Freesurfer June 2018

freesurfer@nmr.mgh.harvard.edu

105 participants
154 discussions

RA position at Ohio State
by Scott Hayes 21 Jun '18

21 Jun '18

External Email - Use Caution Research Assistant Position The Buckeye Brain Aging Lab (B-BAL) Department of Psychology Ohio State University Applications are being sought for a full-time research assistant position, in the Buckeye Brain Aging Lab (B-BAL) directed by Dr. Scott Hayes. The B-BAL studies the relationship among aging, physical activity, cognition and the brain [using Magnetic Resonance Imaging (MRI) metrics]. We also examine the neural correlates of memory in healthy and clinical populations. The Research Assistant 1 assists in the general coordination and conduct of research in the B-BAL, including administration of neuropsychological tests and/or questionnaires to young and older adults; recruits, screens, and schedules human subjects, including coordination of subject appointments (cognitive, MRI, and physical fitness assessments), subject payments, and submission of IRB amendments; assists with participant recruitment efforts between the laboratory and community partners; assists with research lab purchases and maintains lab supplies; assists with cognitive, MRI, and physical fitness data collection, including obtaining informed consent, cognitive testing (computer and paper and pencil based testing), MRI data acquisition, and record keeping; assists with cognitive and MRI data processing and analyses, supervises undergraduate research assistants. Desired qualifications include: Bachelor's degree in psychology, neuroscience, computer science, engineering, or physics; programming experience in either UNIX or MATLAB, as well as experience in neuroimaging data analyses; knowledge of software packages, such as FreeSurfer, FSL, AFNI, or SPM. The position is available for one year with the possibility of extension for additional years based on satisfactory performance and availability of funds. If you are interested in being considered for the position, please apply online at https://www.jobsatosu.com, under job listing #439956 and submit a current CV and the names of three references. If you have questions about the position or the lab, please contact Dr. Scott Hayes at hayes.1074(a)osu.edu *The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status.*

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Linear mixed modeling advice
by Mark Wagshul 20 Jun '18

20 Jun '18

External Email - Use Caution Hi. I am hoping someone out there can give me some advice on an analysis I'd like to try with our Freesurfer data. We have data (1 mm isotropic MPRAGE at 3T) on healthy older individuals, and have run them through the Freesurfer pipeline, generating cortical volume and thickness measurements. We are interested in studying the moderating effects of cortical atrophy on functional measures taken outside of the MRI. Our hypothesis is that the difference between two different functional measures is moderated by cortical volume/thickness. Thus it is really the interaction term = GM volume/thickness * task (binary 0/1) which we are after. So, we have fixed effects = GM volume/thickness, task, GM*task, age, .... Other covariates Random effects = subject. Repeated measure = task We have already run these analyses using mean cortical volume and thickness, as well as regional cortical volume and thickness in the PFC, and found very significant interaction effects. We would now like to refine these analyses with VBM/SBA analysis. I am hoping that someone can provide some guidance for us in terms of setting up such a model? (This is different from the standard LME analyses in which the imaging measure is the dependent variable. Here our dependent variable is our functional measure taken outside of the scanner, while the imaging measure - e.g. cortical thickness - is a moderating effect on the RHS of the equation. I'm not sure why this couldn't be done on a voxel-wise or vertex-wise basis, but hopefully someone can enlighten me if I'm being overly naive). Thanks in advance for the advice! Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einstein.yu.edu<mailto:mark.wagshul@einstein.yu.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

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Error with Hippocampal Subfields and Amygdala Nuclei
by Andrea, Nicolas 20 Jun '18

20 Jun '18

Hello, I am attempting to run two FS commands to provide data on the hippocampal subfields and the amygdala nuclei. I have run this on ~700 cases, but a few seem to have an error with the segmentation (see attached images for examples). Here is the script that I’ve run that shows where the data is and is run on the specific subject whose images are attached. This was written as a csh script. #Hippocampal subfields setenv SUBJECTS_DIR /autofs/space/rincewind_003/users/Amygdala/subjects source /usr/local/freesurfer/nmr-stable6-env recon-all -s HAB_133_FOK_2.1 -hippocampal-subfields-T1 -no-isrunning #Amygdala nuclei cd /autofs/space/rincewind_003/users/Amygdala/hippoAmyg ./segmentSubject.sh HAB_133_FOK_2.1 $SUBJECTS_DIR left ./segmentSubject.sh HAB_133_FOK_2.1 $SUBJECTS_DIR right If you have any insight on what might be going wrong with the segmentation, that would be most helpful. The recon-all.log is included. Thanks! Nick

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problem with mri_convert --conform?
by Weisholtz, Daniel S.,M.D. 20 Jun '18

20 Jun '18

Hello all, I am having a problem running recon-all with a particular subject due to a very large topological defect. I traced the problem to the white matter segmentation it it seems to be due to an inhomogeneity such that the WM is darker in the superior/anterior part of the brain and lighter in the inferior/posterior part of the brain. I was going to try to correct this problem with control points, but I discovered that starting with orig.mgz, all the brain volumes have a very reduced voxel intensity range (~166-168). rawavg.mgz has a much more typical-appearing voxel intensity range. So I think something is going wrong with the mri_convert --conform step that converts rawavg.mgz to orig.mgz. Since the control points seems to be incorporated at the autorecon2 stage, I’m not sure it would help here. I am attaching rawavg.mgz and orig.mgz. I am very grateful for your thoughts. Sincerely, Dan Weisholtz

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Recon-all using T1 & Flair images
by Heidi Lindroth 20 Jun '18

20 Jun '18

External Email - Use Caution Hi there, Does FreeSurfer have any documentation or validation studies published to support the processing of T1-only versus multi-modal T1 & Flair processing? Thank you, Heidi Lindroth BSN RN PhD Candidate| School of Nursing Program Assistant | School of Medicine and Public Health, Department of Anesthesiology Predoctoral Fellow | Veterans Administration (Madison WI) University of Wisconsin-Madison 701 Highland Avenue, Madison WI 53705 608-219-4294 | hlindroth(a)wisc.edu

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Longitudinal processing in v6.0 using manual edits from v5.3.0
by KALEY E ELLIS 19 Jun '18

19 Jun '18

External Email - Use Caution Hello FreeSurfer experts, We have a large dataset (n=140) that is being processed through the longitudinal pipeline. We have already generated the cross-sectionals and conducted manual edits to the bases in v5.3.0. What is the latest stage (cross, base, long) at which we are able to re-process our data in v6.0, and retain our manual edits, in order to reap the benefits of v6.0? It appears a similar question was asked about whether or not manual edits from an older version are retained and can be ran through recon-all with the newer version (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51197.html) and it appears yes they can. However, since we are using the longitudinal pipeline, we want to confirm the stage at which we can to run recon-all in v6.0. Thank you! Kaley Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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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. >

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Freesurfer June 2018