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 mreuter@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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