What is your command-line and what is the terminal output? Also, please post to the list instead of to me directly. thanks doug
On 6/6/12 5:24 AM, lordowen wrote: > Dear Prof. Greve: > > Sorry to reply this very old post, but we encountered the same > problem. We processed our data following the instructions in > PairedAnaylsis page on Wiki. Everything is fine but we can't perform > mri_glmfit using command-line. So we need your advise to seek possible > solutions for this problem. > > We are using FS 5.1 under Mac OS 10.7.4. We have 12GB memory and about > 500GB HD space. > > Thanks you for your kindly help. > > 2011/3/16 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: >> So you re-ran mris_preproc and you still get the error? If so, try running >> >> mris_preproc --debug <Your Options> |& tee mris_preprog.err.log >> >> Send me the mris_preprog.err.log, but don't email it as it will likely >> be huge. Instead drop it to me a the file drop listed at the end of this >> email. >> >> doug >> >> >> Andrew Mendlowitz wrote: >>> The mri_prepoc runs fine still but the glmfit still says can not >>> allocate memory, there is 8gb of ram and very little disk space is >>> used up, there is 876.1 gb still free. >>> >>> On Fri, Mar 11, 2011 at 12:49 PM, Douglas N Greve >>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> >>> If you re-run mris_preproc does the same thing happen? Are you >>> running out of disk space? >>> doug >>> >>> Andrew Mendlowitz wrote: >>> >>> The code for the lh.paired-diff.thickness.mgh file is >>> mris_preproc --target fsaverage --hemi lh \ >>> >>> --meas thickness --out lh.paired-diff.thickness.mgh \ >>> >>> --fsgd pairss.fsgd --paired-diff >>> >>> >>> On Thu, Mar 10, 2011 at 10:13 AM, Douglas N Greve >>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: >>> >>> There appears to be something wrong with the >>> lh.paired-diff.thickness.mgh file. How was it created? >>> doug >>> >>> Andrew Mendlowitz wrote: >>> >>> Hello All, >>> I get the following error while trying to run >>> mri_glmfit. I am >>> running a 2.93 ghz imac with 8gb of ram. I am also running >>> freesurfer version 5.0.0 on Snow >>> Leopard OS version 10.6. >>> >>> >>> /Applications/freesurfer/subjects/qdec$ mri_glmfit >>> --glmdir >>> lh.paired-diff --fsgd paired-diff.fsgd --C mean.mtx --y >>> lh.paired-diff.thickness.mghgdfReadHeader: reading >>> paired-diff.fsgd >>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT >>> be done. >>> Continuous Variable Means (all subjects) >>> 0 Age 1.5 >>> Class Means of each Continuous Variable >>> 1 Main 1.5000 >>> INFO: gd2mtx_method is dods >>> >>> $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve >>> Exp $ >>> cwd /Applications/freesurfer/subjects/qdec >>> cmdline mri_glmfit --glmdir lh.paired-diff --fsgd >>> paired-diff.fsgd --C mean.mtx >>> --y lh.paired-diff.thickness.mgh >>> sysname Darwin >>> hostname larry >>> machine i386 >>> user amend >>> FixVertexAreaFlag = 1 >>> UseMaskWithSmoothing 1 >>> OneSampleGroupMean 0 >>> y >>> /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh >>> logyflag 0 >>> usedti 0 >>> FSGD paired-diff.fsgd >>> glmdir lh.paired-diff >>> IllCondOK 0 >>> DoFFx 0 >>> Creating output directory lh.paired-diff >>> Loading y from >>> >>> /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh >>> mri_glmfit(79576) malloc: *** mmap(size=2563764224) failed >>> (error code=12) >>> *** error: can't allocate region >>> *** set a breakpoint in malloc_error_break to debug >>> MRIallocIndices: could not allocate 1714511945 elt >>> index array >>> Cannot allocate memory >>> >>> The mri_info for the file is : >>> >>> >>> mghRead(/Applications/freesurfer/subjects/qdec/fsgd_input.mgh, >>> -1): could not >>> open file >>> amend@larry /Applications/freesurfer/subjects/qdec$ >>> mri_info >>> >>> /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh >>> Volume information for >>> >>> /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh >>> type: MGH >>> dimensions: 1714510945 x 1853057372 x 1634628457 x >>> 1668310833 >>> voxel sizes: 72950800688805540228332034981888.0000, >>> 0.0000, >>> 70387746064971392794503413760.0000 >>> type: UNKNOWN (842347100) >>> fov: inf >>> dof: 1668244335 >>> xstart: -inf, xend: inf >>> ystart: -39.8, yend: 39.8 >>> zstart: >>> -57528904905339976080461439864148066304.0, zend: >>> 57528904905339976080461439864148066304.0 >>> TR: 71446969504754118412748034408448.00 >>> msec, TE: >>> 17862977898376175754203558313984.00 msec, TI: >>> 4464583905807213894543171649536.00 msec, flip angle: >>> 4128358109894647822155776.00 degrees >>> nframes: 1668310833 >>> PhEncDir: UNKNOWN >>> ras xform present >>> xform info: x_r = >>> 19441367164500690594879212879872.0000, y_r = >>> 282670772483715414097920.0000, z_r = >>> 4630517930517356511053742080.0000, c_r = >>> 18179207505345150839094025125888.0000 >>> : x_a = >>> 72953300747400503281465327353856.0000, y_a = >>> 71756401321839400437789128392704.0000, z_a = >>> 4721224652433019196440490016768.0000, c_a = 0.0000 >>> : x_s = 0.0000, y_s = >>> 208210237828607676252160.0000, z_s = >>> 4286666299869639999488.0000, c_s = >>> 4622889417339745644740714954752.0000 >>> >>> talairach xfm : >>> Orientation : AAA >>> Primary Slice Direction: coronal >>> >>> voxel to ras transform: >>> inf 12133604733747200.0000 inf >>> -inf >>> inf 3080133850722982464323584.0000 >>> inf >>> -inf >>> 36752183205510726549504.0000 >>> 8937395835633664.0000 inf -inf >>> 0.0000 0.0000 0.0000 1.0000 >>> >>> voxel-to-ras determinant nan >>> >>> ras to voxel transform: >>> mat = NULL! >>> Invalid argument >>> MatrixFree: NULL mat POINTER! >>> >>> Invalid argument >>> >>> -Andrew >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> >>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> -- Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>> >>> Phone Number: 617-724-2358 <tel:617-724-2358> >>> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 >>> <tel:617-726-7422> >>> <tel:617-726-7422 <tel:617-726-7422>> >>> >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> >>> FileDrop: >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> >>> >>> >>> 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 <mailto:gr...@nmr.mgh.harvard.edu> >>> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 >>> <tel:617-726-7422> >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> >> -- >> 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
