Dear Martin,
the RAS coordinates and voxel to ras transforms are indeed slightly different.
Should I change this and if so, how?
Please find the output of mri_info for each of the two acquisitions at the end
of this email.
Thanks again!
Irene
***********************************************************************************
Volume information for gsTP1/mri/rawavg.mgz
type: MGH
dimensions: 256 x 256 x 176
voxel sizes: 1.0000, 1.0000, 1.0000
type: FLOAT (3)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -88.0, zend: 88.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = 0.0000, y_r = -0.0436, z_r = 0.9990, c_r = -3.5493
: x_a = -1.0000, y_a = 0.0000, z_a = 0.0000, c_a = 12.8739
: x_s = 0.0000, y_s = 0.9990, z_s = 0.0436, c_s = -16.0490
talairach xfm :
Orientation : PSR
Primary Slice Direction: sagittal
voxel to ras transform:
0.0000 -0.0436 0.9990 -85.8823
-1.0000 0.0000 0.0000 140.8739
0.0000 0.9990 0.0436 -147.7657
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-0.0000 -1.0000 -0.0000 140.8739
-0.0436 0.0000 0.9990 143.8789
0.9990 -0.0000 0.0436 92.2460
0.0000 0.0000 0.0000 1.0000
***********************************************************************************
Volume information for gsTP2/mri/rawavg.mgz
type: MGH
dimensions: 256 x 256 x 176
voxel sizes: 1.0000, 1.0000, 1.0000
type: FLOAT (3)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -88.0, zend: 88.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = 0.0000, y_r = 0.0000, z_r = 1.0000, c_r = -1.5339
: x_a = -1.0000, y_a = 0.0000, z_a = 0.0000, c_a = 11.5254
: x_s = 0.0000, y_s = 1.0000, z_s = 0.0000, c_s = -19.3390
talairach xfm :
Orientation : PSR
Primary Slice Direction: sagittal
voxel to ras transform:
0.0000 0.0000 1.0000 -89.5339
-1.0000 0.0000 0.0000 139.5254
0.0000 1.0000 0.0000 -147.3390
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-0.0000 -1.0000 -0.0000 139.5254
-0.0000 -0.0000 1.0000 147.3390
1.0000 0.0000 0.0000 89.5339
0.0000 0.0000 0.0000 1.0000
Selon Martin Reuter <mreu...@nmr.mgh.harvard.edu>:
> Hi Irene,
>
> since those images are not from the longitudinal runs, it really is a
> cross sectional question:
>
> You have two images and the raw average look both similarly noisy, but
> the orig (which is the first image in the recon-all stream) is smoother
> for one than the other.
>
> That means that the conform step (that interpolates the isotropic orig
> from the rawavg) introduces the different smoothing. Not sure why it is
> different.
> You can check (with mri_info) the voxel sizes of your rawavg and the RAS
> coordinates. If they are the same, smoothing should also be the same.
>
> Best, Martin
>
> On Thu, 2011-11-03 at 17:48 +0100, Irene Altarelli wrote:
> > Dear Martin,
> >
> > thanks for your quick reply.
> >
> > I am using version 5.1. I only have two timepoints per subject and I
> > took the snapshots from the independent runs. What bothers me is that
> > the difference is not present in the 001.mgz images, but seems to appear
> > later in the workflow.
> >
> > Thanks again,
> > Irene
> >
> > Le jeudi 03 novembre 2011 à 10:40 -0400, Martin Reuter a écrit :
> > > Hi Irene,
> > >
> > > both images should be smoothed the same. You only have two time points
> > > in each subject? Which FreeSurfer version are you using? And these
> > > images are from the *.long.base directories (or are they from the
> > > independent runs)?
> > >
> > > -Martin
> > >
> > > On Thu, 2011-11-03 at 15:20 +0100, Irene Altarelli wrote:
> > > > Dear Fs experts,
> > > >
> > > > I am running a longitudinal dataset through the longitudinal pipeline,
> > > > and noticed that for one subject, although we kept everything the same
> > > > (sequence, coil etc) the two timepoints' brainmasks look different:
> > > > timepoint one (in the attached snapshot, gs_tp1) looks as if it has
> been
> > > > smoothed, compared to timepoint two (gs_tp2). I have checked some other
> > > > images from this subject, and the same seems to occur for orig.mgz, but
> > > > not for rawavg.mgz.
> > > >
> > > > Any idea on what could be causing the difference would be greatly
> > > > appreciated.
> > > >
> > > > Thanks in advance,
> > > > Irene
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