[Freesurfer] ERROR: Talairach failed!
External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon_all my subjects which is .nii file. But I usually meet this error. talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0079, pval=0. < threshold=0.0050) Command exited with non-zero status 1 @#@FSTIME 2019:04:04:10:30:25 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 50% M 6252 F 7 R 243 W 0 c 1 w 8 I 1384 O 0 L 1.11 0.48 0.21 @#@FSLOADPOST 2019:04:04:10:30:25 talairach_afd N 4 1.11 0.48 0.21 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See:http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach ERROR: Talairach failed! Linux abby-virtual-machine 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 0306A_T1_w4 exited with ERRORS at Thu Apr 4 10:30:25 CST 2019 For more details, see the log file /home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I've searched the list and they advised to check with this website https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview. however,my subject's recon_all folder doesn't have T1.mgz and brainmask.mgz. it just has mri_nu_correct.mni.log orig orig_nu.mgz transformsmri_nu_correct.mni.log.bak orig.mgz rawavg.mgz I run ten files, and almost all of them go wrong, which is very strange.I need your help. please give some advises with program statements in detail. I really appreciate your help 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz 2) Platform: ubuntu 18 3) recon-all.log:see attached Thu Apr 4 10:27:46 CST 2019 /home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4 /usr/local/freesurfer/bin/recon-all -i 0306A_T1_w4.nii -s 0306A_T1_w4 -all subjid 0306A_T1_w4 setenv SUBJECTS_DIR /home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-linux-centos7_x86_64-dev-20190402-8622e54 Linux abby-virtual-machine 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 16384 kbytes maxproc 15449 maxlocks unlimited maxsignal15449 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited totalusedfree shared buff/cache available Mem:4015684 1296860 900516 12656 1818308 2447140 Swap: 3999740 435200 3564540 program versions used $Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $ $Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $ ProgramName: lta_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02 Id: $Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $ User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02 Id: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_annotation2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02 Id: $Id: mri_annotation2label.c,v 1.32 2016/08/02 21:20:27 nicks Exp $ User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_aparc2aseg ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02 Id: $Id: mri_aparc2aseg.c,v 1.54 2016/12/26 15:29:30 fischl Exp $ User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_aparc2wmseg ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02 Id: $Id: mri_aparc2wmseg.c,v 1.6 2011/03/02 00:04:13 nicks Exp $ User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 408
[Freesurfer] the problem about XL defect detected...
External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon-all subjects but for some of my subjects I get the following error when I run recon-all command: CORRECTING DEFECT 0 (vertices=18460, convex hull=3400, v0=4) XL defect detected... Killed Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 10:44:52 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux I don't know how to check and amend ?h.orig.nofix. please give me some commands in detail. Thank you for your help. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] the problem about XL defect detected...
External Email - Use Caution Hi， I am sorry. In my recon_all folder, there isn't lh.white, rh.white,lh.pial and rh.pial files, so I can run below command freeview -v topo_defect_before/mri/brainmask.mgz \ topo_defect_before/mri/wm.mgz:colormap=heat:opacity=0.4:visible=0 \ -f topo_defect_before/surf/lh.white:edgecolor=yellow \ topo_defect_before/surf/lh.pial:edgecolor=red \ topo_defect_before/surf/rh.white:edgecolor=yellow \ topo_defect_before/surf/rh.pial:edgecolor=red \ topo_defect_before/surf/lh.orig.nofix:visible=0 Hope you can give me more advises. Thank you very much. Greve, Douglas N.,Ph.D. 于2019年4月11日周四 下午11:23写道： > check out > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview > > > On 4/11/19 10:58 AM, Abby tang wrote: > > > > External Email - Use Caution > > > > Hello FreeSurfer Developers, I'm attempting to recon-all subjects but > > for some of my subjects I get the following error when I run recon-all > > command: CORRECTING DEFECT 0 (vertices=18460, convex hull=3400, v0=4) > > XL defect detected... Killed Linux abby-virtual-machine > > 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 10:44:52 UTC 2019 x86_64 > > x86_64 x86_64 GNU/Linux > > I don't know how to check and amend ?h.orig.nofix. please give me some > commands in detail. > > Thank you for your help. > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] CORRECTING DEFECT 1 problem
