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. Sign up now.