Hi Irene, the voxel sizes are isotropic 1mm (which is good). However for some reason the first image is slightly rotated while the second is perfectly aligned with the axes. Therefore the first gets interpolated while the second stays the same. That explains the different smoothing.
Now the question is why is one image different. Do you collect a single scan for each session or are you averaging several within-session scans? You should look at other subjects and try to find out if and why specific time points are slightly rotated. By the way this is a good example how to potentially mess up a longitudinal study. If for example one of the time points is always (or more frequently) rotated because of a different protocol the study would be severely biased. So it is good that you are checking this. Best, Martin On Fri, 2011-11-04 at 10:28 +0100, irene.altare...@ens.fr wrote: > 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 > > > > > _______________________________________________ > > > > > 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 > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom > > > > it > > is > > > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > > > contains patient information, please contact the Partners Compliance > > HelpLine at > > > > http://www.partners.org/complianceline . If the e-mail was sent to you > > > > in > > error > > > > but does not contain patient information, please contact the sender and > > properly > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