External Email - Use Caution Hello，Bruce I attached my subjects. Please help me. Thank you. Abby 2851A_T1_w4.nii <https://drive.google.com/file/d/16rwuarmjHdyV3cImi_Gy0N71aqGytlzO/view?usp=drive_web> Bruce Fischl 于2019年4月18日周四 下午10:53写道： > Hi Abby > > it's hard to tell from the image, but it looks like there is a big I/S > bias field as well as large amounts of pathology. > > If you upload the subject to our ftp site we will take a look > > cheers > Bruce > On Thu, 18 Apr > 2019, Abby > tang wrote: > > > > > External Email - Use Caution > > > > Hello FreeSurfer Developers, > > > > I'm attempting to recon_all my subjects which is .nii file. But I > usually meet this error. > > > > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950) > > After retessellation of defect 0 (v0=950), euler #=20 > (87340,255044,167724) : difference with theory > > (-32) = -52 > > > > CORRECTING DEFECT 1 (vertices=46367, convex hull=8524, v0=962) > > Segmentation fault (core dumped) > > Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 > 10:44:52 UTC 2019 x86_64 x86_ > > 64 x86_64 GNU/Linux > > > > recon-all -s 2851A_T1_w4 exited with ERRORS at Thu Apr 18 20:25:16 CST > 2019 > > > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > I check files in blow command and attached picture. > > > > freeview -v 2851A_T1_w4/mri/norm.mgz -f 2851A_T1_w4/surf/lh.orig.nofix > 2851A_T1_w4/surf/lh.inflated. > > nofix > > > > almost all of subjects go wrong. I need your help. > > > > please give some advises with program statements in detail. > > > > I really appreciate your help > > > > 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz > > 2) Platform: ubuntu 18 > > 3) recon-all.log:see attached > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] CORRECTING DEFECT 1 problem
External Email - Use Caution Hi Bruce I did't get your reply message yet. I have send the subject file to you. Could you give me your advises? Thank you for your help. Abby Abby tang 于2019年4月19日周五 上午8:32写道： > Hello，Bruce > I attached my subjects. Please help me. > Thank you. > Abby > 2851A_T1_w4.nii > <https://drive.google.com/file/d/16rwuarmjHdyV3cImi_Gy0N71aqGytlzO/view?usp=drive_web> > > Bruce Fischl 于2019年4月18日周四 下午10:53写道： > >> Hi Abby >> >> it's hard to tell from the image, but it looks like there is a big I/S >> bias field as well as large amounts of pathology. >> >> If you upload the subject to our ftp site we will take a look >> >> cheers >> Bruce >> On Thu, 18 Apr >> 2019, Abby >> tang wrote: >> >> > >> > External Email - Use Caution >> > >> > Hello FreeSurfer Developers, >> > >> > I'm attempting to recon_all my subjects which is .nii file. But I >> usually meet this error. >> > >> > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950) >> > After retessellation of defect 0 (v0=950), euler #=20 >> (87340,255044,167724) : difference with theory >> > (-32) = -52 >> > >> > CORRECTING DEFECT 1 (vertices=46367, convex hull=8524, v0=962) >> > Segmentation fault (core dumped) >> > Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 >> 10:44:52 UTC 2019 x86_64 x86_ >> > 64 x86_64 GNU/Linux >> > >> > recon-all -s 2851A_T1_w4 exited with ERRORS at Thu Apr 18 20:25:16 CST >> 2019 >> > >> > To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > >> > I check files in blow command and attached picture. >> > >> > freeview -v 2851A_T1_w4/mri/norm.mgz -f 2851A_T1_w4/surf/lh.orig.nofix >> 2851A_T1_w4/surf/lh.inflated. >> > nofix >> > >> > almost all of subjects go wrong. I need your help. >> > >> > please give some advises with program statements in detail. >> > >> > I really appreciate your help >> > >> > 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz >> > 2) Platform: ubuntu 18 >> > 3) recon-all.log:see attached >> > >> >___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: freesurfer picture
External Email - Use Caution *Hi Bruce* *I have tried freeview, but I don't know what file should be loaded in freeview. After qdec processing, what file format should be selected to load freeview?* *best wish* *Abby* Bruce Fischl 于2019年6月5日周三 下午9:53写道： > Hi Abby > > have you tried using freeview? It is a lot more flexible than qdec and > supports a bunch of different color maps > cheers > Bruce > > > On Wed, 5 Jun 2019, Abby tang wrote: > > > > > External Email - Use Caution > > > > Hello FreeSurfer Developers, > > > > I'm attempting to get some pictures about my results , so QDEC was used. > However I can't adjust thos > > e pictures which QDEC produced, such as picture1. > > > > When I read other's paper, they provided different pictures just like > picture2. If there any other m > > ethods to produce statistic pictures of brain? Can you give me some > advices? > > > > Thank you for your help. > > > > Best regards > > > > Abby > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: freesurfer picture
