The problem is with the mat file, not the input. The matrix should be an
ascii text file.
doug
> *Command line: *
On 11/18/2013 12:09 PM, Laura M. Tully wrote:
> Hello freesurfers,
>
> I'm trying to run mri_glmfit between groups analysis (patients vs.
> controls) with gender, age, medication (continuous), and duration of
> illness as covariates. Because the control group have values of zeros
> for medication and duration of illness (which results in an
> illconditioned matrix), I have created my own design matrix so that
> controls do not have a column for medication or duration of illness
> and am feeding this matrix into mri_glmfit instead of the fsgd file.
> However, this seems to cause a problem with the --y input; when I try
> to run mri_glmfit, i get an error message "error in uncompressing" -
> I'm not quite sure what this means, perhaps I did something wrong in
> creating the design matrix?
>
> See the full output below. I've also attached the design matrix,
> contrast file, and the original fsgd (which results in the ill
> conditioned matrix).
>
> Best,
> Laura.
>
> mri_glmfit --y lh_grpDiffs_thickness10.mgh --X> *Output:*
> new_mat_files/X_lh_grp_thick_med_dur.mat --C
> Contrast1B_grp_Diffs_HCvsSZ_Med_Dur.mtx --surf fsaverage lh --cortex
> --glmdir lh.grp_diffs_thickness_med_dur_112013.glmdir --illcond
>
> Reading source surface> hostname ncfws13.rc.fas.harvard.edu <http://ncfws13.rc.fas.harvard.edu>
> /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/surf/lh.white
> Number of vertices 163842
> Number of faces 327680
> Total area 65416.648438
> AvgVtxArea 0.399267
> AvgVtxDist 0.721953
> StdVtxDist 0.195470
>
> $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
> cwd /ncf/snp/04/SCORE/freesurfer_analysis/glm_analysis
> cmdline mri_glmfit --y lh_grpDiffs_thickness10.mgh --X
> new_mat_files/X_lh_grp_thick_med_dur.mat --C
> Contrast1B_grp_Diffs_HCvsSZ_Med_Dur.mtx --surf fsaverage lh --cortex
> --glmdir lh.grp_diffs_thickness_med_dur_112013.glmdir --illcond
> sysname Linux
> /lib64/ld-2.5.so <http://ld-2.5.so>> machine x86_64
> user ltully
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 0
> y
> /ncf/snp/04/SCORE/freesurfer_analysis/glm_analysis/lh_grpDiffs_thickness10.mgh
> logyflag 0
> X new_mat_files/X_lh_grp_thick_med_dur.mat
> usedti 0
> labelmask
> /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh.cortex.label
> maskinv 0
> glmdir lh.grp_diffs_thickness_med_dur_112013.glmdir
> IllCondOK 1
> ReScaleX 1
> DoFFx 0
> Creating output directory lh.grp_diffs_thickness_med_dur_112013.glmdir
> Loading y from
> /ncf/snp/04/SCORE/freesurfer_analysis/glm_analysis/lh_grpDiffs_thickness10.mgh
> MatrixReadTxT: could not scan value [1][1]
>
> File exists
> ERROR: in uncompressing
> MATFILE5: 0 x 0, type 0, imagf 0, name ''
>
> File exists
> unsupported matlab format 0 (unknown)
>
> File exists
> Saving design matrix to
> lh.grp_diffs_thickness_med_dur_112013.glmdir/Xg.dat
> *** glibc detected *** mri_glmfit: double free or corruption (out):
> 0x000000003b1279c0 ***
> ======= Backtrace: =========
> /lib64/libc.so.6[0x3229470d7f]
> /lib64/libc.so.6(cfree+0x4b)[0x32294711db]
> mri_glmfit[0x99fea2]
> mri_glmfit[0x5bcbe3]
> mri_glmfit[0x433608]
> mri_glmfit[0x433802]
> mri_glmfit[0x40f2f7]
> /lib64/libc.so.6(__libc_start_main+0xf4)[0x322941d994]
> mri_glmfit(__gxx_personality_v0+0x172)[0x40b2ba]
> ======= Memory map: ========
> 00400000-00b86000 r-xp 00400000 00:00 0
> 00b86000-00c86000 ---p 00b86000 00:00 0
> 00c86000-26a08000 rwxp 00c86000 00:00 0
> 35b4b000-3d4fa000 rwxp 35b4b000 00:00 0 [heap]
> 3229000000-322901c000 r-xp 00000000 fd:00 557272
> 322901c000-322921c000 ---p 322901c000 00:00 0> /lib64/ld-2.5.so <http://ld-2.5.so>
> 322921c000-322921d000 r-xp 0001c000 fd:00 557272
> 322921d000-322921e000 rwxp 0001d000 fd:00 557272> /lib64/ld-2.5.so <http://ld-2.5.so>
> 3229400000-322954d000 r-xp 00000000 fd:00 557376> /lib64/libc-2.5.so <http://libc-2.5.so>
> 322954d000-322974d000 ---p 0014d000 fd:00 557376> /lib64/libc-2.5.so <http://libc-2.5.so>
> 322974d000-3229751000 r-xp 0014d000 fd:00 557376> /lib64/libc-2.5.so <http://libc-2.5.so>
> 3229751000-3229752000 rwxp 00151000 fd:00 557376> /lib64/libc-2.5.so <http://libc-2.5.so>
> 3229752000-3229757000 rwxp 3229752000 00:00 0> /lib64/libm-2.5.so <http://libm-2.5.so>
> 3229800000-3229882000 r-xp 00000000 fd:00 557399
> 3229882000-3229a81000 ---p 00082000 fd:00 557399> /lib64/libm-2.5.so <http://libm-2.5.so>
> 3229a81000-3229a82000 r-xp 00081000 fd:00 557399> /lib64/libm-2.5.so <http://libm-2.5.so>
> 3229a82000-3229a83000 rwxp 00082000 fd:00 557399> /lib64/libm-2.5.so <http://libm-2.5.so>
> 3229c00000-3229c02000 r-xp 00000000 fd:00 557398> /lib64/libdl-2.5.so <http://libdl-2.5.so>
> 3229c02000-3229e02000 ---p 00002000 fd:00 557398> /lib64/libdl-2.5.so <http://libdl-2.5.so>
> 3229e02000-3229e03000 r-xp 00002000 fd:00 557398> /lib64/libdl-2.5.so <http://libdl-2.5.so>
> 3229e03000-3229e04000 rwxp 00003000 fd:00 557398> /lib64/libdl-2.5.so <http://libdl-2.5.so>
> 322a000000-322a014000 r-xp 00000000 fd:00 557401> /lib64/libpthread-2.5.so <http://libpthread-2.5.so>
> /lib64/libz.so.1.2.3
> 322a014000-322a213000 ---p 00014000 fd:00 557401
> /lib64/libz.so.1.2.3
> 322a213000-322a214000 rwxp 00013000 fd:00 557401
> /lib64/libz.so.1.2.3
> 322a400000-322a416000 r-xp 00000000 fd:00 557391
> 322a416000-322a615000 ---p 00016000 fd:00 557391> /lib64/libpthread-2.5.so <http://libpthread-2.5.so>
> 322a615000-322a616000 r-xp 00015000 fd:00 557391> /lib64/libpthread-2.5.so <http://libpthread-2.5.so>
> 322a616000-322a617000 rwxp 00016000 fd:00 557391> /lib64/libpthread-2.5.so <http://libpthread-2.5.so>
> 322a617000-322a61b000 rwxp 322a617000 00:00 0> /lib64/libcrypt-2.5.so <http://libcrypt-2.5.so>
> 322f000000-322f00d000 r-xp 00000000 fd:00 557370
> /lib64/libgcc_s-4.1.2-20080825.so.1
> 322f00d000-322f20d000 ---p 0000d000 fd:00 557370
> /lib64/libgcc_s-4.1.2-20080825.so.1
> 322f20d000-322f20e000 rwxp 0000d000 fd:00 557370
> /lib64/libgcc_s-4.1.2-20080825.so.1
