/S1053811910013261?via=ihu
b)?
Thank you!
Markus
2014-03-26 15:36 GMT+01:00 Douglas Greve <greve@nmr.mgh.harvard.edu>:
On 3/26/14 8:24 AM, Markus Gschwind wrote:
Dear Doug and Bruce,
I have three more questions concerning 'pctsurfcon'.
1) The inner sampling distance is set to 1mm by default, but the
outer sampling is done at a 30% of the cortical thickness. I saw
that I could easily change the parameters or modify the script,
but I wonder why this has been chosen like this. What was the
rationale?
A fixed distance of 1mm was used to help prevent the WM sample from
projecting so far back that it samples GM "behind" it. I can't
remember how I choose 30% (instead of 50%). I think David Salat used
slightly different parameters in his paper.
2) I think it is possible to run glmfit on the ?h.w-g.pct.mgh
file in order to get some group stats, right?
Yes
3) Is it also possibe to run the xhemi on the w-g.pct.mgh file?
Yes
doug
Thank you so much!
Markus
2014-03-24 23:51 GMT+01:00 Markus Gschwind
<markus.gschwind@gmail.com>:
Whow that is great!! Thank you so much Doug, I was
not aware of this! That's what I needed it seems.
Thanks Bruce and Doug!
Markus
2014-03-24 23:21 GMT+01:00 Douglas N Greve
<greve@nmr.mgh.harvard.edu>:
you might want to look at the pctsurfcon
script to see if that gets you
where you want to be
On 03/24/2014 06:18 PM, Bruce Fischl wrote:
> it really depends on the size of the
abnormality. I would guess 2 is
> too big, and you want something more like 1,
and sampling not averaging
> On Mon, 24 Mar 2014, Markus Gschwind wrote:
>
>> Hi Bruce!
>> Ok I see, great! Tank you!
>>
>> So to double check, this will be something
like :
>>
>> mri_vol2surf \
>>
>>
>> --mov /mri/nu.mgz \
>> --ref /mri/nu.mgz \
>>
>> --surf /surf/lh.white
>> --projdist mmdist -2 \ # for inside white
>>
>>
>> # --projdist mmdist 2 \ # for outside
white
>> --interp trilinear \
>> --hemi lh \
>> --out lh.nu_inside_white.mgh
>>
>>
>> I am not sure which one to use from those,
as I want to compare stable
>> values but distant from white.
>>
>>
>> --projfrac-avg min max del : average
along normal
>> --projdist mmdist : distance projection
along normal
>> --projdist-avg min max del : average
along normal
>>
>> What would you recommend?
>> Thank you again!
>> Markus
>>
>>
>>
>>
>>
>>
>>
>> 2014-03-24 21:29 GMT+01:00 Bruce Fischl
<fischl@nmr.mgh.harvard.edu>:
>> Hi Markus
>>
>> I wouldn't use brainmask as it has
been normalized too
>> aggressivley. Maybe the nu.mgz. Look
at the difference between
>> values just outside of it and just
inside of it
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 24 Mar 2014, Markus Gschwind
wrote:
>>
>> Dear Bruce,
>> Thanks for the rapid answer!
>>
>> Do you mean that I take the
voxel values of
>> brainmask.mgz at the place
where
>> the ?h.white surface passes,
right?
>>
>> I thought that the ?l.white
surface marks the limit
>> between GM and WM as a
>> result of a binary decision.
>> I would be interested in the
local certainty of this
>> decision. I thought
>> this is represented by the
slope between the values
>> around 70 and those
>> >100.
>>
>> Thanks again,
>> Markus
>>
>>
>>
>>
>>
>>
>> 2014-03-24 19:26 GMT+01:00
Bruce Fischl
>> <fischl@nmr.mgh.harvard.edu>:
>> Hi Markus
>>
>> I would think that
looking at the gray/white
>> contrast across the
>> ?h.white surface would be
more informative
>>
>> cheers
>> Bruce
>> On Mon, 24 Mar 2014,
Markus Gschwind wrote:
>>
>> Dear all,
>> I would like to
capture regions where
>> the gray
>> matter/ white
matter junction is blurred
>> in order to
>> detect possible
focal
>> cortical
dysplasias.
>>
>> As I understood the
WM/GM segmentation
>> is done by
>> the script
mri_segment.
>>
>> Would it be
possible detect those
>> regions where the
>> gradient between GM
and WM regions is
>> low?
>>
>> I imagined that
running mri_segment
>> several times,
>> with each time a
different lower GM
>> threshold and
>> higher WM
threshold, and
>> then calculating
the diference between
>> the results,
>> might give such
information.
>>
>> I am very much
interested in what you
>> think about
>> this approach and
how to do it
>> practically.
>>
>> For info here are
the optional flags of
>> mri_segment:
>>
>> -slope <s>
>>
>> set the curvature
slope (both n and p)
>>
>> -pslope <p>
>>
>> set the curvature
pslope (default=1.0)
>>
>> -nslope <n>
>>
>> set the curvature
nslope (default=1.0)
>>
>> -debug_voxel <x y
z>
>>
>> set voxel for
debugging
>>
>> -auto
>>
>> automatically
detect class statistics
>> (default)
>>
>> -noauto
>>
>> don't automatically
detect class
>> statistics
>>
>> -log
>>
>> log to
./segment.dat
>>
>> -keep
>>
>> keep wm edits.
maintains all values of 0
>> and 255
>>
>> -ghi, -gray_hi <h>
>>
>> set the gray matter
high limit
>> (default=100.000)
>>
>> -wlo, -wm_low <l>
>>
>> set the white
matter low limit
>> (default=90.000)
>>
>> -whi, -wm_hi <h>
>>
>> set the white
matter high limit
>> (default=125.000)
>>
>> -nseg <n>
>>
>> thicken the n
largest thin strands
>> (default=20)
>>
>> -thicken
>>
>> toggle thickening
step (default=ON)
>>
>> -fillbg
>>
>> toggle filling of
the basal ganglia
>> (default=OFF)
>>
>> -fillv
>>
>> toggle filling of
the ventricles
>> (default=OFF)
>>
>> -b <s>
>>
>> set blur sigma
(default=0.25)
>>
>> -n <i>
>>
>> set # iterations of
border
>> classification
>> (default=1)
>>
>> -t <t>
>>
>> set limit to thin
strands in mm
>> (default=4)
>>
>> -v
>>
>> verbose
>>
>> -p <p>
>>
>> set % threshold
(default=0.80)
>>
>> -x <filename>
>>
>> extract options
from filename
>>
>> -w <w>
>>
>> set wsize
(default=11)
>>
>> -u
>>
>> usage
>>
>>
>>
>> Thank you very much
for all comments!
>>
>> Markus
>>
>>
>>
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MGH-NMR Center
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