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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 <fischl@nmr.mgh.harvard.edu <mailto:fischl@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 <fischl@nmr.mgh.harvard.edu <mailto:fischl@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard. edu <mailto:greve@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 Freesurfer@nmr.mgh.harvard. edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@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. 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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. 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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 Doug,
load it as a segmentation & overlay ? how I can specify . -overlay ? is right for overlay ?
tksurfer Sub_ID lh inflated -ov sum_binmap.nii -overlay-reg register.dat
-fthresh 0.01 -fmid 0.3 -fslope 1 changing -fthresh , doesn't change the colors. here when I map now, -fmid 12.3, then I can see red, yellow, orange colors. ,
now I did MNI_1mm autorecon, and used this to register mni space clusters, and calculated register.dat. it improves the sum_binmap.nii display on the surface , but lh.seg.mgh (sum of mri_vol2surf ), still shows no overlay. Still can't figure it out.
is there some option of color opacity ( transperency) in tksurfer.
Thanx
On Wed, Dec 14, 2011 at 7:54 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
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 <greve@nmr.mgh.harvard.edu<mailto: greve@nmr.mgh.harvard.**edu greve@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 --noeditI 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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu <greve@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 <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.**harvard.edu<fischl@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 <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.**harvard.edu<fischl@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard. edu <mailto:greve@nmr.mgh.harvard.**edu<greve@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 Freesurfer@nmr.mgh.harvard. edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>>
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vin .