I just checked the demension information and found they are not same.
Do you think which one is wrong?
Thanks a lot!
Volume information for lh.thickness.fsaverage.mgh
type: MGH
dimensions: 163842 x 1 x 1
voxel sizes: 1.0000, 1.0000, 1.0000
type: FLOAT (3)
fov: 163842.000
dof: 0
xstart: -81921.0, xend: 81921.0
ystart: -0.5, yend: 0.5
zstart: -0.5, zend: 0.5
Volume information for lh.fsaverage.ROI5.mgh
type: MGH
dimensions: 23406 x 1 x 7
voxel sizes: 1.0000, 1.0000, 1.0000
type: FLOAT (3)
fov: 23406.000
dof: 0
xstart: -11703.0, xend: 11703.0
ystart: -0.5, yend: 0.5
zstart: -3.5, zend: 3.5
Xiaochu Zhang PhD
Visiting Research Fellow
Neuroimaging Research Branch
National Institute on Drug Abuse - IRP
Biomedical Research Center
251 Bayview Blvd.
Suite 200 (NIDA)
Baltimore MD
21224
Tel: 443-740-2619
-----Original Message-----
From: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: Friday, December 05, 2008 3:51 PM
To: Zhang, Xiaochu (NIH/NIDA) [F]
Cc: Freesurfer Mailing List
Subject: RE: [Freesurfer] RE: for cortical thickness
Zhang,
You could perform the steps you show in 1., where you sample your ROI
directly to the subjects surface, rather than going through the
fsaverage subject. Ultimately, you would (or should) end-up with the
same result as that from following the steps in the wiki page (going
through fsaverage). The difference is that you only need to do the
sampling of the ROI to fsaverage only once, whereas with what you want
to do, you do it for every subject. Not a big deal if you dont have
that many subjects. btw, fsaverage is in talairach space, so its not
distorting things much by performing that registration (the .dat file
from fslregister has very small values).
I'm not sure about the useful of performing 2., where you sample the
thickness data to the volume. This is not usually done (I dont think).
You will have a volume with voxel values equal to the thickness of the
cortex around that voxel, but there is no hard meaning of that value for
that voxel. Typically mri_surf2vol is used to sample parcellation
labels into volume space.
I'm not sure why you are getting dimension mismatch errors. Use mri_info
on the files in question to get the dimensions. Note this part of the
wiki instructions in the last two steps:
cd $SUBJECTS_DIR/subjid/surf
noting that 'subjid' is the name of your subject. If you remain in the
$SUBJECTS_DIR/fsaverage/surf directory from the previous steps, you will
get the mismatch error (which i just discovered myself).
Nick
On Fri, 2008-12-05 at 15:06 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote:
> Hi Nick,
> Thank you so much for your help!
> Recently, I tested it strictly following your instruction. However, I
> met a problem in the last step "mri_segstats ". They gave me the error
> information: "ERROR: dimension mismatch between input volume and seg".
> I checked the old mails in the list. Some one talked about dimension
> mismatch but not related to my issue. Could you please do me a favor
> and give some suggestion for the reason?
>
> There are another two issues:
> 1. I noted you transfer ROI5.nii to fsaverage space. Because my
> ROI5.nii have been in the Talairach space, can I transfer it to
> subjects's space directly?
> For example:
> cd $SUBJECTS_DIR/subjid/surf
> Fslregister --s subjid --mov /path/to/TT_avg152T1.nii --reg
> TT_avg152T1_to_subjid.dat Mri_vol2surf --mov /path/to/ROI5.nii --reg
> TT_avg152T1_to_subjid.dat --projdist 0 1 0.1 --interp nearest --hemi
> lh --out lh.ROI5.mgh Mri_segstats --seg lh.ROI5.mgh --in lh.thickness
> --sum segstats-ROI5.txt
>
> Is it OK? What is the benefit for using fsaverage data?
> BTW, I got the same dimension mismatch error information in the last
> step.
>
> 2. Can we transfer all data into the volume space. i.e., Mri_surf2vol
> --surfval lh.thickness --hemi lh --fillribbon --template orig.mgz
> --volregidentity subjid --outvol lh.ribbon.nii Mri_convert
> lh.ribbon.nii --apply_transform transforms/talairach.auto.xfm -o
> lh-talairach.ribbon.nii
>
> I tried it and no error information appear. However, I don't know it
> is correct or not.
