Hi Irene, To add to what Martin wrote, the issue is that the conform stage of mri_convert automatically interpolates "oblique acquisitions" and the user has no control to turn off this behavior. You may be interested in the following thread in which I inquired about this interpolation:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18123.html In our case, we have 1 mm isotropic data acquired aligned to the AC/PC, and we didn't want FS to interpolate/rotate this data during the creation of orig.mgz. So, we have taken to manually editing the sform/qform of the input nii file so that no rotation is coded in the sform/qform. In our case, we are accomplishing this editing using FSL tools, although I'm sure that you could accomplish the same using appropriate flags with mri_convert. As to whether such editing would break any assumptions of the longitudinal stream I don't know. (I wouldn't think so, because zeroing out a small rotation in the sform/qform is basically akin to rotating the subject's head in the magnet and then acquiring an image with its read/phase/slice axes aligned with the canonical gradient axes). cheers, -MH On Fri, 2011-11-04 at 11:07 -0400, Martin Reuter wrote: > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
