Freesurfer September 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
200 discussions

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

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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

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

12 Sep '16

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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

Getting Waveform from Label - dim mismatch
by ERIK JAHNER 12 Sep '16

12 Sep '16

(sorry if you got this multiple times this morning I had some server issues) I had not seen a post based on this email, so I am resending it. It is my understanding that I can use freesurfer and FSfast to get activation levels after data has been smoothed across the surface instead of 3D volume. Is the mir_segstats only able to use the 3D volume and not the surface data stored within vertices? Sorry if this questions is obvious to everyone. I want to basically get the average activation for a set of vertices at each time point included in a label from the surface mapped functional data. See below for additional details of the parameters I entered. Thanks Erik Jahner > On Sep 9, 2016, at 8:20 AM, ERIK JAHNER <erik.jahner(a)icloud.com <mailto:erik.jahner@icloud.com>> wrote: > > >> Dear Freesurfer experts, >> >> I am attempting to get the waveform from a subject (401)using the preprocessed data (fmcpr.siemens.sm5.fsaverage.lh.nii.gz) by means of a label I created from the icosahedron 3 (lh.ic3.tri_vertex_638). This label was created from the subjects “sphere.reg" file. >> >> I am using the following command: >> >> mri_segstats >> --slabel 401 lh /Applications/freesurfer/subjects/fsaverage/label/ic3/lh.ic3.tri_vertex_638.label >> --avgwf out.dat >> --id 1 >> --i /Applications/freesurfer/LagStructure/401/rest/007/fmcpr.siemens.sm5.fsaverage.lh.nii.gz >> >> However I am getting the following error: >> >> ERROR: dimension mismatch between input volume and seg >> input 163842 1 1 >> seg 140104 1 1 >> >> Obviously there is something wrong with my file dimensions. But, I am unsure of how to fix this. I checked some of the files in my subject anatomical folder like the thickness file and they also have 140104 1 1 as the dimensions. But, as would be predicted the "fmcpr.siemens.sm5.fsaverage.lh.nii.gz” file has the dimensions 163842 1 1 210. Is there an easy way to fix this problem? I am unsure what I did to create this discrepancy. >> >> Thanks for your continued support, >> Erik Jahner

2 1

Re: [Freesurfer] Tracula movement
by Lars M. Rimol 12 Sep '16

12 Sep '16

Re: [Freesurfer] Tracula movement <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subje…> Anastasia Yendiki <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Mon, 12 Sep 2016 04:24:56 -0700 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Hi Lars - This sounds like the subject was trying to climb out of the scanner: 3cm average translational motion and 24% of the slices in the series have drop-out. How do the images look? a.y Hi, I don't have a lot of experience looking at dwi scans, but they don't seem crazy to me. I have attached screenshots of the dwi, FA, and brain_anat_mni images, and the gross anatomy looks fine to me. There are stripes in brain_anat_mni, which I would guess indicate motion.. Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

2 1

Re: [Freesurfer] [martinos-tech] Trobles witg GLM Surface-based Cluster Summary Table
by Douglas N Greve 12 Sep '16

