What version are you using? One of our versions had a problem with creating bad mgzs. You probably don't need to convert it to mgz. Can you run mri_label2vol with the original nii and see if it works? doug
On 04/04/2012 04:50 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. >>>> > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
