if you email me the .mgz I'll fix it. On Fri, 6 Apr 2012, Anthony Dick wrote:
> 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. >>>>> >> >> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
