Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

Re: [Freesurfer] Recon-all exited with errors
by Hoopes, Andrew 19 Jun '18

19 Jun '18

Hi Ryan, this issue should be fixed in the freesurfer development version, but as a temporary fix to get things working in v6, I would suggest disabling SIP and rerunning: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection… best Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Ryan Flores <ryan10(a)stanford.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, June 18, 2018 at 1:07 PM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Recon-all exited with errors External Email - Use Caution Dear FS developers, I tried running recon-all using the -parallel flag over the weekend, but to my surprise they all exited with errors. I’m hoping the problem is something subtle, but I’m having trouble understanding the error log (please see attached). Can someone point out the issue? Thank you for your help. Best, Ryan -- Ryan Flores Clinical Research Coordinator

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Postdoctoral Fellowship in Neurobiological Bases of Reading (MRI and DTI)
by Clint Johns 19 Jun '18

19 Jun '18

External Email - Use Caution Dear colleagues, POSTDOCTORAL FELLOWSHIP IN NEUROIMAGING (MRI and DTI) The LandiLab (PI: Nicole Landi, PhD https://landi.lab.uconn.edu/) at Haskins Laboratories https://haskinslabs.org/ (which is closely affiliated with Yale University and the University of Connecticut) is seeking to hire a full-time postdoctoral research fellow. This postdoc will join a project investigating the neurobiological basis (brain structure, genetics) of reading. The successful applicant will be responsible for conducting and interpreting analyses of neuroimaging data (structural and diffusion imaging data). This position is part of a multi-site project (Haskins Laboratories, University of Houston, Baylor College of Medicine) that is aggregating and analyzing neuroimaging and genotyping data from multiple locations to explore gene-brain-behavior relationships. Applicants must have a background conducting research using MRI. The ideal candidate will also have experience with diffusion weighted imaging (DWI) and experience with advanced statistical analysis of imaging data (e.g. imaging-genetic analyses, Bayesian methods, machine learning). For details regarding required qualifications and application procedure, please visit: https://haskinslabs.org/postdoctoral-fellowship-neuroimaging-mri-and-dti Thank you! Clinton L. Johns, Ph.D. Research Scientist, Haskins Laboratories 300 George Street New Haven CT 06511 speech: 203-865-6163 x240 fax: 203-865-8963 net: johns(a)haskins.yale.edu

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Huge triangles in average template
by Dr. Konstantin Weise 19 Jun '18

19 Jun '18

External Email - Use Caution Dear Freesurfer team, in the left hemisphere of the average template in Brodmann area 4 (M1), there are some huge triangles, which make data analysis hard. I attached an example image to it. I was able to complete the whole pipeline, i.e. generating the template from some subjects and mapping the data to it using the following commands: > make_average_subject --out avg_template --subjects ... > mri_surf2surf --srcsubject ... --trgsubject ... --srcsurfval ... --trgsurfval ... --hemi lh --src_type curv --trg_type curv I already saw the bug in the shipped version of the freesurfer average template. Is there any way to solve this problem? Thank you very much for your assistance and best regards! Konstantin ----------------------------------------------------------- Dr.-Ing. Konstantin Weise Research group "Cortical Networks and Cognitive Functions" Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A, 04103 Leipzig, Germany Phone: +49 341 9940-2580 Fax: +49 341 9940-2624 Email: kweise(a)cbs.mpg.de

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Re: [Freesurfer] [Request of response] Fwd: Error during QDEC
by Douglas Greve 19 Jun '18

19 Jun '18

Those are the qdec tables, not the fsgd file. Look in the qdec output folder for a file called y.fsgd. Also please remember to post to the list and not to us personally On 6/15/18 12:40 AM, Seung-Gul Kang (강승걸) wrote: > > External Email - Use Caution > > Hi Doug, > > Thank you for your reply. > > I send my FSGD files. > sui3_qdec.table > sui5_qdec.table - This file contains the normalization of SSI score > (nrSSI). > > I want to see the correlation (or regression) between the brain > surface areas with significant difference between two groups and SSI > score. > When I enter 'SSI' or 'nrSSI' into covariate in QDEC, then error occurs. > > Best regards, > Seung-Gul > > *S**eung-Gul Kang, M.D., Ph.D. * > Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center > 연구부학장. Dean, Department of Research Affairs; Gachon University > College of Medicine > 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center > 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea > > ᐧ > > 2018년 6월 15일 (금) 오전 12:26, Douglas N. Greve <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>님이 작성: > > Please send the y.fsgd file > > > On 06/13/2018 09:30 PM, Seung-Gul Kang (강승걸) wrote: > > > > External Email - Use Caution > > > > Dear Freesurfer experts, > > > > I send you this e-mail again in anticipation of your help. > > > > I see the error message when I perform QDEC. > > The error message is as below. > > > > Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ > > > > cwd /home/sgk > > > > cmdline mri_glmfit --y > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods > > --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf > fsaverage lh > > --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > > > sysnameLinux > > > > hostname localhost.localdomain > > > > machinex86_64 > > > > usersgk > > > > FixVertexAreaFlag = 1 > > > > UseMaskWithSmoothing1 > > > > OneSampleGroupMean 0 > > > > y/mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > > > logyflag 0 > > > > usedti0 > > > > FSGD /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd > > > > labelmask/mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label > > > > maskinv 0 > > > > glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > > > IllCondOK 0 > > > > ReScaleX 1 > > > > DoFFx 0 > > > > Creating output directory /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > > > Loading y from /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > > > INFO: gd2mtx_method is dods > > > > Saving design matrix to > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/Xg.dat > > > > Normalized matrix condition is 24522.5 > > > > Design matrix ------------------ > > > > > 1.0000.0000.0000.00015.0000.0000.0000.00024.0000.0000.0000.00021.0000.0000.0000.000149457.5940.0000.0000.000; > > > > > 1.0000.0000.0000.00019.0000.0000.0000.00050.0000.0000.0000.00020.0000.0000.0000.000161540.2030.0000.0000.000; > > > > > 1.0000.0000.0000.0007.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000167295.9060.0000.0000.000; > > > > > 0.0000.0001.0000.0000.0000.00010.0000.0000.0000.00031.0000.0000.0000.00027.0000.0000.0000.000175241.7030.000; > > > > > 0.0000.0001.0000.0000.0000.00015.0000.0000.0000.00059.0000.0000.0000.00023.0000.0000.0000.000165616.7970.000; > > > > > 0.0000.0001.0000.0000.0000.00011.0000.0000.0000.00057.0000.0000.0000.00022.0000.0000.0000.000183255.5940.000; > > > > > 1.0000.0000.0000.00026.0000.0000.0000.00037.0000.0000.0000.00023.0000.0000.0000.000159212.2030.0000.0000.000; > > > > > 0.0000.0001.0000.0000.0000.00014.0000.0000.0000.00050.0000.0000.0000.00022.0000.0000.0000.000170017.0940.000; > > > > > 0.0000.0001.0000.0000.0000.00016.0000.0000.0000.00026.0000.0000.0000.00019.0000.0000.0000.000190217.9060.000; > > > > > 0.0000.0001.0000.0000.0000.0001.0000.0000.0000.00039.0000.0000.0000.00019.0000.0000.0000.000156341.0000.000; > > > > > 1.0000.0000.0000.00018.0000.0000.0000.00049.0000.0000.0000.00032.0000.0000.0000.000168844.2970.0000.0000.000; > > > > > 1.0000.0000.0000.00021.0000.0000.0000.00039.0000.0000.0000.00026.0000.0000.0000.000149945.4060.0000.0000.000; > > > > > 1.0000.0000.0000.00011.0000.0000.0000.00039.0000.0000.0000.00022.0000.0000.0000.000166132.9060.0000.0000.000; > > > > > 1.0000.0000.0000.00017.0000.0000.0000.00041.0000.0000.0000.00025.0000.0000.0000.000139924.4060.0000.0000.000; > > > > > 1.0000.0000.0000.00027.0000.0000.0000.00045.0000.0000.0000.00034.0000.0000.0000.000133331.7970.0000.0000.000; > > > > > 1.0000.0000.0000.00011.0000.0000.0000.00047.0000.0000.0000.00024.0000.0000.0000.000164844.7030.0000.0000.000; > > > > > 1.0000.0000.0000.00023.0000.0000.0000.00046.0000.0000.0000.00026.0000.0000.0000.000163024.2030.0000.0000.000; > > > > > 0.0000.0001.0000.0000.0000.00031.0000.0000.0000.00042.0000.0000.0000.00033.0000.0000.0000.000140203.7970.000; > > > > > 0.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00029.0000.0000.0000.000186282.2970.000; > > > > > 0.0000.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00017.0000.0000.0000.000171746.094; > > > > > 0.0001.0000.0000.0000.00017.0000.0000.0000.00034.0000.0000.0000.00015.0000.0000.0000.000145005.2030.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.00015.0000.0000.0000.00054.0000.0000.0000.00027.0000.0000.0000.000168633.203; > > > > > 0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00027.0000.0000.0000.00020.0000.0000.0000.000186731.297; > > > > > 0.0001.0000.0000.0000.0001.0000.0000.0000.00061.0000.0000.0000.00028.0000.0000.0000.000154627.5000.0000.000; > > > > > 0.0001.0000.0000.0000.00010.0000.0000.0000.00044.0000.0000.0000.00022.0000.0000.0000.000154626.2970.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.0004.0000.0000.0000.00059.0000.0000.0000.00020.0000.0000.0000.000177918.500; > > > > > 0.0001.0000.0000.0000.0004.0000.0000.0000.00056.0000.0000.0000.00027.0000.0000.0000.000157687.7970.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.0008.0000.0000.0000.00058.0000.0000.0000.00032.0000.0000.0000.000173899.094; > > > > > 0.0000.0000.0001.0000.0000.0000.00021.0000.0000.0000.00020.0000.0000.0000.00018.0000.0000.0000.000175980.500; > > > > > 0.0001.0000.0000.0000.0000.0000.0000.0000.00059.0000.0000.0000.00028.0000.0000.0000.000162526.7030.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.0002.0000.0000.0000.00037.0000.0000.0000.00020.0000.0000.0000.000198622.797; > > > > > 0.0001.0000.0000.0000.0003.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000157633.9060.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00021.0000.0000.0000.00021.0000.0000.0000.000164236.297; > > > > > 0.0001.0000.0000.0000.00022.0000.0000.0000.00046.0000.0000.0000.00023.0000.0000.0000.000144559.7030.0000.000; > > > > > 0.0001.0000.0000.0000.0007.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000156151.5000.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.00016.0000.0000.0000.00046.0000.0000.0000.00027.0000.0000.0000.000154306.406; > > > > > 0.0000.0000.0001.0000.0000.0000.0000.0000.0000.0000.00019.0000.0000.0000.00020.0000.0000.0000.000188334.203; > > > > > 0.0001.0000.0000.0000.00020.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000134977.4060.0000.000; > > > > -------------------------------- > > > > ERROR: matrix is ill-conditioned or badly scaled, condno = 24522.5 > > > > -------------------------------- > > > > Possible problem with experimental design: > > > > Check for duplicate entries and/or lack of range of > > > > continuous variables within a class. > > > > If you seek help with this problem, make sure to send: > > > > 1. Your command line: > > > > mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > --fsgd > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh > --label > > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > > > 2. The FSGD file (if using one) > > > > 3. And the design matrix above > > > > Error in Analyze: command failed: mri_glmfit --y > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh > --label > > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > > > I also attach the error message. > > > > Could you tell me how I can fix this problem? > > > > I am sincerely looking forward to receiving your reply. > > > > Best regards, > > Seung-Gul > > > > *S**eung-Gul