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
>>
>>
>> _______________________________________________
>> 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
>> 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.
>>
>>
>>
>>
>> _______________________________________________
>> 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
>> 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.
>>
>>
>>
>>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer