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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contains patient information, please contact the Partners Compliance HelpLine at
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