Kang, M.D., Ph.D. * > > Psychiatrist, Professor; Department of Psychiatry, Gil Medical > Center > > 연구부학장. Dean, Department of Research Affairs; Gachon University > > College of Medicine > > 인천광역시자살예방센터장. Director, Incheon Suicide Prevention > Center > > 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, > South Korea > > > > ---------- Forwarded message --------- > > From: Seung-Gul Kang (강승걸) <sg.kang422(a)gmail.com > <mailto:sg.kang422@gmail.com> > > <mailto:sg.kang422@gmail.com <mailto:sg.kang422@gmail.com>>> > > Date: 2018년 6월 12일 (화) 오후 3:32 > > Subject: Error during QDEC > > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > > > > Dear Freesurfer experts, > > > > I see the error message when I perform QDEC. > > The error message is as below. > > > > Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ > > > > cwd /home/sgk > > > > cmdline mri_glmfit --y > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods > > --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf > fsaverage lh > > --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C > > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > > > > > > sysnameLinux > > > > hostname localhost.localdomain > > > > machinex86_64 > > > > usersgk > > > > FixVertexAreaFlag = 1 > > > > UseMaskWithSmoothing1 > > > > OneSampleGroupMean 0 > > > > y/mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > > > logyflag 0 > > > > usedti0 > > > > FSGD /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd > > > > labelmask/mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label > > > > maskinv 0 > > > > glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > > > IllCondOK 0 > > > > ReScaleX 1 > > > > DoFFx 0 > > > > Creating output directory /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > > > Loading y from /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > > > INFO: gd2mtx_method is dods > > > > Saving design matrix to > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/Xg.dat > > > > Normalized matrix condition is 24522.5 > > > > Design matrix ------------------ > > > > > 1.0000.0000.0000.00015.0000.0000.0000.00024.0000.0000.0000.00021.0000.0000.0000.000149457.5940.0000.0000.000; > > > > > 1.0000.0000.0000.00019.0000.0000.0000.00050.0000.0000.0000.00020.0000.0000.0000.000161540.2030.0000.0000.000; > > > > > 1.0000.0000.0000.0007.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000167295.9060.0000.0000.000; > > > > > 0.0000.0001.0000.0000.0000.00010.0000.0000.0000.00031.0000.0000.0000.00027.0000.0000.0000.000175241.7030.000; > > > > > 0.0000.0001.0000.0000.0000.00015.0000.0000.0000.00059.0000.0000.0000.00023.0000.0000.0000.000165616.7970.000; > > > > > 0.0000.0001.0000.0000.0000.00011.0000.0000.0000.00057.0000.0000.0000.00022.0000.0000.0000.000183255.5940.000; > > > > > 1.0000.0000.0000.00026.0000.0000.0000.00037.0000.0000.0000.00023.0000.0000.0000.000159212.2030.0000.0000.000; > > > > > 0.0000.0001.0000.0000.0000.00014.0000.0000.0000.00050.0000.0000.0000.00022.0000.0000.0000.000170017.0940.000; > > > > > 0.0000.0001.0000.0000.0000.00016.0000.0000.0000.00026.0000.0000.0000.00019.0000.0000.0000.000190217.9060.000; > > > > > 0.0000.0001.0000.0000.0000.0001.0000.0000.0000.00039.0000.0000.0000.00019.0000.0000.0000.000156341.0000.000; > > > > > 1.0000.0000.0000.00018.0000.0000.0000.00049.0000.0000.0000.00032.0000.0000.0000.000168844.2970.0000.0000.000; > > > > > 1.0000.0000.0000.00021.0000.0000.0000.00039.0000.0000.0000.00026.0000.0000.0000.000149945.4060.0000.0000.000; > > > > > 1.0000.0000.0000.00011.0000.0000.0000.00039.0000.0000.0000.00022.0000.0000.0000.000166132.9060.0000.0000.000; > > > > > 1.0000.0000.0000.00017.0000.0000.0000.00041.0000.0000.0000.00025.0000.0000.0000.000139924.4060.0000.0000.000; > > > > > 1.0000.0000.0000.00027.0000.0000.0000.00045.0000.0000.0000.00034.0000.0000.0000.000133331.7970.0000.0000.000; > > > > > 1.0000.0000.0000.00011.0000.0000.0000.00047.0000.0000.0000.00024.0000.0000.0000.000164844.7030.0000.0000.000; > > > > > 1.0000.0000.0000.00023.0000.0000.0000.00046.0000.0000.0000.00026.0000.0000.0000.000163024.2030.0000.0000.000; > > > > > 0.0000.0001.0000.0000.0000.00031.0000.0000.0000.00042.0000.0000.0000.00033.0000.0000.0000.000140203.7970.000; > > > > > 0.