Hello, there,
If I have the label file of a ROI, and I want to convert the RAS coordinate of each vertex to volume index, which command I can use?
Thanks! Guang
Date: Fri, 18 Dec 2009 14:18:44 -0500 From: greve@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com Subject: Re: [Freesurfer] a question about mris_ca_train
I don't have any more suggestions except to play with the projection fraction. You can load the data simultaneously in tkmedit and tksurfer, click on a hole in tksurfer, then use the "Save/Go To Point" feature to see in tkmedit why the surface does not pass through your label.
doug
Guang Zeng wrote:
Hello, Doug,
Thanks a lot for your suggestion, I added --projfrac 0.5 to my vol2surf command, the result looks much better now, but there are still some regions among ROIs have no label, please see the attached figure.
Could you give some suggestions to fix this problem. Thanks a lot! Guang
Date: Thu, 17 Dec 2009 12:22:28 -0500 From: greve@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com Subject: Re: [Freesurfer] a question about mris_ca_train
When you run vol2surf, try specifying --projfrac 0.5 to sample in the middle of the ribbon.
doug
Guang Zeng wrote:
Hello, Doug,
Fix that dimension dismtach problem now, and got my annot.file, but I still have problems, I attached the images which show my atals and annotation file loaded into tkmedit and tksurfer, the surface is broken.
Could you tell me what I need to do?
Thanks a lot! Guang
Date: Wed, 16 Dec 2009 18:05:03 -0500 From: greve@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com Subject: Re: [Freesurfer] a question about mris_ca_train
Load it again in tkmedit to make sure you have the color table
right,
then re-run you mris_seg2annot command with your color table.
doug
Guang Zeng wrote:
Hello, Doug,
I am transfering my color lookup table to FreeSurfer ColorLUT
now. It
may need a little while. I load the a.anat.mgz using tkmedit and FreeSurfer lookup table, although the label and the colors looks a little bit strange, but all the other things look fine to me such as the segmentation results are registered pretty well.
Could you tell me what I need to do next, once my color lookup
table
is ready,
Thanks! Guang
> Date: Wed, 16 Dec 2009 17:39:07 -0500 > From: greve@nmr.mgh.harvard.edu > To: freesurfer_zg@hotmail.com > Subject: Re: [Freesurfer] a question about mris_ca_train > > First, work in the volume instead of the surface because the
surface is
> too hard to determine what is going on. Convert a.nii to the
anatomical
> space with > > mri_vol2vol --mov a.nii --reg > $FREESURFER_HOME/subjects/sub1/compare/register_raw.dat --interp > nearest --fstarg \ > --o $FREESURFER_HOME/subjects/sub1/mri/a.anat.mgz > > Then look at the output in tkmedit: > > tkmedit sub1 orig.mgz -surfs -seg a.anat.mgz YOURLUT > > where YOURLUT is a color lookup table for your segmentation
(model it
> using FreeSurferColotLUT.txt). > > let me know if that looks ok > > doug > > Guang Zeng wrote: > > Hello, Doug, > > > > Thanks a lot for your quick reply, I removed that "ico 7",
now
it is:
> > > > mri_vol2surf --src a.nii --src_type nifti --srcreg > > $FREESURFER_HOME/subjects/sub1/compare/register_raw.dat
--hemi
rh --o
> > ./atlas-rh.mgz --out_type mgh --float2int round --interp
nearest
> > > > and I rerun the two commands, it finished without problems. > > > > But I tried to take a look at this annotation file, I load
the
volume
> > use tksurfer, then import my myatalas.annot, a multiple-line
warning
> > is showed as > > : Warning: vertex 132436 with annotation ffffffff - out of
range!