>
> Thanks, again!
>
> Xiaochu Zhang PhD
>
> Visiting Research Fellow
>
> Neuroimaging Research Branch
>
> National Institute on Drug Abuse - IRP
>
> Biomedical Research Center
>
> 251 Bayview Blvd.
>
> Suite 200 (NIDA)
>
> Baltimore MD
>
> 21224
>
> Tel: 443-740-2619
>
>
> -----Original Message-----
> From: Nick Schmansky [mailto:[EMAIL PROTECTED]
> Sent: Friday, November 21, 2008 5:15 PM
> To: Zhang, Xiaochu (NIH/NIDA) [F]
> Cc: Freesurfer Mailing List; Allison Stevens
> Subject: RE: [Freesurfer] RE: for cortical thickness
>
> Zhang,
>
> The web page describing the steps to extract cortical thickness data
> for your volume-space defined ROI is found here:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
>
> Nick
>
>
> On Mon, 2008-11-17 at 14:02 -0500, Zhang, Xiaochu (NIH/NIDA) [F]
wrote:
> > Thank you so much for your response, Nick!
> > I uploaded "ROI5.nii" (i.e., abc.nii) just now. This ROI has been in
> > Talarich space.
> > Actually, it is from my group functional data. So I did not have
> > corresponding T1-data.
> >
> > BTW: when can I read the web page describing the steps taken to get
> > cortical thickness from an ROI defined by a volume mask? I hope I
> > can read it ASAP. If it is possible, could you please do me a favor
> > and send the draft to me?
> > Thanks, again!
> >
> >
> > Xiaochu Zhang PhD
> >
> > Visiting Research Fellow
> >
> > Neuroimaging Research Branch
> >
> > National Institute on Drug Abuse - IRP
> >
> > Biomedical Research Center
> >
> > 251 Bayview Blvd.
> >
> > Suite 200 (NIDA)
> >
> > Baltimore MD
> >
> > 21224
> >
> > Tel: 443-740-2619
> >
> >
> > -----Original Message-----
> > From: Nick Schmansky [mailto:[EMAIL PROTECTED]
> > Sent: Monday, November 17, 2008 12:59 PM
> > To: Zhang, Xiaochu (NIH/NIDA) [F]
> > Cc: Freesurfer Mailing List
> > Subject: Re: [Freesurfer] RE: for cortical thickness
> >
> > Xiaochu,
> >
> > I'm putting together a web page describing the steps taken to get
> > cortical thickness from an ROI defined by a volume mask. Can you
> > send
>
> > me these two files so that I can make sure the steps work correctly?
> >
> > 1) the ROI mask file (what you are calling 'abc.nii')
> > 2) the T1-weighted anatomical volume of the subject from which
> > abc.nii
>
> > was created. i need this file to register to a template volume.
> >
> > You can post those files (available only to me) by uploading to our
> > file
> > drop:
> >
> > https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> >
> > Nick
> >
> >
> > On Sat, 2008-11-15 at 00:48 -0500, Zhang, Xiaochu (NIH/NIDA) [F]
> wrote:
> > > Hi, FreeSurfer export,
> > >
> > > Thank you very much for response!
> > > Now, under some export's help, I used to the mri_surf2vol to
> > > transfer
> > cortex thickness into nifti.
> > > The below line is what I used.
> > > mri_surf2vol --surfval ../surf/lh.thickness --hemi lh --fillribbon
> > > --template orig.mgz --volregidentity ${subid} --outvol
> > > lh.ribbon.nii
> > >
> > > I checked the result and found the voxel outside the gray matter
> > > is
> > always zero and in the gray matter is about 0-3. Could you please do
> > me a favor and tell me whether these data is cortex thickness or
not?
> > > If they are cortex thickness, why are they always different. In my
> > mind, it should be same in one direction because we calculate the
> > distance between the white matter line and the gray matter line.
> > >
> > > Thanks a lot!
> > > All the best,
> > > Xiaochu
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> >
> >
> >
>
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
