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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
