Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

colour scale
by Trisanna Sprung-Much 13 Sep '16

13 Sep '16

Hi there is there a way to view a colour scale bar in Freeview rather than Tksurfer, for instance, for a probability map? I can alter the Min and Max by "Configure Overlay" but cannot seem to display the bar next to my surface. Many thanks Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

2 6

Pial surface vs. aparc+aseg
by Nosal, Eryka [PSY] 13 Sep '16

13 Sep '16

Hi, I'm very new to Freesurfer, and I am trying to get subject-specific masks from the output of recon all that I can use on my functional data. I was going to isolate regions from the aparc+aseg files to create the ROIs. In my visual checks, I noticed that the pial surface often leaves off parts of the amygdala and hippocampus even though they are contained within the correct label of the aparc+aseg image. For my purposes, should I be concerned that these regions are not contained within the surface? Sincerely, Eryka Nosal Research Tech The University of Chicago Department of Psychiatry & Behavioral Neuroscience Clinical Neuroscience & Psychopharmacology Research Unit (CNPRU) Phone: (773) 834-4113 Website: http://cnpru.bsd.uchicago.edu/research.html ******************************************************************************** This e-mail is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this e-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is prohibited. If you have received this e-mail in error, please notify the sender and destroy all copies of the transmittal. Thank you University of Chicago Medicine and Biological Sciences ********************************************************************************

2 1

Some volumes not loading (corrupted?)
by Rachel Romeo 13 Sep '16

13 Sep '16

Hi all, After doing some manual edits to the wm and pial masks, I recently had a recon fail with the following error: mghRead(/subject_177/mri/brainmask.mgz, -1): read error Invalid argument mri_em_register: could not open mask volume brainmask.mgz. When trying to load either the brainmask.mgz or wm.mgz into freeview, these also fail, e.g.: mghRead(/subject_177/mri/brainmask.mgz, -1): read error MRIread failed: Unable to read from /subject_177/mri/brainmask.mgz All other volumes load fine. Can you think of what I might have done to corrupt these volumes? And is there a way to revert to the most recent version, so that I don't lose previous edits? Thanks so much, Rachel

2 1

cannot read white surface
by Claudia Dacquino 13 Sep '16

13 Sep '16

Hi freesurfers, I'm trying to create an average subject for GLM analysis from my group, using make_average_subject --out newtemplate and I got this error: Reading surface /media/TREKSTOR/SUBJ/newtemplate/surf/lh.white No such file or directory ERROR: could not read /media/TREKSTOR/SUBJ/newtemplate/surf/lh.white ERROR: make_average_surface Any ideas on what the problem is? Why cannot find white surface? I'm using 5.1 version, but I got the same problem with version 5.3. Thanks to all. Claudia -- Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia Laboratorio di Neuropsichiatria Dipartimento di Neurologia Clinica e Comportamentale IRCCS Fondazione Santa Lucia via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 51501575 web: http://www.neuropsichiatrialab.com <http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli>

