External Email - Use Caution Hi Dr. Greve,
Yes, it seems like the output folder and some output files were created. After running the mri_glmfit, 'three_group_comparison.area.lh.glmdir' folder was created. In the glmdir folder, 'three_group_comparison.area' folder was created, and the following files were also created: beta.mgh, dof.dat, eres.mgh, fwhm.dat, mask.mgh, mri_glmfit.log, rstd.mgh, rvar.mgh, sar1.mgh, surface, and Xg.dat. In the 'three_group_comparison.area' folder, the following files were created: C.dat, F.mgh, gamma.mgh, maxvox.dat, sig.mgh, and z.mgh. Do you have any idea what could have been the problem? Thanks, Hyunwoo Jeong 2022년 2월 17일 (목) 오전 12:36, Douglas N. Greve <dgr...@mgh.harvard.edu>님이 작성: > Did it create the output folder and some output files? I noticed that > there is a "error: No such file or directory" error .... > > On 2/14/2022 8:46 PM, 정현우 wrote: > > External Email - Use Caution > Hi Dr. Greve, > > Thank you for your reply. I attached the fsgd file, mtx file and the > Xg.dat file below. > > Hyunwoo Jeong > > 2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve <dgr...@mgh.harvard.edu>님이 작성: > >> can you send your fsgd file and the Xg.dat file? >> >> On 2/14/2022 1:21 AM, 정현우 wrote: >> >> External Email - Use Caution >> Hello FreeSurfer Developers, >> >> I'm attempting to compare cortical surface area among three groups while >> controlling for estimated total intracranial volume (eTIV), as described on >> the Surface Based Group Analysis tutorial (*MailScanner has detected a >> possible fraud attempt from "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1duGCJ8g5oDH3kWtV2kE_IgOGbDv-Z7Oo1gugv3XGOPXCC_aHdLHeX_zWXCHyKuJTkhfKuLFJtTDCYzVitgEvcVchnOFddw57_ZJLQoy0-g2GSfjMtY0GaGQDOOed0PMy0iPrA3jB3gq2wx5hD3SExMDjKcx5lU881z3dQUOs-_kjzPapCw8TJr-brYJqmsshYuuweI_6hU6aixWkmw2o_yQSDK9be99hU89ZEV-lJkESCYdvWyl-8MW8ksqKo3V2WDdcU6gwnVMvOiFnCPc3QTSuMZnwinjJyETm_qhtviOSLT_aygP3eptRkxXNZdVLSIuhDFG55Q0BXXRCMvsGIg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0 >> <https://secure-web.cisco.com/1A0QSPCwnovVVVsFNKDP8OXxiBFqZ78jELzRvCgQt7us3rKayy2caTMVKC0nI4ildx0WJqzN5lLz1i-T5FHTbnyaiJAYj3f4mSQ4YHgEnKgBthfsubdAmofQmb_wxbJARZK70-yJh-Q-zB-SO-qUOdB5mSbQ71p0R-muUphnBpsvIZSn12rCp8u9iFutHnHZiR2SHvMYZrtWgA2qG1HwIVF7eXEz_S43Y9x_BasmQivW7O0E14rKYKn2Hc6i1PPi-krEJ-p90KuI4uEnOqU2T3HEQaZ4yicZdxZVpeFkSkL2Taw7LCrmTuBUijdwzR0I8MhzyhVIWFnyo-WUBgBXiig/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0> >> ). >> >> I ran the following command: >> >> mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd >> three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx >> --surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir >> --eres-save >> >> Then I got the following error: >> >> gdfRead(): reading three_group_comparison.area.fsgd >> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. >> Continuous Variable Means (all subjects) >> 0 eTIV 1.53351e+06 139455 >> Class Size and Means of each Continuous Variable >> 1 0 42 1566070.5417 >> 2 1 34 1515147.1360 >> 3 2 15 1483959.5000 >> INFO: gd2mtx_method is dods >> Reading source surface >> /media/sjkim/hd2/subject_data/fsaverage/surf/lh.white >> Number of vertices 163842 >> Number of faces 327680 >> Total area 65417.000000 >> AvgVtxArea 0.399269 >> AvgVtxDist 0.721953 >> StdVtxDist 0.195472 >> >> 7.2.0 >> cwd /media/sjkim/hd2/subject_data/glm >> cmdline mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd >> three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx >> --surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir >> --eres-save >> sysname Linux >> hostname sjkim-System-Product-Name >> machine x86_64 >> user sjkim >> FixVertexAreaFlag = 1 >> UseMaskWithSmoothing 1 >> OneSampleGroupMean 0 >> y >> /media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh >> logyflag 0 >> usedti 