Thanx Bruce for quick reply. you are right, it's surface based file after mri_vol2surf. yeah, tried with following command.
>tksurfer Sub_ID lh inflated -annot lh.seg.annot -ov lh.seg.mgh -fthresh 0.01 -fmid 0.3 -fslope 1 On Wed, Dec 14, 2011 at 3:33 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Vin > > it looks like your lh.seg.mgh is a surface-based .mgz not a volume one. > Did you try loading it into tksurfer? > > cheers > Bruce > > > On Wed, 14 Dec 2011, vin . wrote: > > Thank you Doug, >> >> >tkregister2 --mov $d/T1.nii.gz --targ $d/mri/brain.mgz \ >> --regheader --reg $d/register.dat --noedit >> >> after creating register.dat, I followed the explained procedure, >> Which resulted in "lh.seg.mgh". can't view this file. ( appears a line ) >> >> >mri_info lh.seg.mgh >> Volume information for lh.seg.mgh >> type: MGH >> dimensions: 163842 x 1 x 1 x 17 >> voxel sizes: 1.0000, 1.0000, 1.0000 >> type: FLOAT (3) >> fov: 163842.000 >> >> >mri_info 3b.nii >> Volume information for 3b.nii >> type: nii >> dimensions: 182 x 218 x 182 >> voxel sizes: 1.0000, 1.0000, 1.0000 >> >> #binary maps looks okay >> >> may be I am doing mistake in registration or mri_vol2surf ? >> >mri_vol2surf --reg register.dat --mov Nb.nii --interp nearest --hemi lh >> --o >> lh.Nb.mgh >> >> Greetings! >> >> On Tue, Dec 13, 2011 at 5:56 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu> >> wrote: >> It's a little involved but possible. >> 1. Binarize Nth cluster to have a binary value of N >> mri_binarize --i N.nii --min 0.5 --binval N --o Nb.nii >> 2. Sample Nth cluster to the surface >> mri_vol2surf --reg register.dat --mov Nb.nii --interp >> nearest --hemi lh lh.Nb.mgh >> After doing that will all clusters, combine them together with >> mri_concat lh.1b.mgh lh.2b.mgh ... --vote --o lh.seg.mgh >> Now create a surface annotation >> mris_seg2annot --seg lh.seg.mgh --hemi lh --s subject --o >> lh.seg.annot --ctab yourctab >> yourctab is a color table like >> $FREESURFER_HOME/**FreeSurferColorLUT.txt. You list your regions >> and give them the colors you want. >> >> doug >> >> vin . wrote: >> Hi Doug, >> sorry for confusing names. >> >> - 1.nii is name of the cluster, which I want to >> overlay. it's a coritical region, resulted from >> fsl-probtrackx. >> I want to have few color codes in RGB >> R G B >> 1. 255 0 255 >> 2. 116 0 116 >> 3. 0 0 255 >> ... >> >> in this way, I would like to overlay 20 cortical >> regions in different colours on inflated brain. >> >> -fthresh 0.3 here >> (1/(10^0.3) == 50.12 % >> in freesurfer email archieve, I found this. hope >> it's correct. >> >> Thank you >> >> >> >> >> On Mon, Dec 12, 2011 at 11:11 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> >> >> wrote: >> >> Hi Vin, why do you say it's a 50% threshold? What is the >> 1.nii >> data? What colors do you want? >> doug >> >> vin . wrote: >> >> Dear FreeSurfer list, >> Greetings! >> >> a newbie to freesurfer. >> -- would like to overlay tracking group results (Sum from >> all >> subjects)-(from FSL ) in the inflated lh & rh. -- >> >> - it works with one region (hope it's correct), with >> following command, where, -fthresh ?? means it shows 50 % >> threshold based on intensity / only voxels which are >> overlaid >> by atleast half of the subjects ?? >> >> >tksurfer #Sub_ID lh inflated -annot aparc.annot -ov >> 1.nii >> -ovreg register.dat -fthresh 0.3 -fmid 0.3 -fslope 1 >> >> - How I can overlay multiple regions, in specific >> colours, >> with 50% thr. ? , >> Thank you :) >> Vin >> -----------------------------**- >> ------------------------------ >> ------------ >> >> _____________________________**_ _________________ >> Freesurfer mailing list >> freesur...@nmr.mgh.harvard.**edu <Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ >> freesurfer >> >> >> <https://mail.nmr.mgh.**harvard.edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: www.nmr.mgh.harvard.edu/ >> facility/filedrop/index.html >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> >> >> 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 >> >> <http://www.partners.org/**complianceline<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. >> >> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> >>
_______________________________________________ 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.