2 1

cannot read white surface
by Claudia Dacquino 13 Sep '16

13 Sep '16

1 0

Job posting
by Ansgar Furst 12 Sep '16

12 Sep '16

DEPARTMENT OF VETERANS AFFAIRS Palo Alto WRIISC Special Postdoctoral Fellowship Program in Advanced Neuroimaging The Office of Academic Affiliations, Department of Veterans Affairs (VA), is now accepting applications for a two-year Postdoctoral Fellowship Training Program in advanced neuroimaging with an emphasis on Traumatic Brain Injury (TBI), Posttraumatic stress disorder (PTSD), cognitive impairment and chronic pain. The Fellowship can begin between January 1st and August 31st, 2017. This is a joint fellowship between VA Palo Alto War Related Illness and Injury Study Center (WRIISC) and the Department of Psychiatry and Behavioral Sciences at Stanford University. The VAPA-WRIISC-SFP site is linked to the two other WRIISC fellowship sites (Washington, DC, East Orange, NJ) as well as the VA Mental Illness Research, Education, and Clinical Center (MIRECC) fellowship program (based at Palo Alto) for didactic, academic, and research efforts. The Palo Alto WRIISC specializes in integrating anatomical/functional Magnetic Resonance Imaging (MRI) and Positron Emission Tomography (PET) to improve the diagnostic/prognostic value of neuroimaging in the clinical setting. The fellowship provides a unique opportunity to (a) receive training in Diffusion Tensor Imaging (DTI), functional Magnetic Resonance Imaging (fMRI), Voxel-based morphometry (VBM) and amyloid imaging from a team of experienced neuroimagers and (b) relate neuroimaging findings to clinical cases in consensus conferences with our team of neurologists, nurse practitioners, psychiatrists & psychologists. We are interested in the relationship between TBI/PTSD and a potentially increased risk for Alzheimer’s disease and have recently received funding to explore this question using amyloid PET imaging. Our team of investigators is also part of the Alzheimer’s Disease Neuroimaging Initiative (ADNI). There are additional opportunities to explore projects in psychology and dementia with WRIISC, MIRECC, and Stanford faculty. In collaboration with their mentors, fellows will develop and conduct a research project, publish and present findings, participate in grant writing, and utilize the latest technologies for research (5 MRI scanners including a brand new PET-MR unit). Applicants must be US citizens. The ideal candidate will have a Ph.D. in cognitive neuroscience, computer science, psychology, or a related discipline. Prior experience in neuroimaging is essential. Experience with Linux, MATLAB, SPM8/12, FreeSurfer v5.3.0 & FSL v5.0 is highly desirable and programming skills would be a big plus. A. To be eligible to apply for the WRIISC Fellowship Program you must hold a PhD in one of the above described disciplines and be able to provide evidence of U.S. citizenship. B. Applications must be received by December 1st, 2016. Applicants must submit: a) a letter confirming they can fulfill the eligibility requirements; b) a personal statement describing their interest in the Fellowship; c) 3 letters of recommendation; and d) a current curriculum vitae. These materials can be submitted directly to the PhD Fellowship Program Director: Ansgar Furst, PhD at ansgar.furst(a)va.gov. C. If the applicant is identified as the candidate of choice for this site, they will be required to produce all documents listed in the above section A and the following additional documents: Transcripts from all educational institutions VA Form 10-2850d, “Application for Health Professions Trainees.” For more information, please contact Ansgar Furst, PhD at the WRIISC Palo Alto Fellowship site, (650) 493-5000, "1", "1" then x68652 or ansgar.furst(a)va.gov. See also: http://www.warrelatedillness.va.gov/

1 0

Postdoc and Research Assistant openings in cognitive neuroscience at UCSF/Stanford
by Zhichao Xia 12 Sep '16

