Dear Martin and all, I had actually checked the RAS coordinates for all of my subjects and timepoints, and the one I mentioned is the only one in which the rotation is present.
I created a uchar image from rawavg.mgz and tried to run recon-all from that without the motioncor step and without talairach (creating talairach.xfm manually from scratch using tkregister2), but recon-all crashes during mri_nu_correct (see error below). One strange observation: I had been running this subject in version 5.0 previously and noticed that, although the RAS coordinates and transform are the same as the ones I get in version 5.1, I do not see any smoothing effect when comparing rawavg.mgz and orig.mgz. I guess the best we can do at this stage is to manually edit the input nii file so that no rotation is coded in there (by changing the sform/qform as suggested by Michael Harm) - unless you have other suggestions... Thanks very much again for your help, Irene $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp.mri_nu_correct.mni.22469/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (-0.0436194, 0, 0.999048) k_ras = (0.999048, 0, 0.0436194) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz MRIvoxelToTalairachVoxel: unsupported slice direction 1 MRIvoxelToTalairachVoxel: unsupported slice direction 1 Numerical result out of range MRIvoxelToTalairachVoxel: unsupported slice direction 1 Numerical result out of range MRIvoxelToTalairachVoxel: unsupported slice direction 1 Numerical result out of range Le vendredi 04 novembre 2011 à 16:17 -0400, Martin Reuter a écrit : > Irene, > > I don't really know why the RAS coordinates are slightly rotated. I > checked and they are orthogonal. I don't know where this comes from > (autoalign on the scanner, but then why would it be only in one of your > volumes). > > Maybe Doug knows a trick how to avoid the interpolation as it seems > unnecessary? > > > Also, when you say you checked the other subject, did you look at the > images, or did you check the RAS coordinates in the mri_info output. It > can be that rotation is small and you won't see it the image but it is > still there. The RAS xform x_r,x_a,x_s, y_r, y_a, y_s and z_r z_a z_s > should only be +-1 or zero. > > Best, Martin > > > On Fri, 2011-11-04 at 17:46 +0100, irene.altare...@ens.fr wrote: > > Dear Martin, > > > > I have a single scan per session, so no averaging. Also, this is the only > > image > > in my longitudinal data for which I am encountering this problem. I have > > checked all other subjects and none of them is rotated/smoothed. > > > > I am not sure I understand precisely why this scan needs to be rotated, is > > it to > > establish RAS coordinates' center and axes? Do you think there is a way I > > can > > fix it? I don't have many subjects in this protocol, so dropping one would > > be a > > real pity. > > > > Thanks very much again for your help. > > Best, > > Irene > > > > > > > > > > > > Selon Martin Reuter <mreu...@nmr.mgh.harvard.edu>: > > > > > 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 Ã 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
