Hi Yawu, the base stream tests if the header geometries are the same across time points. For example, it is a bad idea to change the resolution (voxel size) of your inputs across time. Can you send the output of
mri_info /usr/local/src/freesurfer/subjects/K_EL03_1/mri/rawavg.mgz and mri_info /usr/local/src/freesurfer/subjects/K_EL03_2/mri/rawavg.mgz Thanks, Martin On Jan 30, 2015, at 8:45 AM, Liu Y <liuy8...@gmail.com> wrote: > Hi Bruce, > I run recon-all -base K_El03_base -tp K_EL03_1 -tp K_EL03_2 -all. > It gives a warning, you can find it from the recon-all.log : > mri_diff --notallow-pix > /usr/local/src/freesurfer/subjects/K_EL03_2/mri/rawavg.mgz > /usr/local/src/freesurfer/subjects/K_EL03_1/mri/rawavg.mgz > > Volumes differ in geometry row=1 col=4 diff=4.745766 (4.74577) > WARNING: Image geometries differ across time, maybe due to aquisition changes? > This can potentially bias a longitudinal study! Will continue in 10s. > Have a nice weekend, > Yawu > > On Fri, Jan 30, 2015 at 3:36 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > Hi Yawu > > the recon-all.log indicates that building the base finished without error. > What command did you run that gave you the error? The original nifti files > will have different geometries since the subject will be in a different > location in the scanner, but that should be normalized out by the > longitudinal stream. > > cheers > Bruce > > > On Fri, 30 Jan 2015, Liu Y wrote: > > 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. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu
_______________________________________________ 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.