12 Sep '16

Please respond to info(a)brainlens.org *Research Assistant Position at UCSF in California, USA on Multilingualism* The Hoeft Lab (http://brainLENS.org <http://brainlens.org/> PI: Fumiko Hoeft MD PhD) is looking for an exceptional research assistant interested in the developmental cognitive neuroscience of multilingualism. This NIH-funded research is in collaboration with Cammie McBride PhD of Chinese Univ of Hong Kong, Ken Pugh PhD of Haskins/Yale/UConn, Linda Siegel of UBC, Manolo Carreiras PhD of BCBL, Ioulia Kovelman PhD of U Michigan, and Yuuko Uchikoshi EdD of UC Davis. The position is suited for a self-motivated, organized and independent thinker, with good interpersonal and multitasking skills, as well as proficiency in the English language and computer software. Neuroimaging, computational, statistical, programming, and neuropsych testing skills are highly desired but not necessary. Native-like proficiency in Spanish or Cantonese is a plus. A major strength of our lab is that there are plenty of opportunities to conduct independent research, to be first author on publications and to give conference presentations as a novice RA (e.g. Myers et al. Psychol Sci ’14, Myers et al. SCAN ’16, Haft et al. Curr Opin Behav Sci ’16). The position begins in January but start date can be sooner and is negotiable. Please email info(a)brainlens.org with a cover letter and your CV. Please add “[RA job]” and your full name in the Subject of the email. Qualified candidates will be asked to have 2-3 letters of reference forwarded. *Joint Postdoctocal Position at UCSF and Stanford University in California, USA* The Hoeft Lab (http://brainLENS.org <http://brainlens.org/> PI: Fumiko Hoeft MD PhD) at the UCSF Dept of Psychiatry and Weill Institute for Neurosciences in collaboration with the Stanford Mood and Anxiety Disorders Lab in the Dept of Psychology (http://goo.gl/dc96Cx PI: Ian Gotlib PhD) is looking for an exceptional postdoc in the field of affective neuroscience, with advanced neuroimaging, psychophysiology, computational, programming and organizational skills. Training in genetics is a plus. The primary project that the postdoc will be responsible for is the examination of intergenerational neuroimaging using a ‘natural’ cross-fostering design that allows dissociation of genetic, prenatal and postnatal environment on brain networks that are transmitted across generations. Related articles from our lab can be found here - Yamagata et al. J Neurosci 2016 (http://goo.gl/vMK8iy) Ho et al. Trends in Neurosci 2016 (http://goo.gl/SyXLcK) and Scientific American (http://goo.gl/YTiH6D) There are other funded opportunities to be involved in research that examines the impact of anxiety and stereotype on psychophysiology and cognitive processes. The position can begin immediately. Please email info(a)brainlens.org with your CV, and with brief paragraphs of research interests, career goals and why you feel you are a good fit for the lab. Please add “[Postdoc job]” and your full name in the Subject of the email. Qualified candidates will be asked to have 3 letters of reference forwarded. -- *Zhichao Xia* National Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University Center for Collaboration and Innovation in Brain and Learning Sciences, Beijing Normal University Division of Child and Adolescent Psychiatry, Department of Psychiatry, UCSF Mobile: +1 (415) 712-3749; +86 13720002046 E-mail: <xiazc_psy(a)163.com>xiazc_psy(a)163.com; xiazc.psy(a)gmail.com; Zhichao.Xia(a)ucsf.edu

1 0

Re: [Freesurfer] mris_anatomical_stats
by Arkadiy Maksimovskiy 12 Sep '16

12 Sep '16

Hi Bruce, Thank you so much for this suggestion. In case anyone searches for this thread in the future, I am writing back to report that it worked and thickness indices remain the same (although other indices, which are of no interest to me for this analysis, did change). Best, Arkadiy

