Hi Martin, Many thanks, Yawu 2015 年 1 月 30 日 下午 5:04于 "Martin Reuter" <mreu...@nmr.mgh.harvard.edu>写道：
> Hi Yawu, > > I looked it up based on the data you send us. You are fine, your voxel > sizes and image dimensions are the same, only the RAS coords differ and > that is OK. I'll see if I can update the test in a way that it does not > warn in these cases. > > Best, Martin > > > On Jan 30, 2015, at 9:47 AM, Martin Reuter <mreu...@nmr.mgh.harvard.edu> > wrote: > > 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 > > > --------------------------------- > 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. > >
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