12 Sep '16

you can find it here fsaverage/surf/?h.white.avg.area.mgh On 09/12/2016 11:26 AM, Claudia Dacquino claudia.dacquino(a)gmail.com [martinos-tech] wrote: > Thanks Doug! > Yes, I realized I was wrong and I wrote to the freesurfer list too. > Just another question,as you were so prompt in replying... Where can I > find the average surface area of the inputsubjects? > Thanks. > Clauia > > > 2016-09-12 17:15 GMT+02:00 Douglas N Greve greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> [martinos-tech] > <martinos-tech(a)yahoogroups.com <mailto:martinos-tech@yahoogroups.com>>: > > Hi Claudia, it is better to post these things to the freesurfer > list as > martinos-tech is no longer active. The total cortical surface area > (65416.6mm2) is incorrect. The total should be 82219.960938. The > reported value is the actual surface area of the fsaverage white > surface. However, the average white surface has a much lower surface > area than areas of any of the input subjects because the surface > coordinate averaging causes minor folding to be smoothed out. To get > around this, we keep track of the average surface area of the input > subjects (rather than the surface area of the average surface, if > that > is not too confusing). The size of the cluster reported > (76467.08mm2) is > accurate. > > doug > > On 09/12/2016 07:52 AM, Claudia Dacquino > claudia.dacquino(a)gmail.com <mailto:claudia.dacquino@gmail.com> > > [martinos-tech] wrote: > > > > Hi all, > > > > I've run GLM surface analysis and I've got a summary table like > this: > > > > > > # Cluster Growing Summary (mri_surfcluster) > > > > # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ > > > > # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ > > > > # CreationTime 2016/09/12-08:47:18-GMT > > > > # cmdline mri_surfcluster --in lh.Compr.glmdir/SZSI-SZNO/sig.mgh > --csd > > > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th40/mc-z.csd > > > --mask lh.Compr.glmdir/mask.mgh --cwsig > > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.mgh --vwsig > > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.voxel.mgh --sum > > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.summary --ocn > > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.mgh --oannot > > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.annot --annot > aparc > > --csdpdf lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.pdf.dat > > --cwpvalthresh 0.05 --o > > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.masked.mgh --no-fixmni > > --bonferroni 2 --surf white > > > > # cwd /media/TREKSTOR/SUBJ/CI_Compr_Contrasts > > > > # sysname Linux > > > > # hostname Piras-TC2 > > > > # machine x86_64 > > > > # FixVertexAreaFlag 1 > > > > # FixSurfClusterArea 1 > > > > # > > > > # Input lh.Compr.glmdir/SZSI-SZNO/sig.mgh > > > > # Frame Number 0 > > > > # srcsubj fsaverage > > > > # hemi lh > > > > # surface white > > > > # annot aparc > > > > # SUBJECTS_DIR /media/TREKSTOR/SUBJ > > > > # SearchSpace_mm2 65416.6 > > > > # SearchSpace_vtx 149953 > > > > # Bonferroni 2 > > > > # Minimum Threshold 4 > > > > # Maximum Threshold infinity > > > > # Threshold