External Email - Use Caution *Hi Bruce* *I want to compare the relationship between age and thickness, which is controlled the effect about sex,education and eTIV. I want to get more beautiful pictures, but the ability of QDEC is limited.* *I have tried freeview, but I don't know what file should be loaded in freeview. After qdec processing, what file format should be selected to load freeview? Or if there are other method to use frreview direct to regressive age and thickness?* *Could you give me some advices?* *Thank you! Hope your reply.* *best wish * *Abby* Abby tang 于2019年6月5日周三 下午10:32写道： > *Hi Bruce* > *I have tried freeview, but I don't know what file should be loaded in > freeview. After qdec processing, what file format should be selected to > load freeview?* > *best wish* > *Abby* > > Bruce Fischl 于2019年6月5日周三 下午9:53写道： > >> Hi Abby >> >> have you tried using freeview? It is a lot more flexible than qdec and >> supports a bunch of different color maps >> cheers >> Bruce >> >> >> On Wed, 5 Jun 2019, Abby tang wrote: >> >> > >> > External Email - Use Caution >> > >> > Hello FreeSurfer Developers, >> > >> > I'm attempting to get some pictures about my results , so QDEC was >> used. However I can't adjust thos >> > e pictures which QDEC produced, such as picture1. >> > >> > When I read other's paper, they provided different pictures just like >> picture2. If there any other m >> > ethods to produce statistic pictures of brain? Can you give me some >> advices? >> > >> > Thank you for your help. >> > >> > Best regards >> > >> > Abby >> > >> >___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] picture edit
External Email - Use Caution Dear Dr. Tim Schäfer Thank you for your help and websites. I will try to do with them. Thank you! Best wish Abby Tim Schäfer 于2019年6月19日周三 上午2:37写道： > External Email - Use Caution > > The picture style you want looks very similar (though not identical) to > the ones produces by SurfStat: > > http://www.math.mcgill.ca/keith/surfstat/ > > Scroll down on the page to see some example figures produced with it. > SurfStat is a matlab toolbox, and it's quite easy to plot arbitrary data to > brain surfaces with it. See the examples on the website. One can load > freesurfer data and surfaces in Matlab, so it should be no problem to do > what you want. > > If you prefer python over matlab, you could use pysurfer from > https://pysurfer.github.io/ instead, but getting the style you want with > it requires a bit more custom code I guess. > > Tim > > > On June 18, 2019 at 2:57 AM Abby tang wrote: > > > > > > External Email - Use Caution > > > > Hello FreeSurfer Developers, > > > > I'm attempting to get some pictures about my results , so QDEC was > > used. However I can't adjust those pictures which QDEC produced, such > > as picture1. When I read other's paper, they provided different > > pictures just like picture2. > > I want to compare the relationship between age and thickness, which is > > controlled the effect about sex,education and eTIV. I want to get more > > beautiful pictures, but the ability of QDEC is limited. I have tried > > freeview, but I don't know what file should be loaded in freeview. > > After qdec processing, what file format should be selected to load > > freeview? Or if there are other method to use freeview direct to > > regressive age and thickness? Could you give me some advices? > > Thank you! Hope your reply. > > > > Thank you for your help. > > > > Best regards > > > > Abby > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Dr. Tim Schäfer > Postdoc Computational Neuroimaging > Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error in analyze (Qdec)
External Email - Use Caution Hi I have uploaded it in ftp, the file name is /home/abby/QDEC.tar.gz or QDEC.tar.gz. Thank you. Greve, Douglas N.,Ph.D. 于2019年7月9日周二 下午10:42写道： > Can you tar or compress /home/abby/Desktop/qdecyoung/qdec/Untitled/ and > upload it here > ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming > Let me know when it is there and what the file name is > > On 7/9/19 6:35 AM, Abby tang wrote: > > > > External Email - Use Caution > > > > Hello FreeSurfer Developers, > > I want to compare the relationship between age and thickness, which is > > controlled the effect about sex,education and eTIV, so QDEC was used. > > However I met a problem when I use it, such as picture1. > > I get the wrong message, Error in Analyze: command failed: mri_glmfit > > --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd > > /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir > > /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label > > /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C > > > /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat > > > --C > > > /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat > > > --C > > > /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat > > > --C > > > /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat. > > So I tried to put those to terminal, the feedback is: > > gdfRead(): reading /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd > > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > > Continuous Variable Means (all subjects) > > 0 age 80.3537 2.43637 > > 1 education 12.189 3.6099 > > 2 eTIV 1.33934e+06 242446 > > Class Means of each Continuous Variable > > 1 sexFemale 80.0568 11.4773 1265564.4638 > > 2 sexMale 80.6974 13.0132 1424768.7681 > > INFO: gd2mtx_method is dods > > Reading source surface > > /usr/local/freesurfer/subjects/fsaverage/surf/lh.white > > Number of vertices 163842 > > Number of faces327680 > > Total area 65416.984375 > > AvgVtxArea 0.399269 > > AvgVtxDist 0.721953 > > StdVtxDist 0.195470 > > > > $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ > > cwd /home/abby/Desktop/qdecyoung/qdec > > cmdline mri_glmfit.bin --y > > /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd > > /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir > > /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label > > /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C > > > /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat > > > --C > > > /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat > > > --C > > > /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat > > > --C > > > /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat > > > > > sysname Linux > > hostname abby-virtual-machine > > machine x86_64 > > user abby > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y/home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh > > logyflag 0 > > usedti 0 > > FSGD /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd > > labelmask /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label > > maskinv 0 > > glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory /home/abby/Desktop/qdecyoung/qdec/Untitled > > Loading y from /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh > >... done reading. > > INFO: gd2mtx_method is dods > > Saving design matrix to /home/abby/Desktop/qdecyoung/qdec/Untitled/Xg.dat > > Computing normalized matrix > > Normalized matrix condition is 9294.65 > > Matrix condition is 1e+08 > > Found 148151 points in label. > > Pruning voxels by thr: 1.175494e-38 > > Found 139197 voxels in mask > > Saving mask to /home/abby/Desktop/qdecyoung/qdec/Untitled/mask.mgh > > Reshaping mriglm->mask... > > search space = 69257.619818 > > DOF = 156 > > Starting fit and test > > Fit completed in 0.338183 minutes > > Computing spatial AR1 on surface > > Residual: ar1mn
Re: [Freesurfer] Error in analyze (Qdec)
External Email - Use Caution Hi Greve Can you download those files? I have uploaded it in ftp, the file name is QDEC.tar.gz. Hope you can help me. Thank you very much. Abby Abby tang 于2019年7月10日周三 上午9:46写道： > Hi > I have uploaded it in ftp, the file name is /home/abby/QDEC.tar.gz or > QDEC.tar.gz. > Thank you. > > Greve, Douglas N.,Ph.D. 于2019年7月9日周二 下午10:42写道： > >> Can you tar or compress /home/abby/Desktop/qdecyoung/qdec/Untitled/ and >> upload it here >> ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming >> Let me know when it is there and what the file name is >> >> On 7/9/19 6:35 AM, Abby tang wrote: >> > >> > External Email - Use Caution >> > >> > Hello FreeSurfer Developers, >> > I want to compare the relationship between age and thickness, which is >> > controlled the effect about sex,education and eTIV, so QDEC was used. >> > However I met a problem when I use it, such as picture1. >> > I get the wrong message, Error in Analyze: command failed: mri_glmfit >> > --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd >> > /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir >> > /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label >> > /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C >> > >> /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat >> >> > --C >> > >> /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat >> >> > --C >> > >> /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat >> >> > --C >> > >> /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat. >> > So I tried to put those to terminal, the feedback is: >> > gdfRead(): reading /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd >> > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. >> > Continuous Variable Means (all subjects) >> > 0 age 80.3537 2.43637 >> > 1 education 12.189 3.6099 >> > 2 eTIV 1.33934e+06 242446 >> > Class Means of each Continuous Variable >> > 1 sexFemale 80.0568 11.4773 1265564.4638 >> > 2 sexMale 80.6974 13.0132 1424768.7681 >> > INFO: gd2mtx_method is dods >> > Reading source surface >> > /usr/local/freesurfer/subjects/fsaverage/surf/lh.white >> > Number of vertices 163842 >> > Number of faces327680 >> > Total area 65416.984375 >> > AvgVtxArea 0.399269 >> > AvgVtxDist 0.721953 >> > StdVtxDist 0.195470 >> > >> > $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ >> > cwd /home/abby/Desktop/qdecyoung/qdec >> > cmdline mri_glmfit.bin --y >> > /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd >> > /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir >> > /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label >> > /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C >> > >> /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat >> >> > --C >> > >> /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat >> >> > --C >> > >> /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat >> >> > --C >> > >> /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat >> >> > >> > sysname Linux >> > hostname abby-virtual-machine >> > machine x86_64 >> > user abby >> > FixVertexAreaFlag = 1 >> > UseMaskWithSmoothing 1 >> > OneSampleGroupMean 0 >> > y/home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh >> > logyflag 0 >> > usedti 0 >> > FSGD /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd >> > labelmask /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label >> > maskinv 0 >> > glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled >> > IllCondOK 0 >> > ReScaleX 1 >> > DoFFx 0 >> > Creating output directory /home/abby/Desktop/qdecyoung/qdec/Untitled >> > Loading y from /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh >> >... done reading. >> > INFO: gd2mtx_method is dods >> > Saving design matrix to >> /home/abby/Desktop/qdecyoung/q
Re: [Freesurfer] Error in analyze (Qdec)
External Email - Use Caution Hi Greve Can you download those files? I have uploaded it in ftp website and send to your email, the file name is Untitled.rar. Hope you can help me. Thank you very much. Abby Greve, Douglas N.,Ph.D. 于2019年7月15日周一 下午12:07写道： > I see the file there, but it has zero length. Check whether your source > file actually has something in it. If it does, try uploading it again (you > may have to use a different file name) > > On 7/10/2019 9:17 PM, Abby tang wrote: > > External Email - Use Caution > Hi Greve > Can you download those files? I have uploaded it in ftp, the file name is > QDEC.tar.gz. > Hope you can help me. Thank you very much. > Abby > > Abby tang 于2019年7月10日周三 上午9:46写道： > >> Hi >> I have uploaded it in ftp, the file name is /home/abby/QDEC.tar.gz or >> QDEC.tar.gz. >> Thank you. >> >> Greve, Douglas N.,Ph.D. 于2019年7月9日周二 下午10:42写道： >> >>> Can you tar or compress /home/abby/Desktop/qdecyoung/qdec/Untitled/ and >>> upload it here >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming >>> Let me know when it is there and what the file name is >>> >>> On 7/9/19 6:35 AM, Abby tang wrote: >>> > >>> > External Email - Use Caution >>> > >>> > Hello FreeSurfer Developers, >>> > I want to compare the relationship between age and thickness, which is >>> > controlled the effect about sex,education and eTIV, so QDEC was used. >>> > However I met a problem when I use it, such as picture1. >>> > I get the wrong message, Error in Analyze: command failed: mri_glmfit >>> > --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd >>> > /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir >>> > /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label >>> > /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C >>> > >>> /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat >>> >>> > --C >>> > >>> /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat >>> >>> > --C >>> > >>> /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat >>> >>> > --C >>> > >>> /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat. >>> > So I tried to put those to terminal, the feedback is: >>> > gdfRead(): reading /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd >>> > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. >>> > Continuous Variable Means (all subjects) >>> > 0 age 80.3537 2.43637 >>> > 1 education 12.189 3.6099 >>> > 2 eTIV 1.33934e+06 242446 >>> > Class Means of each Continuous Variable >>> > 1 sexFemale 80.0568 11.4773 1265564.4638 >>> > 2 sexMale 80.6974 13.0132 1424768.7681 >>> > INFO: gd2mtx_method is dods >>> > Reading source surface >>> > /usr/local/freesurfer/subjects/fsaverage/surf/lh.white >>> > Number of vertices 163842 >>> > Number of faces327680 >>> > Total area 65416.984375 >>> > AvgVtxArea 0.399269 >>> > AvgVtxDist 0.721953 >>> > StdVtxDist 0.195470 >>> > >>> > $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ >>> > cwd /home/abby/Desktop/qdecyoung/qdec >>> > cmdline mri_glmfit.bin --y >>> > /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd >>> > /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir >>> > /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label >>> > /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C >>> > >>> /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat >>> >>> > --C >>> > >>> /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat >>> >>> > --C >>> > >>> /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat >>> >>> > --C >>> > >>> /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat >>> >>> > >>> > sysname Linux >>> > hostname abby-virtual-machine >>> &g
