Have you tried to change the threshold to see if you see more colors? Don't load it as a segmentation, just look at the overlay. doug
vin . wrote: > Thank you so much Doug, > > you are right, it doesn't match exactly, however there is some match. > so, now I am running recon-all T1_1mmMNI.nii, probably it will improve > the registration. > > -extend to previous email - > just to check, I also summed, all binary files. (attached > sum_binarymap.tif : output from tksurfer) > >tksurfer Sub_ID lh inflated -ov sum_binmap.nii -overlay-reg > register.dat -fthresh 0.01 -fmid 0.3 -fslope 1 > > here sum_binmap : > >mri_binarize --i N.nii --min 0.1 --binval N --o Nb.nii > >fscalc 1b.nii add 2b.nii add 3b.nii ... -o sum_binmap.nii > >mris_seg2annot --seg sum_binmap.nii --hemi lh --s vin --o > lh.seg.annot --ctab vin_colortable.txt > > I just wonder, why I only see one color in sum_binmap overlay. > > > > On Wed, Dec 14, 2011 at 6:01 AM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > The fsaverage surface does not intersect very well with the MNI > brain (the problem is that the average surface does not have as > deep folds as an individual). You can see what is going on if you > convert your label to fsaverage space with > > tkmedit fsaverage orig.mgz -surfs -fmin 0.5 -overlay 1.nii > -overlay-reg register.dat > > This will show you the surfaces and the label. If the label does > not intersect the surfaces, at all, then there's not much you can > do. If there is some intersection, then you can run mri_vol2surf > with --projfrac-max -.1 1.1 .1 > > doug > > > > On 12/13/11 10:53 PM, vin . wrote: >> #Registration >> >tkregister2 --mov $d/T1.nii.gz --targ >> $d/mri/brain.mgz \ >> --regheader --reg $d/vin_register.dat --noedit >> >> I have cortical-clusters in 1mm MNI space so, I took 1mm MNI >> brain and registered this on the "fsaverage" default subject's >> /mri/brain.mgz" >> >> Find attached register.dat >> >> #checking registration >> > >> tkregister2 --targ $d/mri/brain.mgz \ >> --mov T1.nii.gz --reg vin_register.dat >> >> find attached register.tiff >> >> Regards, >> vin >> >> >> On Wed, Dec 14, 2011 at 4:40 AM, Douglas Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> Is your register.dat correct? >> >> >> On 12/13/11 10:33 PM, vin . wrote: >>> Thanx Doug, >>> >>> atleast I see, now something. (see attached "seg.mgh -annot >>> seg.annot.tiff) >>> > tksurfer Sub_ID lh inflated -annot seg.annot -ov >>> lh.seg.mgh -fthresh 0.01 -fmid 0.3 -fslope 1 >>> >>> just to check, I also summed, all binary files. (attached >>> sum_binarymap) >>> >tksurfer Sub_ID lh inflated -ov sum_binmap.nii >>> -overlay-reg register.dat -fthresh 0.01 -fmid 0.3 -fslope 1 >>> >>> also find colortable. >>> >>> Greetings! >>> >>> On Wed, Dec 14, 2011 at 4:18 AM, Douglas Greve >>> <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> >>> Try tksurfer Sub_ID lh inflated -annot seg.annot >>> doug >>> >>> >>> On 12/13/11 9:39 PM, vin . wrote: >>>> no, in tksurfer, just inflated lh appears (no >>>> overlay). so, I viewed lh.seg.mgh in freeview and >>>> converted it to .nii and viewed in fslview. >>>> >>>> On Wed, Dec 14, 2011 at 3:37 AM, Bruce Fischl >>>> <fis...@nmr.mgh.harvard.edu >>>> <mailto:fis...@nmr.mgh.harvard.edu>> wrote: >>>> >>>> oh, so you mean you see a line on the surface? >>>> >>>> On Wed, 14 Dec 2011, vin . wrote: >>>> >>>> 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 >>>> <mailto: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 >>>> <mailto: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> >>>> <mailto:gr...@nmr.mgh.harvard. edu >>>> <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> <mailto:freesur...@nmr.mgh. >>>> harvard.edu >>>> <mailto: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> >>>> <mailto:gr...@nmr.mgh.harvard. edu >>>> <mailto:gr...@nmr.mgh.harvard.edu>> >>>> Phone Number: 617-724-2358 >>>> <tel:617-724-2358> <tel:617-724-2358 >>>> <tel:617-724-2358>> >>>> Fax: >>>> 617-726-7422 <tel:617-726-7422> >>>> <tel:617-726-7422 <tel:617-726-7422>> >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/ >>>> <http://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/ >>>> <http://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 >>>> <mailto: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> >>>> 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 >> <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. >> >> > -- 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 FileDrop: 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
