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
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
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
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 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.
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 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.
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
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 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.
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.
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 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.
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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.
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.eduhttps://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.
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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.
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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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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.
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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.
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-- 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/
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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?
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?
3) Is it also possibe to run the xhemi on the w-g.pct.mgh file?
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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.
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.
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
On 3/26/14 8:24 AM, Markus Gschwind wrote:
Dear Doug and Bruce,
I have three more questions concerning 'pctsurfcon'.
- 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.
- 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
- 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 mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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. >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto: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. >> >> >> >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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=ihub )?
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'.
- 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.
- 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
- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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.
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.
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
Freesurfer mailing listFreesurfer@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.
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'.
- 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.
- 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
- 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 >> >> >> _______________________________________________ >> 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. >> >> >> >> >> _______________________________________________ >> 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. >> >> >> >> > > > _______________________________________________ > 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
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Thank you Bruce, this works great.
This is just for the records:
$ 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
Thanks again!
2014-03-27 13:29 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
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'.
- 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.
- 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
- 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 >> >> >> _______________________________________________ >> 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. >> >> >> >> >> _______________________________________________ >> 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. >> >> >> >> > > > _______________________________________________ > 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
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glad it worked out Bruce On Fri, 28 Mar 2014, Markus Gschwind wrote:
Thank you Bruce, this works great. This is just for the records:
$ 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
Thanks again!
2014-03-27 13:29 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: 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 Figure1(http://www.sciencedirect.com/science/article/pii/S1053811910013261?via=ih u 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 >> >> >> _______________________________________________ >> 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. >> >> >> >> >> _______________________________________________ >> 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. >> >> >> >> > > > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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. 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Hi Doug, Is 'pctsurfcon' intended to supersede 'mri_cnr'? If not, what are the intended situations in which one would be used over the other?
thanks, -MH
-- Michael Harms, Ph.D.
----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu
On 3/24/14 5:21 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
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.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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