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00029.0000.0000.0000.000186282.2970.000; > > > > > 0.0000.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00017.0000.0000.0000.000171746.094; > > > > > 0.0001.0000.0000.0000.00017.0000.0000.0000.00034.0000.0000.0000.00015.0000.0000.0000.000145005.2030.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.00015.0000.0000.0000.00054.0000.0000.0000.00027.0000.0000.0000.000168633.203; > > > > > 0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00027.0000.0000.0000.00020.0000.0000.0000.000186731.297; > > > > > 0.0001.0000.0000.0000.0001.0000.0000.0000.00061.0000.0000.0000.00028.0000.0000.0000.000154627.5000.0000.000; > > > > > 0.0001.0000.0000.0000.00010.0000.0000.0000.00044.0000.0000.0000.00022.0000.0000.0000.000154626.2970.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.0004.0000.0000.0000.00059.0000.0000.0000.00020.0000.0000.0000.000177918.500; > > > > > 0.0001.0000.0000.0000.0004.0000.0000.0000.00056.0000.0000.0000.00027.0000.0000.0000.000157687.7970.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.0008.0000.0000.0000.00058.0000.0000.0000.00032.0000.0000.0000.000173899.094; > > > > > 0.0000.0000.0001.0000.0000.0000.00021.0000.0000.0000.00020.0000.0000.0000.00018.0000.0000.0000.000175980.500; > > > > > 0.0001.0000.0000.0000.0000.0000.0000.0000.00059.0000.0000.0000.00028.0000.0000.0000.000162526.7030.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.0002.0000.0000.0000.00037.0000.0000.0000.00020.0000.0000.0000.000198622.797; > > > > > 0.0001.0000.0000.0000.0003.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000157633.9060.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00021.0000.0000.0000.00021.0000.0000.0000.000164236.297; > > > > > 0.0001.0000.0000.0000.00022.0000.0000.0000.00046.0000.0000.0000.00023.0000.0000.0000.000144559.7030.0000.000; > > > > > 0.0001.0000.0000.0000.0007.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000156151.5000.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.00016.0000.0000.0000.00046.0000.0000.0000.00027.0000.0000.0000.000154306.406; > > > > > 0.0000.0000.0001.0000.0000.0000.0000.0000.0000.0000.00019.0000.0000.0000.00020.0000.0000.0000.000188334.203; > > > > > 0.0001.0000.0000.0000.00020.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000134977.4060.0000.000; > > > > -------------------------------- > > > > ERROR: matrix is ill-conditioned or badly scaled, condno = 24522.5 > > > > -------------------------------- > > > > Possible problem with experimental design: > > > > Check for duplicate entries and/or lack of range of > > > > continuous variables within a class. > > > > If you seek help with this problem, make sure to send: > > > > 1. Your command line: > > > > mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > --fsgd > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh > --label > > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C > > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat--C > > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > > > > > > 2. The FSGD file (if using one) > > > > 3. And the design matrix above > > > > Error in Analyze: command failed: mri_glmfit --y > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh > --label > > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C > > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > > > I also attach the error message. > > > > Could you tell me how I can fix this problem? > > > > I am looking forward to receiving your reply. > > > > Best regards, > > Seung-Gul > > > > *S**eung-Gul Kang, M.D., Ph.D. * > > Psychiatrist, Professor; Department of Psychiatry, Gil Medical > Center > > 연구부학장. Dean, Department of Research Affairs; Gachon University > > College of Medicine > > 인천광역시자살예방센터장. Director, Incheon Suicide Prevention > Center > > 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, > South Korea > > > > ᐧ > > ᐧ > > > > 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. >