1 0

Re: [Freesurfer] Qdec Error: Couldn't open qcache file
by Jana Dinges 12 Sep '16

12 Sep '16

1 0

ERROR again
by Seung Gul Kang 12 Sep '16

12 Sep '16

Dear Douglas Greve and FS team, I send this e-mail again since I was afraid that you would not receive my previous e-mail. I am sorry if you got the previous e-mail and are figuring this problem out. I am looking forward to receive your reply regarding to the solution. Thank you. Best, Seung-Gul --- *Seung Gul Kang, M.D., Ph.D. * *Psychiatrist, Associate Professor*; Department of Psychiatry, Gil Medical Center, Gachon University, School of Medicine, 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea *Research scholar*; Sleep Disorders Clinical Research Program, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 1 Bowdoin Square, 9th floor, Boston, MA 02114, USA *Collaboration researcher*; Division of Sleep & Circadian Disorders, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston MA 02115 ---------- Forwarded message ---------- From: Seung Gul Kang <sg.kang422(a)gmail.com> Date: 2016-09-10 17:49 GMT-04:00 Subject: Re: [Freesurfer] ERROR: matrix is ill-conditioned or badly scaled, condno = 22801.1 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Dear Douglas Greve, Thank you so much for your answer. But, unfortunately it did not work. The problem develops when I put bhth (global thickness) as a covariate. (I want to control age, sex, BDINS, and bhth for the comparison between two groups.) If I don't put bhth as a covariate, there is no problem. And, inerestingly, if I put only bhth as a covariate (without putting other covariates), the error does not develop. Does the normalization mean the log (bhth)? I changed the bhth into log (bhth) and ran qdec again. However, the error appeared again as below. (Actually, the bhth already shows normal distribution in spss.) I am afraid that normalization would not be solution. Please see the file 1 (my FSGD file) and 2 (FSGD file made in qdec folder). Normalized matrix condition is 16920.4 Design matrix ------------------ 1.000 0.000 0.000 0.000 27.000 0.000 0.000 0.000 3.000 0.000 0.000 0.000 0.415 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 28.000 0.000 0.000 0.000 4.000 0.000 0.000 0.000 0.387 0.000; 1.000 0.000 0.000 0.000 25.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.400 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 26.000 0.000 0.000 0.000 7.000 0.000 0.000 0.000 0.399 0.000; 1.000 0.000 0.000 0.000 35.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.390 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 30.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.376 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.385 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.379 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 28.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.372 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 33.000 0.000 0.000 0.000 2.000 0.000 0.000 0.000 0.379 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 45.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.362 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 38.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.362 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.394 0.000; 1.000 0.000 0.000 0.000 28.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.364 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 30.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.390 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 39.000 0.000 0.000 0.000 3.000 0.000 0.000 0.000 0.348 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 48.000 0.000 0.000 0.000 4.000 0.000 0.000 0.000 0.382 0.000; 1.000 0.000 0.000 0.000 32.000 0.000 0.000 0.000 3.000 0.000 0.000 0.000 0.374 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 32.000 0.000 0.000 0.000 4.000 0.000 0.000 0.000 0.399 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 31.000 0.000 0.000 0.000 2.000 0.000 0.000 0.000 0.376 0.000; 1.000 0.000 0.000 0.000 33.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.378 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 33.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.405 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 44.000 0.000 0.000 0.000 4.000 0.000 0.000 0.000 0.359 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 41.000 0.000 0.000 0.000 2.000 0.000 0.000 0.000 0.384 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 41.