> 3237200000-32372e6000 r-xp 00000000 fd:00 3309621
> /usr/lib64/libstdc++.so.6.0.8
> 32372e6000-32374e5000 ---p 000e6000 fd:00 3309621
> /usr/lib64/libstdc++.so.6.0.8
> 32374e5000-32374eb000 r-xp 000e5000 fd:00 3309621
> /usr/lib64/libstdc++.so.6.0.8
> 32374eb000-32374ee000 rwxp 000eb000 fd:00 3309621
> /usr/lib64/libstdc++.so.6.0.8
> 32374ee000-3237500000 rwxp 32374ee000 00:00 0
> 3239600000-3239609000 r-xp 00000000 fd:00 557404
> 3239609000-3239808000 ---p 00009000 fd:00 557404> /lib64/libcrypt-2.5.so <http://libcrypt-2.5.so>
> 3239808000-3239809000 r-xp 00008000 fd:00 557404> /lib64/libcrypt-2.5.so <http://libcrypt-2.5.so>
> 3239809000-323980a000 rwxp 00009000 fd:00 557404> /lib64/libcrypt-2.5.so <http://libcrypt-2.5.so>
> 323980a000-3239838000 rwxp 323980a000 00:00 0> Phone: (916) 734-7927 <tel:%28916%29%20734-7927>
> 2b1225c45000-2b1225c48000 rwxp 2b1225c45000 00:00 0
> 2b1225c69000-2b1225c6d000 rwxp 2b1225c69000 00:00 0
> 2b1225c6d000-2b1225ca2000 r-xs 00000000 fd:00 3703836
> /var/run/nscd/dbC3ggnz (deleted)
> 2b1225d6d000-2b12952bb000 rwxp 2b1225d6d000 00:00 0
> 7fff44349000-7fff44362000 rwxp 7ffffffe5000 00:00 0
> [stack]
> 7fff443cb000-7fff443ce000 r-xp 7fff443cb000 00:00 0
> [vdso]
> ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0
> [vsyscall]
> Aborted
>
>
> --
> --
> Laura M. Tully, PhD
> Post-Doctoral Fellow in Psychiatry
> UC Davis Imaging Research Center
> 4701 X Street,
> Sacramento, CA 95817
> Fax: (916) 734-8750 <tel:%28916%29%20734-8750>
>> ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu>
> Alumnus of Social Neuroscience & Psychopathology Lab, Harvard University
>> *Confidentiality Notice:* This e-mail message, including any
> Follow me on twitter: @tully_laura
> --
> attachments, is for the sole use of the intended recipient(s) and may> ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu>
> contain confidential and privileged information. Any unauthorized
> review, use, disclosure or distribution is prohibited. If you are not
> the intended recipient, please contact the sender by reply e-mail and
> destroy all copies of the original message.
>
>
>
> --
> --
> Laura M. Tully, PhD
> Post-Doctoral Fellow in Psychiatry
> UC Davis Imaging Research Center
> 4701 X Street,
> Sacramento, CA 95817
> Phone: (916) 734-7927
> Fax: (916) 734-8750
>
> Alumnus of Social Neuroscience & Psychopathology Lab, Harvard University
>> *Confidentiality Notice:* This e-mail message, including any
> Follow me on twitter: @tully_laura
> --
> attachments, is for the sole use of the intended recipient(s) and may> _______________________________________________
> contain confidential and privileged information. Any unauthorized
> review, use, disclosure or distribution is prohibited. If you are not
> the intended recipient, please contact the sender by reply e-mail and
> destroy all copies of the original message.
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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