3 3

Can freesurfer work well to T1 images without TR/TE/TI and flip angle information？
by He Chen 18 Jun '18

18 Jun '18

External Email - Use Caution Hi freesurfer experts, The recon-all command was conducted to my data by: recon-all -all -s sub1 -i anat.nii . But freesurfer seems to not be able to read the TR/TE/TI and flip angle information in the .nii file. Or there is no information about TR/TE/TI or flip angle stored in the .nii file. Although the terminal told me recon-all finished without errors, I think there still may be some implicit and fatal errors. I want to know whether all the processing steps in 'recon-all -all' command can work appropriately without TR/TE/TI and flip angle information? See the recon-all.log file: +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ... reading from /media/emily/DATA_Storage/test_freeview/sub1/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 ... recon-all -s sub1 finished without error at Fri Jun 15 04:36:11 CST 2018 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Thank you! He

3 2

Re: [Freesurfer] Questions regarding Permutation and Monte Carlo simulation
by Douglas N. Greve 18 Jun '18

18 Jun '18

Hi Lea, I'm cc'ing the list so that others can benefit. On 06/13/2018 12:28 PM, Backhausen, Lea wrote: > > > Hey Doug, > > Thanks for your helpful suggestions on Monte Carlo simulation and > permutation you gave in the Mailing List! > > I have some follow-up questions, also regarding your recently > published paper about false positive rates > (https://www.sciencedirect.com/science/article/pii/S1053811917310960) > > 1) Concerning Monte Carlo simulation where you said even 1000 > iterations would be okay: What will the difference be between 1000 and > 10,000 iterations? I read in the tutorial that >5000 are recommended? > This has to do with the precision of the cluster p-value Since you are doing a simulation, the p-value is subject to sampling error. If you look in the output file, you will see that I give 95% confidence intervals for the p-value, so as long as the high range is less than .05, then it should be ok. I think 1000 is probably fine. > > 2) In your paper you write that permutation requires that data is > exchangeable across subjects and that age effects may be a problem. In > our study we want to compare adolescent patients with ADHD and conduct > disorder with typically developing adolescents. In this context, data > would not be exchangeable across subjects, right? Could we still use > permutation? > Exchangeability is a very complicated subject and not very intuitive. It is too complicated to get into here. I suggest reading up on it a little. It does not mean that you can swap groups without there being any effect. > > 3) When using the CFT thresholds with Monte Carlo simulation you > recommend in your paper, do you still only report clusters with > CWP<.05 or is the CWP less important when using stricter thresholds? > Generally, CWP must be less than 0.05 for publication. Sometimes people will show results with more liberal p-values (eg, 0.1) to show "trends". It all depends on what you can get past your reviewers:). doug > > Thank you so much for your input! > > Best > > Lea Backhausen > > ------------------------------ > > Lea Backhausen > > Research Assistant > > Department of Child and Adolescent Psychiatry, Faculty of Medicine of > the TU Dresden, Germany > http://www.uniklinikum-dresden.de <http://www.uniklinikum-dresden.de/> >

1 0

mri_glmfit ERROR no voxels found
by Marine Boudot de la Motte 18 Jun '18

18 Jun '18

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to do a Surface-based analysis on Freesurfer while projecting MTR MRI sequences. I have followed all the steps explained in the group analysis tutorials, and the mri_preproc seems to have ran correctly but once the mri_glmfit is launched i get the following error : Computing normalized matrix Normalized matrix condition is 38.1502 Matrix condition is 1.78431e+12 Found 149926 points in label. Pruning voxels by thr: 1.175494e-38 Found 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input I've searched the list but didn't find an answer. Does anyone have any clue on how to solve this problem ? Thank you very much for your help, Marine

3 3

Re: [Freesurfer] Longitudinal analysis of multiple scanner acquisitions
by zalewk 18 Jun '18

18 Jun '18

External Email - Use Caution Hello Freesurfer Team, Sorry to bother you guys again, any word on what you think is the best approach going forward here? Best, Kody Zalewski ________________________________ From: zalewk Sent: Thursday, June 7, 2018 10:39 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Longitudinal analysis of multiple scanner acquisitions Good afternoon Freesurfer team, I want to run the longitudinal pipeline on multiple groups of subjects, the problem is we are at the mercy of the scanners available to us at the various time-points. We have two different Siemens 1.5 scanners (same type of scanner, there was an effort made to match them) at time point 1 and 2 with a Phillips 3T at time point 3. Is it worth the time to attempt a longitudinal analysis on this cohort? Best, Kody Zalewski

2 1

Running qcache on old FS data
by Jamie Hanson 18 Jun '18

18 Jun '18

External Email - Use Caution Hello all, I was trying to run qcache on some previously processed Freesurfer data from a colleague, but ran into some issues with missing files and wondered how best to proceed. Details: -The data was processed with (Freesurfer) v4.5.0 and I would ideally like to not reprocess it with a newer version (to keep in concordance with past published work, and also it's a large number of subjects, n=800+). -The qcache flag was not used with the data previously (to my knowledge), so I was attempting to run this command: recon-all -s $subj -qcache -When I try that command, I get an error regarding a missing lh.white.K file. I've uploaded the log file here: https://www.dropbox.com/s/94mnsy7wrps5ce2/recon-all.log?dl=0 I wondered if it was possible to complete qcache with the data as is? I searched on the list previously and saw one or two other folks had run into this issues; I, however, didn't see a final solution to things. Any thoughts or suggestions are greatly appreciated! Thanks much! Best, Jamie. -- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh Personal website: jamiehanson.org

2 4

Recon-all exited with errors
by Ryan Flores 18 Jun '18

18 Jun '18

External Email - Use Caution Dear FS developers, I tried running recon-all using the -parallel flag over the weekend, but to my surprise they all exited with errors. I’m hoping the problem is something subtle, but I’m having trouble understanding the error log (please see attached). Can someone point out the issue? Thank you for your help. Best, Ryan -- Ryan Flores Clinical Research Coordinator

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