Hello, Doug,
I convert the wmparc.mgz of a FS processed subject to a .nii file using mri_vol2vol and then use it to go through my command lines again, the created annotation file also have similar problem (please see the attached figs) , do I miss some refinement steps?
My converted .nii file is called wmparc.nii, and my command line are:
mri_vol2surf --src $FREESURFER_HOME/subjects/sub1/compare/wmparc.nii --src_type nifti --srcreg $FREESURFER_HOME/subjects/sub1/compare/register_raw.dat --hemi lh --o ./atlas-lh.mgh --out_type mgh --float2int round --interp nearest --projfrac 0.5
mris_seg2annot --seg atlas-lh.mgh --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --s sub1 --h lh --o myfsatalas.annot
Then I load the annot file in tksurfer.
Do I miss some refinement steps?
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
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> > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > > >
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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 > > > FileDrop:
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> > 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 >
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