Thank you Doug, that worked a treat! I knew it must have been something simple I was missing.
Best.
LT
On Tue, Nov 19, 2013 at 8:45 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
The problem is with the mat file, not the input. The matrix should be an ascii text file. doug
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.
*Command line: * 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
*Output:* Reading source surface /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 hostname ncfws13.rc.fas.harvard.edu http://ncfws13.rc.fas.harvard.edu 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 /lib64/ld-2.5.so http://ld-2.5.so 322901c000-322921c000 ---p 322901c000 00:00 0 322921c000-322921d000 r-xp 0001c000 fd:00 557272 /lib64/ld-2.5.so http://ld-2.5.so 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 3229800000-3229882000 r-xp 00000000 fd:00 557399 /lib64/libm-2.5.so http://libm-2.5.so 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/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 /lib64/libpthread-2.5.so http://libpthread-2.5.so 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 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 /lib64/libcrypt-2.5.so http://libcrypt-2.5.so 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 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 Phone: (916) 734-7927 tel:%28916%29%20734-7927 Fax: (916) 734-8750 tel:%28916%29%20734-8750
Alumnus of Social Neuroscience & Psychopathology Lab, Harvard University ltully@fas.harvard.edu mailto:ltully@fas.harvard.edu
Follow me on twitter: @tully_laura
*Confidentiality Notice:* This e-mail message, including any 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.
--
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 ltully@fas.harvard.edu mailto:ltully@fas.harvard.edu
Follow me on twitter: @tully_laura
*Confidentiality Notice:* This e-mail message, including any 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.