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