> > > > Could you give me some suggestions to fix it? > > > > The original input file I loaded into tksurfer has been
converted
into > > the anatomical space, and my first-command line input a.nii
has been
> > registered to it using tksurfer. > > > > Thanks a lot! > > Gaung > > > > > Date: Wed, 16 Dec 2009 17:12:50 -0500 > > > From: greve@nmr.mgh.harvard.edu > > > To: freesurfer_zg@hotmail.com > > > Subject: Re: [Freesurfer] a question about mris_ca_train > > > > > > Sample it to the native subject's space with
mri_vol2surf (not
to ico > > > 7). Is the input file a.nii already in the anatomical space
(ie,
256^3, > > > 1mm^3)? If not, make sure that your registration matrix is
correct
> > using > > > tkregister2. > > > > > > doug > > > > > > Guang Zeng wrote: > > > > Hello, Doug, > > > > > > > > Thanks a lot for your help, I am following your
instruction now,
> > > > > > > > First Step: mri_vol2surf > > > > my command line is > > > > mri_vol2surf --src a.nii --src_type nifti --srcreg > > > > $FREESURFER_HOME/subjects/sub1/compare/register_raw.dat
--hemi
rh --o > > > > ./atlas-rh.mgz --out_type mgh --float2int round
--trgsubject ico
> > > > --icoorder 7 --interp nearest > > > > > > > > Second step: mris_seg2annot > > > > my command line is > > > > mris_seg2annot --seg atlas-rh.mgz --ctab > > > > $FREESURFER_HOME/FreeSurferColorLUT.txt --s sub1 --h
rh --o
> > > > myatalas.annot > > > > > > > > But I got error like, > > > > ERROR: dimension mismatch. Surface has 132464
vertices, seg
has 163842 > > > > Make sure the surface segmentation matches the subject
and
hemi
> > > > > > > > Could you give me some suggestions to fix it? > > > > > > > > Thanks! > > > > Guang > > > > > > > > > > > > > Date: Wed, 16 Dec 2009 13:12:59 -0500 > > > > > From: greve@nmr.mgh.harvard.edu > > > > > To: freesurfer_zg@hotmail.com > > > > > CC: freesurfer@nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] a question about mris_ca_train > > > > > > > > > > You can use mri_vol2surf with the --interp nearest
option to
sample > > > > your > > > > > volume segmentations onto the surface. You can then use > > mris_seg2annot > > > > > to convert this segmentation directly to an annotation,
then use
> > > > > mri_annotation2label to convert the annotation into a
set of
labels. > > > > > Nothing here guarantees that labels will be connected or > > contiguous nor > > > > > is it sure that all vertices on the surface will be
labeled.
> > > > > > > > > > doug > > > > > > > > > > Guang Zeng wrote: > > > > > > Hi, there, > > > > > > > > > > > > Recently, I sent sseveral emails to you to ask same
kind of
> > question > > > > > > about building our own template and atlas. > > > > > > Thanks a lot for your quick reply, they helps me a
lot.
> > > > > > > > > > > > Currently, I still have a question about building
our own
> > atlas using > > > > > > mris_ca_train, sorry to bother you again. > > > > > > > > > > > > We have a surface labeling atlas in our lab, we'd
like to
use this > > > > > > atlas instead of using FS's
desikan_killiany.2007-06-20gcs.
> > > > > > It is kind of difficult for us to load every subject
in our
> > training > > > > > > set to tksurfer, and manually label each ROI based
on our
ATLAS. > > > > > > > > > > > > What we try to do is: > > > > > > 1. Send each subject in the training set to our
toolbox which
> > will > > > > use > > > > > > our atlas to do surface labeling. For each subject
it will
> > output a > > > > > > file just like > > > > > > wmparc.mgz in FS, but it is NIfTI file. > > > > > > > > > > > > 2. Send each subject to FS pipeline to get the
?h.sphere.reg,
> > ?h.sulc > > > > > > files. > > > > > > > > > > > > 3. Find a method to get my ?h. mylabels. annot files,
and use
> > > > > > mris_ca_train to build a new atlas. > > > > > > > > > > > > First of all, do you think what I try to do is
reasonable?
> > > > > > > > > > > > If yes, I know I need to get the FS .label files
for each
ROI, > > then I > > > > > > can call mris_label2annot to get ?h. mylabels. annot
files.
> > > > > > > > > > > > But how can I get the FS .label files for each ROI
from our
> > toolbox > > > > > > output ROI labeled NIfTI file? > > > > > > > > > > > > These qurstions trouble me for a long time, your
help are
really > > > > > > appreciate. > > > > > > > > > > > > Thanks a lot! > > > > > > Guang > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
> > > > > > Your E-mail and More On-the-Go. Get Windows Live
Hotmail Free.
> > > > Sign up > > > > > > now.
http://clk.atdmt.com/GBL/go/171222985/direct/01/
> > > > > > > > > > > >
> > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > > > > > > > -- > > > > > 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
> > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > > > > > > >
> > > > Your E-mail and More On-the-Go. Get Windows Live
Hotmail Free.
> > Sign up > > > > now. http://clk.atdmt.com/GBL/go/171222985/direct/01/ > > > > > > -- > > > 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
> > > > > > >
> > Hotmail: Trusted email with Microsoft’s powerful SPAM
protection.
Sign > > up now. http://clk.atdmt.com/GBL/go/177141664/direct/01/ > > -- > 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 >
Hotmail: Free, trusted and rich email service. Get it now. http://clk.atdmt.com/GBL/go/171222984/direct/01/
-- 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
Hotmail: Free, trusted and rich email service. Get it now. http://clk.atdmt.com/GBL/go/171222984/direct/01/
-- 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
Hotmail: Powerful Free email with security by Microsoft. Get it now. http://clk.atdmt.com/GBL/go/171222986/direct/01/
-- 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
_________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/
freesurfer@nmr.mgh.harvard.edu
-
Guang Zeng