Hello--was wondering if you guys have any ideas. I am a bit stumped. 
Thanks for the help!

Anthony

On 4/4/12 4:50 PM, Anthony Dick wrote:
> No, but the conversion from the original .nii works...
>
> [miles:[PATH]] adick% mri_convert chuman_1.mgz junk.mgh
> mri_convert chuman_1.mgz junk.mgh
> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
> reading from chuman_1.mgz...
> MRIallocIndices: could not allocate 1701979223 elt index array
> Cannot allocate memory
>
> [miles:[PATH]] adick% mri_convert chuman_1.nii chuman_1_new.mgz
> mri_convert chuman_1.nii chuman_1_new.mgz
> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
> reading from chuman_1.nii...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (0.999687, 0.0236858, -0.00800704)
> j_ras = (-0.0228015, 0.995052, 0.0967044)
> k_ras = (0.0102579, -0.0964916, 0.995281)
> writing to chuman_1_new.mgz...
>
>
> On 4/4/12 4:47 PM, Douglas N Greve wrote:
>> Can you successfully run mri_convert on chuman_1.mgz, eg
>> mri_convert chuman_1.mgz junk.mgh
>>
>> doug
>>
>>
>>
>> On 04/04/2012 12:29 PM, Anthony Dick wrote:
>>> 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
>>>>>>
>>>>>
>>>> The information in this e-mail is intended only for the person to whom
>>>> it is
>>>> addressed. If you believe this e-mail was sent to you in error and the
>>>> e-mail
>>>> contains patient information, please contact the Partners Compliance
>>>> HelpLine at
>>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>>> in error
>>>> but does not contain patient information, please contact the sender
>>>> and properly
>>>> dispose of the e-mail.
>>>>
>
>


-- 
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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