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
- 255 0 255
- 116 0 116
- 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> 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> 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 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: 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> . 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.
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.eduwrote:
It's a little involved but possible.
- Binarize Nth cluster to have a binary value of N mri_binarize --i N.nii --min 0.5 --binval N --o Nb.nii
- 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
- 255 0 255
- 116 0 116
- 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.**edugreve@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>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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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/**BugReportinghttp://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.**htmlhttp://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/**compliancelinehttp://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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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 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 youOn Mon, Dec 12, 2011 at 11:11 PM, Douglas N Greve <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 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 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: 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 . 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 greve@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
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.eduwrote:
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> 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 youOn Mon, Dec 12, 2011 at 11:11 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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 fromall 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 areoverlaid by atleast half of the subjects ??
>tksurfer #Sub_ID lh inflated -annot aparc.annot -ov1.nii -ovreg register.dat -fthresh 0.3 -fmid 0.3 -fslope 1
- How I can overlay multiple regions, in specificcolours, with 50% thr. ? , Thank you :) Vin -----------------------------**-
------------ _____________________________**_ _________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.**edu <Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@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/**freesurferhttps://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.**edugreve@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/**BugReportinghttp://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.**htmlhttp://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/**compliancelinehttp://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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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 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> 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>> 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> 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 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: 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> . 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 greve@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
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.eduwrote:
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
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> 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>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<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<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<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>
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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<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>
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. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard. edu <mailto:greve@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 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: www.nmr.mgh.harvard.edu/ facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Douglas N Greve
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vin .