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
> 
>                  
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---------------------------------
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 

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