Thanks you for your quick reply. Here is the command-line and below it is the terminal output. In the beginning we follow the instructions on PairedAnalysis page, but the "lh.paired-diff.thickness.sm05.mgh" can't be loaded (error message is the same with what we listed below). So we pre-processed our data individually (as past below) and meet the same problem. We very appreciated any suggestion to fix this problem.
======================================================= mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.c02.mgh --y lh.paired-diff.thickness.c03.mgh --y lh.paired-diff.thickness.c04.mgh --y lh.paired- diff.thickness.c06.mgh --y lh.paired-diff.thickness.c07.mgh --y lh.paired- diff.thickness.c08.mgh --y lh.paired-diff.thickness.c09.mgh --y lh.paired- diff.thickness.c10.mgh --y lh.paired-diff.thickness.c11.mgh --y lh.paired- diff.thickness.c16.mgh --y lh.paired-diff.thickness.c17.mgh --y lh.paired- diff.thickness.c18.mgh --y lh.paired-diff.thickness.c19.mgh --y lh.paired- diff.thickness.c20.mgh --y lh.paired-diff.thickness.c21.mgh --y lh.paired- diff.thickness.c22.mgh --y lh.paired-diff.thickness.c23.mgh --y lh.paired- diff.thickness.c25.mgh --y lh.paired-diff.thickness.c28.mgh --y lh.paired- diff.thickness.c29.mgh --y lh.paired-diff.thickness.c31.mgh --y lh.paired- diff.thickness.c32.mgh --y lh.paired-diff.thickness.c33.mgh --y lh.paired- diff.thickness.c34.mgh --y lh.paired-diff.thickness.c35.mgh --y lh.paired- diff.thickness.c36.mgh --y lh.paired-diff.thickness.c38.mgh --y lh.paired- diff.thickness.c41.mgh --y lh.paired-diff.thickness.c42.mgh --y lh.paired- diff.thickness.c43.mgh --y lh.paired-diff.thickness.c44.mgh --fsgd paired- diff_control.fsgd --osgm --surface c10_LinSG_MC.long.c10_LinSG lh --surface c10_LinSG_OV.long.c10_LinSG lh --surface c11_ZhuangC_MC.long.c11_ZhuangC lh --surface c11_ZhuangC_OV.long.c11_ZhuangC lh --surface c16_SwenST_MC.long.c16_SwenST lh --surface c16_SwenST_OV.long.c16_SwenST lh --surface c17_YouPG_MC.long.c17_YouPG lh --surface c17_YouPG_OV.long.c17_YouPG lh --surface c18_WainYP_MC.long.c18_WainYP lh --surface c18_WainYP_OV.long.c18_WainYP lh --surface c19_LeeSC_MC.long.c19_LeeSC lh --surface c19_LeeSC_OV.long.c19_LeeSC lh -- surface c20_LanYZ_MC.long.c20_LanYZ lh --surface c20_LanYZ_OV.long.c20_LanYZ lh --surface c21_DwanSP_MC.long.c21_DwanSP lh --surface c21_DwanSP_OV.long.c21_DwanSP lh --surface c22_ChangYH_MC.long.c22_ChangYH lh --surface c22_ChangYH_OV.long.c22_ChangYH lh --surface c23_HsiehWC_MC.long.c23_HsiehWC lh --surface c23_HsiehWC_OV.long.c23_HsiehWC lh --surface c25_ChenYG_MC.long.c25_ChenYG lh --surface c25_ChenYG_OV.long.c25_ChenYG lh --surface c28_ChenYR_MC.long.c28_ChenYR lh --surface c28_ChenYR_OV.long.c28_ChenYR lh --surface c29_LinSG_MC.long.c29_LinSG lh -- surface c29_LinSG_OV.long.c29_LinSG lh --surface c2_YangWZ_MC.long.c2_YangWZ lh --surface c2_YangWZ_OV.long.c2_YangWZ lh - -surface c31_LinIG_MC.long.c31_LinIG lh --surface c31_LinIG_OV.long.c31_LinIG lh --surface c32_YanYH_MC.long.c32_YanYH lh --surface c32_YanYH_OV.long.c32_YanYH lh --surface c33_ZhuangHT_MC.long.c33_ZhuangHT lh --surface c33_ZhuangHT_OV.long.c33_ZhuangHT lh --surface c34_SuWT_MC.long.c34_SuWT lh --surface c34_SuWT_OV.long.c34_SuWT lh -- surface c35_LuYH_MC.long.c35_LuYH lh --surface c35_LuYH_OV.long.c35_LuYH lh --surface c36_LaiYZ_MC.long.c36_LaiYZ lh --surface c36_LaiYZ_OV.long.c36_LaiYZ lh --surface c37_ChouYT_MC.long.c37_ChouYT lh -- surface c37_ChouYT_OV.long.c37_ChouYT lh --surface c38_HsuBY_MC.long.c38_HsuBY lh --surface c38_HsuBY_OV.long.c38_HsuBY lh -- surface c3_HuangSW_MC.long.c3_HuangSW lh --surface c3_HuangSW_OV.long.c3_HuangSW lh --surface c41_PaiJS_MC.long.c41_PaiJS lh --
