Hi Bruce, I run the command recon-all -base K_EL03_base -tp K_EL03_1 -tp K_EL03_2 -all.I am to upload the recon_all.log to you. Thanks, Yawu
On Thu, Jan 29, 2015 at 6:07 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Yawu > > what was the freesurfer command you ran that gave you the error? Can you > send us the command and the full screen output? > > thanks > Bruce > > On Thu, 29 Jan 2015, Liu Y wrote: > > Hi Bruce, >> >> I have uploaded the baseline K_EL03_1.nii.gz and followup K_EL03_2.nii.gz >> via FTP File Exchange. >> >> Thanks, >> >> Yawu >> >> >> On Thu, Jan 29, 2015 at 3:28 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu >> > >> wrote: >> Hi Yawu >> >> Can you upload those two volumes so we can take a look? >> Cheers >> Bruce >> >> >> >> On Jan 28, 2015, at 4:33 PM, Liu Y <liuy8...@gmail.com> wrote: >> >> Dear experts, >> Recently I run freesurfer longitudinal analysis >> (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0), >> during the creation of the BASE, I get the following error >> "Volumes differ in geometry row=1 col=4 >> diff=4.745766(4.74577)". We did not change the protocol >> during the study period. I check the baseline and >> follow-up images with mri_info, it shows like this for >> baseline images . >> Volume information for K_EL03_1.nii.gz >> type: nii >> dimensions: 208 x 256 x 160 >> voxel sizes: 1.1719, 1.1719, 1.2000 >> type: FLOAT (3) >> fov: 243.750 >> dof: 0 >> xstart: -121.9, xend: 121.9 >> ystart: -150.0, yend: 150.0 >> zstart: -96.0, zend: 96.0 >> TR: 2400.00 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 = 1.9559 >> : x_a = -1.0000, y_a = 0.0000, z_a = 0.0000, c_a >> = 24.3864 >> : x_s = 0.0000, y_s = 1.0000, z_s = 0.0000, c_s = >> -21.0540 >> Orientation : PSR >> Primary Slice Direction: sagittal >> >> voxel to ras transform: >> 0.0000 0.0000 1.2000 -94.0441 >> -1.1719 0.0000 0.0000 146.2614 >> 0.0000 1.1719 0.0000 -171.0540 >> 0.0000 0.0000 0.0000 1.0000 >> >> voxel-to-ras determinant -1.64795 >> ras to voxel transform: >> -0.0000 -0.8533 -0.0000 124.809 -0.0000 -0.0000 >> 0.8533 145.9661 >> 0.8333 0.0000 0.0000 78.3701 >> 0.0000 0.0000 0.0000 1.0000 >> > >> and for followup images:Volume information for >> K_EL03_2.nii.gz >> type: nii >> dimensions: 208 x 256 x 160 >> voxel sizes: 1.1719, 1.1719, 1.2000 >> type: FLOAT (3) >> fov: 243.750 >> dof: 0 >> xstart: -121.9, xend: 121.9 >> ystart: -150.0, yend: 150.0 >> zstart: -96.0, zend: 96.0 >> TR: 2400.00 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 = -2.7898 >> : x_a = -1.0000, y_a = 0.0000, z_a = 0.0000, c_a >> = 17.2881 >> : x_s = 0.0000, y_s = 1.0000, z_s = 0.0000, c_s = >> -34.7603 >> Orientation : PSR >> Primary Slice Direction: sagittal >> >> voxel to ras transform: >> 0.0000 0.0000 1.2000 -98.7898 >> -1.1719 0.0000 0.0000 139.1631 >> 0.0000 1.1719 0.0000 -184.7603 >> 0.0000 0.0000 0.0000 1.0000 >> >> voxel-to-ras determinant -1.64795 >> >> ras to voxel transform: >> -0.0000 -0.8533 -0.0000 118.7526 >> -0.0000 -0.0000 0.8533 157.6622 >> 0.8333 0.0000 0.0000 82.3249 >> 0.0000 0.0000 0.0000 1.0000 >> >> I have no ideal what is going wrong. Please help. >> By the way I used dcm2nii Gui (compressed FSL 4DNIfTInii) >> convert dcm to nii.gz. >> Thanks, >> >> Yawu >> >> _______________________________________________ >> 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 > > > 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 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.