Sign pos > > > > # AdjustThreshWhenOneTail 1 > > > > # CW PValue Threshold: 0.05 > > > > # Area Threshold 0 mm^2 > > > > # CSD thresh 4.000000 > > > > # CSD nreps 10000 > > > > # CSD simtype null-z > > > > # CSD contrast NA > > > > # CSD confint 90.000000 > > > > # Overall max 1e+10 at vertex 3 > > > > # Overall min 0 at vertex 8 > > > > # NClusters 1 > > > > # Total Cortical Surface Area 65416.6 (mm^2) > > > > # FixMNI = 0 > > > > # > > > > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP > > CWPLow CWPHi NVtxs Annot > > > > 1 10000000000.000 3 76467.08 -22.1 41.5 24.1 0.00020 > > 0.00000 0.00040 149953 rostralmiddlefrontal > > > > > > Is it possible to have a Cluster Size (76467.08 mm2) greater > than the > > Total Cortical Surface (65416.6 mm2). > > > > Are there some errors in this? > > > > Thanks a lot to all of you. > > > > 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> > > <http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli > <http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli>> > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > 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 > <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. > > > > > -- > > 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> > > > > __._,_.___ > ------------------------------------------------------------------------ > Posted by: Claudia Dacquino <claudia.dacquino(a)gmail.com> > ------------------------------------------------------------------------ > Reply via web post > <https://groups.yahoo.com/neo/groups/martinos-tech/conversations/messages/58…> > • Reply to sender > <mailto:claudia.dacquino@gmail.com?subject=Re%3A%20%5Bmartinos-tech%5D%20Trobles%20witg%20GLM%20Surface-based%20Cluster%20Summary%20Table> > • Reply to group > <mailto:martinos-tech@yahoogroups.com?subject=Re%3A%20%5Bmartinos-tech%5D%20Trobles%20witg%20GLM%20Surface-based%20Cluster%20Summary%20Table> > • Start a New Topic > <https://groups.yahoo.com/neo/groups/martinos-tech/conversations/newtopic;_y…> > • Messages in this topic > <https://groups.yahoo.com/neo/groups/martinos-tech/conversations/topics/5882…> > (3) > > ------------------------------------------------------------------------ > Have you tried the highest rated email app? <https://yho.com/1wwmgg> > With 4.5 stars in iTunes, the Yahoo Mail app is the highest rated > email app on the market. What are you waiting for? Now you can access > all your inboxes (Gmail, Outlook, AOL and more) in one place. Never > delete an email again with 1000GB of free cloud storage. > ------------------------------------------------------------------------ > Visit Your Group > <https://groups.yahoo.com/neo/groups/martinos-tech/info;_ylc=X3oDMTJlYnY4dWI…> > > > Yahoo! Groups > <https://groups.yahoo.com/neo;_ylc=X3oDMTJkMnJybTJmBF9TAzk3NDc2NTkwBGdycElkA…> > > • Privacy > <https://info.yahoo.com/privacy/us/yahoo/groups/details.html> • > Unsubscribe > <mailto:martinos-tech-unsubscribe@yahoogroups.com?subject=Unsubscribe> > • Terms of Use <https://info.yahoo.com/legal/us/yahoo/utos/terms/> > > . > > __,_._,___ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