surface c41_PaiJS_OV.long.c41_PaiJS lh --surface c42_HsuPY_MC.long.c42_HsuPY lh --surface c42_HsuPY_OV.long.c42_HsuPY lh --surface c43_ChengYS_MC.long.c43_ChengYS lh --surface c43_ChengYS_OV.long.c43_ChengYS lh --surface c44_WangYG_MC.long.c44_WangYG lh --surface c44_WangYG_OV.long.c44_WangYG lh --surface c4_HsuTY_MC.long.c4_HsuTY lh -- surface c4_HsuTY_OV.long.c4_HsuTY lh --surface c6_HoHS_MC.long.c6_HoHS lh -- surface c6_HoHS_OV.long.c6_HoHS lh --surface c7_ChenDY_MC.long.c7_ChenDY lh --surface c7_ChenDY_OV.long.c7_ChenDY lh --surface c8_YuFY_MC.long.c8_YuFY lh --surface c8_YuFY_OV.long.c8_YuFY lh --surface c9_HoJF_MC.long.c9_HoJF lh --surface c9_HoJF_OV.long.c9_HoJF lh
==============================================================
gdfReadHeader: reading paired-diff_control.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 stai -2.21875 7.24454
1 cesd -0.59375 4.96777
Class Means of each Continuous Variable
1 control -2.2188 -0.5938
INFO: gd2mtx_method is dods
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c10_LinSG_MC.long.c10_LinSG/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c10_LinSG_OV.long.c10_LinSG/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c11_ZhuangC_MC.long.c11_ZhuangC/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c11_ZhuangC_OV.long.c11_ZhuangC/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c16_SwenST_MC.long.c16_SwenST/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c16_SwenST_OV.long.c16_SwenST/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c17_YouPG_MC.long.c17_YouPG/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c17_YouPG_OV.long.c17_YouPG/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c18_WainYP_MC.long.c18_WainYP/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c18_WainYP_OV.long.c18_WainYP/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c19_LeeSC_MC.long.c19_LeeSC/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c19_LeeSC_OV.long.c19_LeeSC/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c20_LanYZ_MC.long.c20_LanYZ/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c20_LanYZ_OV.long.c20_LanYZ/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c21_DwanSP_MC.long.c21_DwanSP/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c21_DwanSP_OV.long.c21_DwanSP/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c22_ChangYH_MC.long.c22_ChangYH/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c22_ChangYH_OV.long.c22_ChangYH/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c23_HsiehWC_MC.long.c23_HsiehWC/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c23_HsiehWC_OV.long.c23_HsiehWC/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c25_ChenYG_MC.long.c25_ChenYG/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c25_ChenYG_OV.long.c25_ChenYG/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c28_ChenYR_MC.long.c28_ChenYR/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c28_ChenYR_OV.long.c28_ChenYR/surf/lh.white
Reading source surface /Applications/freesurfer/subjects/ PDM_cortical_thickness//c29_LinSG_MC.long.c29_LinSG/surf/lh.white
mri_glmfit(58169) malloc: *** mmap(size=2097152) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
mrisFindNeighbors: could not allocate list of 7 dists at v=25644
Cannot allocate memory
2012/6/7 Douglas Greve greve@nmr.mgh.harvard.edu:
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.