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