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.381 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 43.000 0.000 0.000 0.000 3.000 0.000 0.000 0.000 0.384 0.000; 0.000 1.000 0.000 0.000 0.000 21.000 0.000 0.000 0.000 10.000 0.000 0.000 0.000 0.382 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 46.000 0.000 0.000 0.000 13.000 0.000 0.000 0.000 0.382; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 41.000 0.000 0.000 0.000 8.000 0.000 0.000 0.000 0.379; 0.000 1.000 0.000 0.000 0.000 29.000 0.000 0.000 0.000 13.000 0.000 0.000 0.000 0.382 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 39.000 0.000 0.000 0.000 12.000 0.000 0.000 0.000 0.376 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 27.000 0.000 0.000 0.000 6.000 0.000 0.000 0.000 0.374 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 57.000 0.000 0.000 0.000 11.000 0.000 0.000 0.000 0.368 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000 7.000 0.000 0.000 0.000 0.374 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 31.000 0.000 0.000 0.000 11.000 0.000 0.000 0.000 0.366; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 23.000 0.000 0.000 0.000 11.000 0.000 0.000 0.000 0.402; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 34.000 0.000 0.000 0.000 11.000 0.000 0.000 0.000 0.373; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 32.000 0.000 0.000 0.000 10.000 0.000 0.000 0.000 0.411; 0.000 1.000 0.000 0.000 0.000 37.000 0.000 0.000 0.000 2.000 0.000 0.000 0.000 0.409 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 46.000 0.000 0.000 0.000 5.000 0.000 0.000 0.000 0.380; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 48.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.375; 0.000 1.000 0.000 0.000 0.000 42.000 0.000 0.000 0.000 3.000 0.000 0.000 0.000 0.392 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 54.000 0.000 0.000 0.000 8.000 0.000 0.000 0.000 0.388; 0.000 1.000 0.000 0.000 0.000 30.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.394 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 36.000 0.000 0.000 0.000 12.000 0.000 0.000 0.000 0.379; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 34.000 0.000 0.000 0.000 9.000 0.000 0.000 0.000 0.362; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 38.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.407; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 16920.4 -------------------------------- 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/kang_fs/qdec/Untitled/y.mgh --fsgd /mnt/hgfs/share/kang_fs/qdec/Untitled/qdec.fsgd dods --glmdir /mnt/hgfs/share/kang_fs/qdec/Untitled --surf fsaverage lh --label /mnt/hgfs/share/kang_fs/fsaverage/label/lh.aparc.label --C /mnt/hgfs/share/kang_fs/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /mnt/hgfs/share/kang_fs/qdec/Untitled/contrasts/lh-Diff-H-I-Intercept-thickness.mat --C /mnt/hgfs/share/kang_fs/qdec/Untitled/contrasts/lh-Diff-M-F-Intercept-thickness.mat --C /mnt/hgfs/share/kang_fs/qdec/Untitled/contrasts/lh-X- diagnosis-sex-Intercept-thickness.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/kang_fs/qdec/Untitled/y.mgh --fsgd /mnt/hgfs/share/kang_fs/qdec/Untitled/qdec.fsgd dods --glmdir /mnt/hgfs/share/kang_fs/qdec/Untitled --surf fsaverage lh --label /mnt/hgfs/share/kang_fs/fsaverage/label/lh.aparc.label --C /mnt/hgfs/share/kang_fs/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /mnt/hgfs/share/kang_fs/qdec/Untitled/contrasts/lh-Diff-H-I-Intercept-thickness.mat --C /mnt/hgfs/share/kang_fs/qdec/Untitled/contrasts/lh-Diff-M-F-Intercept-thickness.mat --C /mnt/hgfs/share/kang_fs/qdec/Untitled/contrasts/lh-X- diagnosis-sex-Intercept-thickness.mat After error message, I tried to put two lines into my FSGD file (file 3) I put two lines into the below of the variables of the last subject. But, I saw the error message again as below (blue letters). Please check the file 3 (my FSGD file) and file 4 (made by qdec fsgd file). ============================================================ Data table loading completed successfully. SUBJECTS_DIR is '/mnt/hgfs/share/kang_fs' ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels ninputs = 47 Checking inputs nframestot = 47 Allocing output Done allocing nframes = 47 Writing to /mnt/hgfs/share/kang_fs/qdec/Untitled/y.mgh gdfReadHeader: reading /mnt/hgfs/share/kang_fs/qdec/Untitled/qdec.fsgd WARNING: gdfReadV1: class diagnosis1-sexM is defined but not used. INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 34.7021 8.43225 1 BDINS 4.46809 4.30661 2 bhth 2.41468 0.0807373 Class Means of each Continuous Variable 1 diagnosisH-sexM 31.2727 