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 <[email protected]>
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 <[email protected]
>> >
>> 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
>> <[email protected]>
>> 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
>> <[email protected]> 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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