0 >> FSGD three_group_comparison.area.fsgd >> labelmask /media/sjkim/hd2/subject_data/fsaverage/label/lh.cortex.label >> maskinv 0 >> glmdir three_group_comparison.area.lh.glmdir >> IllCondOK 0 >> ReScaleX 1 >> DoFFx 0 >> Creating output directory three_group_comparison.area.lh.glmdir >> Loading y from >> /media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh >> ... done reading. >> INFO: gd2mtx_method is dods >> Saving design matrix to three_group_comparison.area.lh.glmdir/Xg.dat >> Computing normalized matrix >> Normalized matrix condition is 833.575 >> Matrix condition is 1e+08 >> Found 149955 points in label. >> Pruning voxels by thr: 1.175494e-38 >> Found 149953 voxels in mask >> Saving mask to three_group_comparison.area.lh.glmdir/mask.mgh >> Reshaping mriglm->mask... >> search space = 74612.059149 >> DOF = 85 >> Starting fit and test >> Fit completed in 0.0373833 minutes >> Computing spatial AR1 on surface >> Residual: ar1mn=0.997826, ar1std=0.000886, gstd=8.674183, fwhm=20.426140 >> Writing results >> three_group_comparison.area >> maxvox sig=3.0263 F=7.57212 at index 107440 0 0 seed=1645215319 >> error: No such file or directory >> error: MatrixMultiplyD(): m2 is null >> break >> /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596 >> >> I used FreeSurfer version 7.2.0 and Ubuntu 20.04. >> >> I've searched the mail archives and similar errors have been reported in >> qdec, but I could not find any specific solution for this problem. Do you >> have any suggestions to solve this problem? >> >> Thank you in advance, >> >> Hyunwoo Jeong >> >> _______________________________________________ >> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has >> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >> be* >> https://secure-web.cisco.com/1ulpvinyitIUSvjVtOCospKw5F9QAk0aSUu1I9W0LT9zZqmeQh0j3i1_P6BDSKt9FQjGQKm1GLvIR1BUwY6m2WYtmeOqyzUnOC-YSYOCYL_9mXf_yQRucxrykULk2wcgH_NoLncDJEd0o6cqq11JbusP1mncbZfaoT_j0orTXHlQj-NwJdkLeOzR75SznpiPkXIgl4IgTNjMSlgrIhmUwRmWkzOibNYL9WO5NQF5lgYoS0cSkAWhsMhRgVbfVR4DvDBbafLXgiMd1G3rfg15yqTGSAkljmzU9rAyrGCl-0VI0yv8pFnaGMWTRmTVqzA8IRseXLucArSyF4C_qGbp7IA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/1e2hDU-pnYJe1fZTYbCeBlfK68223y1O5DfBiwonrpaQSHY6Q3j3VKqXalKmXdsw9HmjYobBacaJAbaLnwTVgOfS1T8UlU40dkXAg_-wzY1-G3mi1doiY7vN21PStBnUczf8W4RHQs3SFLbtfc48KvoLzx6TJwv8kpW1tj8GpAUYBhn3OeH1hFQJqOBFGOiJTbVp9WbBhBn3ZXEn5Vw5LG24yxSw2rn-qJgw_tGDCIQ64Ab0bhJ1CB_avlMMLTABTi_pEGsLnkTnF0NgwN5v8hw8I3Ad2ks8uLacaRoPZzlpSBGVhwWaqU3reLUTgjRnsKy5HR9yiNEycyT7B-jP6Pw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1ulpvinyitIUSvjVtOCospKw5F9QAk0aSUu1I9W0LT9zZqmeQh0j3i1_P6BDSKt9FQjGQKm1GLvIR1BUwY6m2WYtmeOqyzUnOC-YSYOCYL_9mXf_yQRucxrykULk2wcgH_NoLncDJEd0o6cqq11JbusP1mncbZfaoT_j0orTXHlQj-NwJdkLeOzR75SznpiPkXIgl4IgTNjMSlgrIhmUwRmWkzOibNYL9WO5NQF5lgYoS0cSkAWhsMhRgVbfVR4DvDBbafLXgiMd1G3rfg15yqTGSAkljmzU9rAyrGCl-0VI0yv8pFnaGMWTRmTVqzA8IRseXLucArSyF4C_qGbp7IA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1e2hDU-pnYJe1fZTYbCeBlfK68223y1O5DfBiwonrpaQSHY6Q3j3VKqXalKmXdsw9HmjYobBacaJAbaLnwTVgOfS1T8UlU40dkXAg_-wzY1-G3mi1doiY7vN21PStBnUczf8W4RHQs3SFLbtfc48KvoLzx6TJwv8kpW1tj8GpAUYBhn3OeH1hFQJqOBFGOiJTbVp9WbBhBn3ZXEn5Vw5LG24yxSw2rn-qJgw_tGDCIQ64Ab0bhJ1CB_avlMMLTABTi_pEGsLnkTnF0NgwN5v8hw8I3Ad2ks8uLacaRoPZzlpSBGVhwWaqU3reLUTgjRnsKy5HR9yiNEycyT7B-jP6Pw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1ulpvinyitIUSvjVtOCospKw5F9QAk0aSUu1I9W0LT9zZqmeQh0j3i1_P6BDSKt9FQjGQKm1GLvIR1BUwY6m2WYtmeOqyzUnOC-YSYOCYL_9mXf_yQRucxrykULk2wcgH_NoLncDJEd0o6cqq11JbusP1mncbZfaoT_j0orTXHlQj-NwJdkLeOzR75SznpiPkXIgl4IgTNjMSlgrIhmUwRmWkzOibNYL9WO5NQF5lgYoS0cSkAWhsMhRgVbfVR4DvDBbafLXgiMd1G3rfg15yqTGSAkljmzU9rAyrGCl-0VI0yv8pFnaGMWTRmTVqzA8IRseXLucArSyF4C_qGbp7IA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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