1.5455 2.4318 2 diagnosisI-sexM 34.0000 7.1111 2.4200 3 diagnosis1-sexM -nan -nan -nan 4 diagnosisH-sexF 34.5333 2.0000 2.3940 5 diagnosisI-sexF 38.5833 8.2500 2.4208 6 diagnosis1-sexF -nan -nan -nan INFO: gd2mtx_method is dods Reading source surface /mnt/hgfs/share/kang_fs/fsaverage/surf/lh.white ERROR: no contrasts specified. Error in Analyze: command failed: mri_glmfit --y /mnt/hgfs/share/kang_fs/qdec/Untitled/y.mgh --fsgd /mnt/hgfs/share/kang_fs/qdec/Untitled/qdec.fsgd dods --glmdir /mnt/hgfs/share/kang_fs/qdec/Untitled --surf fsaverage lh --label /mnt/hgfs/share/kang_fs/fsaverage/label/lh.aparc.label I hope that you could solve this problem. I will really appreciate if you help. Best, Seung-Gul ᐧ --- *Seung Gul Kang, M.D., Ph.D. * *Psychiatrist, Associate Professor*; Department of Psychiatry, Gil Medical Center, Gachon University, School of Medicine, 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea *Research scholar*; Sleep Disorders Clinical Research Program, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 1 Bowdoin Square, 9th floor, Boston, MA 02114, USA *Collaboration researcher*; Division of Sleep & Circadian Disorders, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston MA 02115 2016-09-10 11:42 GMT-04:00 Douglas Greve <greve(a)nmr.mgh.harvard.edu>: > You can try normalizing your covariates. You can do so before putting them > into the fsgd file or you can add the following two lines to your fsgd file: > > DeMeanFlag 1 > > ReScaleFlag 1 > > > > On 9/9/16 11:25 PM, Seung Gul Kang wrote: > > Hi, > > I am new learner in freesurfer and analyzing the difference of the > thickness between two groups using qdec. > > There is a error as below. > I don't know what is the reason. > > ERROR: matrix is ill-conditioned or badly scaled, condno = 22801.1 > -------------------------------- > 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/kang_fs/qdec/2/y.mgh --fsgd > /mnt/hgfs/share/kang_fs/qdec/2/qdec.fsgd dods --glmdir > /mnt/hgfs/share/kang_fs/qdec/2 --surf fsaverage lh --label > /mnt/hgfs/share/kang_fs/fsaverage/label/lh.aparc.label --C > /mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Avg-Intercept-thickness.mat > --C /mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Diff-H-I-Intercept-thickness.mat > --C /mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Diff-M-F-Intercept-thickness.mat > --C /mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-X-diagnosis-sex- > Intercept-thickness.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/kang_fs/qdec/2/y.mgh --fsgd /mnt/hgfs/share/kang_fs/qdec/2/qdec.fsgd > dods --glmdir /mnt/hgfs/share/kang_fs/qdec/2 --surf fsaverage lh --label > /mnt/hgfs/share/kang_fs/fsaverage/label/lh.aparc.label --C > /mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Avg-Intercept-thickness.mat > --C /mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Diff-H-I-Intercept-thickness.mat > --C /mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Diff-M-F-Intercept-thickness.mat > --C /mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-X-diagnosis-sex- > Intercept-thickness.mat > > matrix > > Design matrix ------------------ > 1.000 0.000 0.000 0.000 27.000 0.000 0.000 0.000 3.000 > 0.000 0.000 0.000 2.600 0.000 0.000 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 28.000 0.000 0.000 > 0.000 4.000 0.000 0.000 0.000 2.440 0.000; > 1.000 0.000 0.000 0.000 25.000 0.000 0.000 0.000 1.000 > 0.000 0.000 0.000 2.510 0.000 0.000 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 26.000 0.000 0.000 > 0.000 7.000 0.000 0.000 0.000 2.500 0.000; > 1.000 0.000 0.000 0.000 35.000 0.000 0.000 0.000 1.000 > 0.000 0.000 0.000 2.450 0.000 0.000 0.000; > 1.000 0.000 0.000 0.000 30.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 2.380 0.000 0.000 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 24.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 2.430 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 24.000 0.000 0.000 > 0.000 1.000 0.000 0.000 0.000 2.390 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 28.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 2.350 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 33.000 0.000 0.000 > 0.000 2.000 0.000 0.000 0.000 2.400 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 45.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 2.300 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 38.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 2.300 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 24.