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 greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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. 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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 greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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