Hi Bruce,
I had tried to run recon-all on the dicoms. But the same errors show up.
This image covering whole brain is obtained (Siemens 3T) actually from a
monkey and looks good. Here is the header information from the dicom image.
According to the suggestion in Freesurfer FAQ, I run "tkregister2 --mgz --s
subj --fstal". Surprisingly, a strange image appears and looks a white line.
Seemingly the brain image is rotated to a invisible orientation. Any
suggestions?
Best,
Liang
#-------------------------------------------
Volume information for 001.mgz
type: MGH
dimensions: 256 x 256 x 160
voxel sizes: 0.5000, 0.5000, 1.0000
type: SHORT (4)
fov: 160.000
dof: 0
xstart: -64.0, xend: 64.0
ystart: -64.0, yend: 64.0
zstart: -80.0, zend: 80.0
TR: 2500.00 msec, TE: 4.38 msec, TI: 1100.00 msec, flip angle:
8.00 degrees
nframes: 1
PhEncDir: ROW
ras xform present
xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r =
2.6988
: x_a = -0.0000, y_a = -0.0000, z_a = -1.0000, c_a =
6.9217
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s =
-1.3494
talairach xfm :
Orientation : LIP
Primary Slice Direction: coronal
voxel to ras transform:
-0.5000 -0.0000 -0.0000 66.6988
-0.0000 -0.0000 -1.0000 86.9217
0.0000 -0.5000 0.0000 62.6506
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.25
ras to voxel transform:
-2.0000 0.0000 0.0000 133.3976
-0.0000 -0.0000 -2.0000 125.3012
0.0000 -1.0000 0.0000 86.9217
0.0000 0.0000 0.0000 1.0000
2010/11/17 Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> can you try running recon-all directly on the dicoms? Also, it's probably
> pretty noisy at .5mm in-plane - how does it look? Is it whole brain?
>
>
> On Wed, 17 Nov 2010, liang wang wrote:
>
> Hi Bruce,
>>
>> I run the command on a NIFTI image converted by dicom files. The image can
>> be skull stripped using bet in FSL, but some skulls were not removed
>> clearly. Here is the information by mri_info. It seems to me normal, but
>> several scan parameters loss. For the nifti image, I use to3d (AFNI code)
>> to
>> convert DICOM to nifti format and use 3drefit to fix up correctly the
>> orientation.
>>
>> #-----------------------------------
>> type: nii
>> dimensions: 256 x 256 x 160
>> voxel sizes: 0.5000, 0.5000, 1.0000
>> type: SHORT (4)
>> fov: 128.000
>> dof: 0
>> xstart: -64.0, xend: -64.0
>> ystart: -64.0, yend: -64.0
>> zstart: -80.0, zend: -80.0
>> TR: 0.00 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 = 1.0000, y_r = -0.0000, z_r = -0.0000, c_r =
>> -2.6988
>> : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a =
>> -1.3494
>> : x_s = 0.0000, y_s = 0.0000, z_s = -1.0000, c_s =
>> 6.9217
>> Orientation : RPI
>> Primary Slice Direction: axial
>>
>> voxel to ras transform:
>> 0.5000 -0.0000 -0.0000 -66.6988
>> -0.0000 -0.5000 -0.0000 62.6506
>> 0.0000 0.0000 -1.0000 86.9217
>> 0.0000 0.0000 0.0000 1.0000
>>
>> voxel-to-ras determinant 0.25
>>
>> ras to voxel transform:
>> 2.0000 -0.0000 -0.0000 133.3976
>> 0.0000 -2.0000 0.0000 125.3012
>> 0.0000 0.0000 -1.0000 86.9217
>> 0.0000 0.0000 0.0000 1.0000
>>
>>
>> 2010/11/17 Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>>
>> wow, that's a completely wacky talairach xform. Did you run this straight
>>> on the dicom images? The talairach clearly failed for some reason. Try
>>> running mri_info on the dicoms to see if there is something strange in
>>> them
>>>
>>>
>>> On Wed, 17 Nov 2010, liang wang wrote:
>>>
>>> Hi FSusers,
>>>
>>>>
>>>> The terminal displays errors when I run "recon-all -autorecon1 -subjid
>>>> ..."
>>>> to get a skull-stripped brain image. The processing exits with the
>>>> following
>>>> errors regarding talairach transformation. Here is the talairach.xfm:
>>>>
>>>> MNI Transform File
>>>> % tkregister2
>>>>
>>>> Transform_Type = Linear;
>>>> Linear_Transform =
>>>> 39.07553864 15.93667889 -36.86604309 -1474.05761719
>>>> 1861.34423828 844.27008057 -1897.87268066 -75416.71093750
>>>> -606.90667725 -274.30368042 622.14581299 24711.26757812 ;
>>>>
>>>>
>>>> Any suggestions would be appreciated.
>>>>
>>>> Best,
>>>> Liang
>>>>
>>>> #--------------------------------------------------------------------
>>>> #...@# Talairach Failure Detection Wed Nov 17 10:15:36 EST 2010
>>>> /mnt/cd/kastner/liang/resting_state/ph_062210/fs_skull/ph/mri
>>>>
>>>> talairach_afd -T 0.005 -xfm transforms/talairach.xfm
>>>>
>>>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
>>>> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
>>>> Linux node37.cluster 2.6.18-128.el5 #1 SMP Wed Jan 21 10:41:14 EST 2009
>>>> x86_64 x86_64 x86_64 GNU/Linux
>>>>
>>>> recon-all -s ph exited with ERRORS at Wed Nov 17 10:15:36 EST 2010
>>>>
>>>>
>>>>
>>>>
>>>>
>>> The information in this e-mail is intended only for the person to whom it
>>> is
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>>
>>
>>
--
Liang Wang, PhD
Neuroscience of Attention and Perception Laboratory
Princeton Neuroscience Institute
Princeton University
Princeton, NJ, 08540
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