Hello Bruce,
Sorry--just getting back to this project. The basic problem is that I am
trying to align a cerebellar parcellation with the underlay in tkmedit.
I was working on this with Doug, and his suggestion actually worked, and
now I can't get it to work again (see thread:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21209.html).
Here is the information you requested.
Anthony
[miles:[PATH]] adick% mri_info chuman_1.mgz
Volume information for chuman_1.mgz
type: MGH
dimensions: 141 x 103 x 87
voxel sizes: 0.8083, 0.9715, 0.8214
type: FLOAT (3)
fov: 113.976
dof: 0
xstart: -57.0, xend: 57.0
ystart: -50.0, yend: 50.0
zstart: -35.7, zend: 35.7
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 = 0.9997, y_r = -0.0228, z_r = 0.0103, c_r
= 4.4598
: x_a = 0.0237, y_a = 0.9951, z_a = -0.0965, c_a
= 15.3835
: x_s = -0.0080, y_s = 0.0967, z_s = 0.9953, c_s
= -6.8289
talairach xfm :
Orientation : RAS
Primary Slice Direction: axial
voxel to ras transform:
0.8081 -0.0222 0.0084 -51.7364
0.0191 0.9666 -0.0793 -32.3006
-0.0065 0.0939 0.8175 -46.7739
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.645035
ras to voxel transform:
1.2367 0.0293 -0.0099 64.4661
-0.0235 1.0243 0.0995 36.5272
0.0125 -0.1175 1.2117 53.5256
0.0000 0.0000 0.0000 1.0000
[miles:[PATH]] adick% mri_info orig.mgz
Volume information for orig.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.0000, 1.0000, 1.0000
type: UCHAR (0)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
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
= 6.0377
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a
= 60.9280
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s
= -1.0000
talairach xfm : /[PATH]/subjects/01/mri/transforms/talairach.xfm
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1.0000 0.0000 0.0000 134.0377
0.0000 0.0000 1.0000 -67.0720
0.0000 -1.0000 0.0000 127.0000
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000 0.0000 0.0000 134.0377
-0.0000 -0.0000 -1.0000 127.0000
-0.0000 1.0000 -0.0000 67.0720
0.0000 0.0000 0.0000 1.0000
[miles:[PATH]] adick% mri_label2vol --seg chuman_1.mgz --temp orig.mgz
--regheader > chuman_1.mgz --o chuman_1.conf.mgz
MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
On 3/7/12 9:17 AM, Bruce Fischl wrote:
> Hi Anthony
>
> sounds like there is something wrong with one of your volumes. Can you
> ru mri_info on them?
>
> Bruce
> On Wed, 7 Mar 2012, Anthony Dick wrote:
>
>> Hello--I am giving this message a bump. Please let me know if there are
>> any suggestions. Thanks!
>>
>> Anthony
>>
>> On 2/15/12 1:43 PM, Anthony Dick wrote:
>>> Hello,
>>>
>>> I have run the following successfully, but when I have moved on to
>>> other
>>> brains I get:
>>>
>>> mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader>
>>> chuman_1.mgz --o chuman_1.conf.mgz
>>> MRIalloc: could not allocate 975187978 frame
>>>
>>> Cannot allocate memory
>>>
>>> I am running a Mac Pro with 8GB RAM.
>>>
>>> Anthony
>>>
>>
>>
>>
>
>
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--
Anthony Steven Dick, Ph.D.
Assistant Professor
Department of Psychology
Florida International University
Modesto A. Maidique Campus DM 296B
11200 S.W. 8th Street
Miami, FL 33199
Phone: 305-348-4202 (try this first)
Lab Phone: 305-348-9057 or 305-348-9055
Fax: 305-348-3879
Email: ad...@fiu.edu
Webpage: http://www.fiu.edu/~adick
Lab Webpage: http://dcn.fiu.edu
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