28 Mar
2014
28 Mar
'14
8:43 a.m.
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 . 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