visualize corrected results
by Caroline Beelen 12 Sep '16

12 Sep '16

Dear FS, I have a question on visualizing results from GLM analysis... How can I visualize corrected results in Freeview after having applied bonferroni/FDR correction (somewhere else)? I saw it is not possible (error: masking file missing) -and was told it is not necessary- to apply monte carlo simulation on results obtained via aparc-files from DK-atlas. Thank you very much! Regards, Caroline

1 0

Re: [Freesurfer] [martinos-tech] Trobles witg GLM Surface-based Cluster Summary Table
by Douglas N Greve 12 Sep '16

12 Sep '16

Hi Claudia, it is better to post these things to the freesurfer list as martinos-tech is no longer active. The total cortical surface area (65416.6mm2) is incorrect. The total should be 82219.960938. The reported value is the actual surface area of the fsaverage white surface. However, the average white surface has a much lower surface area than areas of any of the input subjects because the surface coordinate averaging causes minor folding to be smoothed out. To get around this, we keep track of the average surface area of the input subjects (rather than the surface area of the average surface, if that is not too confusing). The size of the cluster reported (76467.08mm2) is accurate. doug On 09/12/2016 07:52 AM, Claudia Dacquino claudia.dacquino(a)gmail.com [martinos-tech] wrote: > > Hi all, > > I've run GLM surface analysis and I've got a summary table like this: > > > # Cluster Growing Summary (mri_surfcluster) > > # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ > > # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ > > # CreationTime 2016/09/12-08:47:18-GMT > > # cmdline mri_surfcluster --in lh.Compr.glmdir/SZSI-SZNO/sig.mgh --csd > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th40/mc-z.csd > --mask lh.Compr.glmdir/mask.mgh --cwsig > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.mgh --vwsig > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.voxel.mgh --sum > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.summary --ocn > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.mgh --oannot > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.annot --annot aparc > --csdpdf lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.pdf.dat > --cwpvalthresh 0.05 --o > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.masked.mgh --no-fixmni > --bonferroni 2 --surf white > > # cwd /media/TREKSTOR/SUBJ/CI_Compr_Contrasts > > # sysname Linux > > # hostname Piras-TC2 > > # machine x86_64 > > # FixVertexAreaFlag 1 > > # FixSurfClusterArea 1 > > # > > # Input lh.Compr.glmdir/SZSI-SZNO/sig.mgh > > # Frame Number 0 > > # srcsubj fsaverage > > # hemi lh > > # surface white > > # annot aparc > > # SUBJECTS_DIR /media/TREKSTOR/SUBJ > > # SearchSpace_mm2 65416.6 > > # SearchSpace_vtx 149953 > > # Bonferroni 2 > > # Minimum Threshold 4 > > # Maximum Threshold infinity > > # Threshold Sign pos > > # AdjustThreshWhenOneTail 1 > > # CW PValue Threshold: 0.05 > > # Area Threshold 0 mm^2 > > # CSD thresh 4.000000 > > # CSD nreps 10000 > > # CSD simtype null-z > > # CSD contrast NA > > # CSD confint 90.000000 > > # Overall max 1e+10 at vertex 3 > > # Overall min 0 at vertex 8 > > # NClusters 1 > > # Total Cortical Surface Area 65416.6 (mm^2) > > # FixMNI = 0 > > # > > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP > CWPLow CWPHi NVtxs Annot > > 1 10000000000.000 3 76467.08 -22.1 41.5 24.1 0.00020 > 0.00000 0.00040 149953 rostralmiddlefrontal > > > Is it possible to have a Cluster Size (76467.08 mm2) greater than the > Total Cortical Surface (65416.6 mm2). > > Are there some errors in this? > > Thanks a lot to all of you. > > 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> > > > > __._,_.___ > ------------------------------------------------------------------------ > Posted by: Claudia Dacquino <claudia.dacquino(a)gmail.com> > ------------------------------------------------------------------------ > Reply via web post > <https://groups.yahoo.com/neo/groups/martinos-tech/conversations/messages/58…> > • Reply to sender > <mailto:claudia.dacquino@gmail.com?subject=Re%3A%20Trobles%20witg%20GLM%20Surface-based%20Cluster%20Summary%20Table> > • Reply to group > <mailto:martinos-tech@yahoogroups.com?subject=Re%3A%20Trobles%20witg%20GLM%20Surface-based%20Cluster%20Summary%20Table> > • Start a New Topic > <https://groups.yahoo.com/neo/groups/martinos-tech/conversations/newtopic;_y…> > • Messages in this topic > <https://groups.yahoo.com/neo/groups/martinos-tech/conversations/topics/5882…> > (1) > > ------------------------------------------------------------------------ > Have you tried the highest rated email app? <https://yho.com/1wwmgg> > With 4.5 stars in iTunes, the Yahoo Mail app is the highest rated > email app on the market. What are you waiting for? Now you can access > all your inboxes (Gmail, Outlook, AOL and more) in one place. Never > delete an email again with 1000GB of free cloud storage. > ------------------------------------------------------------------------ > Visit Your Group > <https://groups.yahoo.com/neo/groups/martinos-tech/info;_ylc=X3oDMTJlMjRnMGM…> > > > Yahoo! Groups > <https://groups.yahoo.com/neo;_ylc=X3oDMTJkNXQ3dWU2BF9TAzk3NDc2NTkwBGdycElkA…> > > • Privacy > <https://info.yahoo.com/privacy/us/yahoo/groups/details.html> • > Unsubscribe > <mailto:martinos-tech-unsubscribe@yahoogroups.com?subject=Unsubscribe> > • Terms of Use <https://info.yahoo.com/legal/us/yahoo/utos/terms/> > > . > > __,_._,___ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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mris_anatomical_stats
by Arkadiy Maksimovskiy 12 Sep '16

12 Sep '16

Dear Freesurfer Experts, I am trying to run mris_anatomical_stats in order to extra thickness data from my participants' label files. However, I only have access to a subj_recon data (without wm.mgz in that folder). Does anyone know if there is a way to extract the thickness measures for every participant's label, without having the wm.mgz file? Would it be okay to copy that file from fsaverage, in order ot bypass this issue, or would that mess up the calculations of the thickness of the participants' labels? Thank you in advance for your help, Arkadiy

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Freesurfer September 2016