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 2.480 0.000; > 1.000 0.000 0.000 0.000 28.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 2.310 0.000 0.000 0.000; > 1.000 0.000 0.000 0.000 30.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 2.460 0.000 0.000 0.000; > 1.000 0.000 0.000 0.000 39.000 0.000 0.000 0.000 3.000 > 0.000 0.000 0.000 2.230 0.000 0.000 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 48.000 0.000 0.000 > 0.000 4.000 0.000 0.000 0.000 2.410 0.000; > 1.000 0.000 0.000 0.000 32.000 0.000 0.000 0.000 3.000 > 0.000 0.000 0.000 2.370 0.000 0.000 0.000; > 1.000 0.000 0.000 0.000 32.000 0.000 0.000 0.000 4.000 > 0.000 0.000 0.000 2.510 0.000 0.000 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 31.000 0.000 0.000 > 0.000 2.000 0.000 0.000 0.000 2.380 0.000; > 1.000 0.000 0.000 0.000 33.000 0.000 0.000 0.000 1.000 > 0.000 0.000 0.000 2.390 0.000 0.000 0.000; > 1.000 0.000 0.000 0.000 33.000 0.000 0.000 0.000 1.000 > 0.000 0.000 0.000 2.540 0.000 0.000 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 44.000 0.000 0.000 > 0.000 4.000 0.000 0.000 0.000 2.290 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 41.000 0.000 0.000 > 0.000 2.000 0.000 0.000 0.000 2.420 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 41.000 0.000 0.000 > 0.000 1.000 0.000 0.000 0.000 2.400 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 43.000 0.000 0.000 > 0.000 3.000 0.000 0.000 0.000 2.420 0.000; > 0.000 1.000 0.000 0.000 0.000 21.000 0.000 0.000 0.000 > 10.000 0.000 0.000 0.000 2.410 0.000 0.000; > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 46.000 0.000 > 0.000 0.000 13.000 0.000 0.000 0.000 2.410; > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 41.000 0.000 > 0.000 0.000 8.000 0.000 0.000 0.000 2.400; > 0.000 1.000 0.000 0.000 0.000 29.000 0.000 0.000 0.000 > 13.000 0.000 0.000 0.000 2.400 0.000 0.000; > 0.000 1.000 0.000 0.000 0.000 39.000 0.000 0.000 0.000 > 12.000 0.000 0.000 0.000 2.380 0.000 0.000; > 0.000 1.000 0.000 0.000 0.000 27.000 0.000 0.000 0.000 > 6.000 0.000 0.000 0.000 2.370 0.000 0.000; > 0.000 1.000 0.000 0.000 0.000 57.000 0.000 0.000 0.000 > 11.000 0.000 0.000 0.000 2.330 0.000 0.000; > 0.000 1.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000 > 7.000 0.000 0.000 0.000 2.370 0.000 0.000; > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 31.000 0.000 > 0.000 0.000 11.000 0.000 0.000 0.000 2.330; > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 23.000 0.000 > 0.000 0.000 11.000 0.000 0.000 0.000 2.520; > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 34.000 0.000 > 0.000 0.000 11.000 0.000 0.000 0.000 2.360; > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 32.000 0.000 > 0.000 0.000 10.000 0.000 0.000 0.000 2.570; > 0.000 1.000 0.000 0.000 0.000 37.000 0.000 0.000 0.000 > 2.000 0.000 0.000 0.000 2.570 0.000 0.000; > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 46.000 0.000 > 0.000 0.000 5.000 0.000 0.000 0.000 2.400; > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 48.000 0.000 > 0.000 0.000 1.000 0.000 0.000 0.000 2.370; > 0.000 1.000 0.000 0.000 0.000 42.000 0.000 0.000 0.000 > 3.000 0.000 0.000 0.000 2.470 0.000 0.000; > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 54.000 0.000 > 0.000 0.000 8.000 0.000 0.000 0.000 2.450; > 0.000 1.000 0.000 0.000 0.000 30.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 2.480 0.000 0.000; > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 36.000 0.000 > 0.000 0.000 12.000 0.000 0.000 0.000 2.390; > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 34.000 0.000 > 0.000 0.000 9.000 0.000 0.000 0.000 2.300; > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 38.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 2.550; > -------------------------------- > > I attached fsgd file. > > Thank you. > > Best, > Seung-Gul > --- > *Seung Gul Kang, M.D., Ph.D. * > > *Psychiatrist, Associate Professor*; Department of Psychiatry, Gil > Medical Center, Gachon University, School of Medicine, 21, Namdong-daero > 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea > *Research scholar*; Sleep Disorders Clinical Research Program, Department > of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 1 > Bowdoin Square, 9th floor, Boston, MA 02114, USA > *Collaboration researcher*; Division of Sleep & Circadian Disorders, > Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave, > Boston MA 02115 > > > _______________________________________________ > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ᐧ

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer