Freesurfer August 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
233 discussions

Neuroimaging Postdoc at Penn State
by emma jane 14 Aug '17

14 Aug '17

[image: image.png] -- *Emma Jane Rose PhD.* *Assistant Research Professor & * *Associate Director for the **Program for Translational Research on Adversity and Neurodevelopment (P-TRAN)* *Edna Bennett Pierce Prevention Research Center* *The Pennsylvania State University* *308 Biobehavioral Health Building* *University Park, PA 16802* *www.prevention.psu.edu <http://www.prevention.psu.edu/>* *www.npscoalition.org <http://www.npscoalition.org/>*

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white matter ROI mask using an fsaverage label
by Eryilmaz, H. Hamdi 14 Aug '17

14 Aug '17

Hi Anastasia and FS experts, I am trying to create a white matter ROI mask underneath a cortical ROI label (e.g., 2 mm into the white matter) created in fsaverage space. I will then use this mask to extract values from individual dtifit_FA and dtifit_MD maps generated by trac-all. What would be the easiest way to do this? I thought about using mri_aparc2aseg but I am not quite sure about how to specify a label with this command. Thanks so much for your help! Best, Hamdi

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Combining Results of Per-Run GLM?
by Taylor, Johnmark 14 Aug '17

14 Aug '17

Hello, I am trying to do a GLM analysis for a study in which I scanned each participant twice. Currently, to combine the two scanning sessions I am combining the runs from the two sessions into a single session directory and applying per-session motion correction, essentially treating all the data as though it came from a single session. The issue is that when I do this, the GLM analysis takes prohibitively long (with just 8 subjects, the analysis has already been running for two weeks). To speed things up, I had the idea of doing the runwise GLM (getting the betas and contrast values for each run), then combining the runwise results to get t-values and p-values for the whole session. However, I am not entirely sure how to do this last bit; is there some kind of function that can be used to take all the per-run t-values or effect sizes in a session and combine them to get an aggregate t-value and p-value for the whole session, for a given contrast? I believe FSL follows this analysis strategy (doing runwise analyses then combining them into the whole session), so I was wondering whether FSFAST had a way of doing the same. Thank you very much, JohnMark

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Error when trying to compile the code
by Aziz Nanthaamornphong 14 Aug '17

14 Aug '17

Dear FreeSurfer Experts, I was trying to compile the FreeSurfer code by following steps shown in https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page However, I got this error message after I ran ./configure configure: error: FATAL: netcdf lib not found. Set LDFLAGS or --with-mni-dir. I currently use OS X El Capitan as the OS. How can I solve this problem? Thank you in advance. Aziz.

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Question about global mean cortical thickness
by Zhiliang Long 14 Aug '17

14 Aug '17

Dear FS experts: I am writting to ask for help about the computation of global mean thickness. On the FAQ page, one suggestion is that the global mean thickness is equal to the (lh.thickness*lh.surfarea + rh.thickness.rh.surfarea) / (lh.surfarea+rh.surfarea). I am wondering how the ?h.thickness and ?h.surfarea are calculated. Any suggestions are appreciated. Thanks for your time. Best Zhiliang Long

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Re: [Freesurfer] test-retest variability small subcortical regions
by Van Der Deijl, Rosanne 14 Aug '17

14 Aug '17

Hi Bruce, I mean for the longitudinal analysis. Forgot to mention this, sorry! Kind regards, Rose Date: Fri, 11 Aug 2017 12:39:58 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Test-retest reliability small subcortical regions To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1708111239430.24300(a)door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Rose do you mean cross-sectional or longitudinal analysis? cheers Bruce On Fri, 11 Aug 2017, Van Der Deijl, Rosanne wrote: > Dear Freesurfer team, > > I was wondering what the test-retest reliability is of comparing small > regions in the subcortical volume, e.g. the amygdala. Has this improved with > the 6.0 version? > > Thank you! > > Kind regards, > > Rose >

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problem with fsgd glmfit
by Kasper Jessen 14 Aug '17

14 Aug '17

Dear FreeSurfer, I would like to do the long. two stage model (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel) Study design: 2 groups (one control group, one patient group) with gender and age as covariates. Each subject was MRI scanned at baseline and 6 weeks follow-up. I would like to test the difference in structural measures between groups over time. My problem 1. Is the process and setup below correct? 2. When i pass the above command under 3) i get an error where it says: FSGDF Format Error: file = /Volumes/External/P1_FU/GroupDiffLhThickness.fsgd, tag=Input Is there anyone that can help? I have followed the tutorial: FIRST STAGE: Preparing the Data - QCACHE is done. SECOND STAGE: Option mri_glmfit: Then i would like to test the difference between groups, and this is were i have a hard time following the tutorial. I looked at the following guide: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis concerning Group Analysis using mri_glmfit and i understand that i need to use the command below creating my own fsgd file. 1) Since i have a longitudinal setup, i converted it to a cross-sectional steup as you would do if you used the QDEC option. My fsgd file looks as the one below. 1 = patients and 0 = controls. GroupDescriptorFile 1 Title GroupDiff_Lh_Thickness Class 1 Class 0 Variables age gender Input b101_base 1.0 24.0 1.0 Input b103_base 1.0 41.0 0.0 Input b105_base 1.0 22.0 1.0 Input b206_base 0.0 25.0 1.0 Input b207_base 0.0 23.0 0.0 2) To test group difference between groups regressing out the effect of age and gender i have made a .mtx file with the following input: 1 -1 0 0 0 0 3) Therenext, i ran the following but something is wrong with my fsgd file: mri_glmfit --y lh.thickness-spc.stack.fwhm15.mgh --fsgd GroupDiffLhThickness.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex --glmdir lh_thickness_spc_fwhm15_groupdiff I hoper there is someone who can help. Best wishes Kasper Jessen

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Post-Doctoral Position: Molecular Imaging in Geriatric Neuropsychiatry
by Gwenn Smith 13 Aug '17

13 Aug '17

[JHM2.gif] Post-Doctoral Position: Molecular Imaging in Geriatric Neuropsychiatry An immediate full-time opening is available for an outstanding, highly motivated post-doctoral research fellow in the laboratory of Gwenn S. Smith, PhD. The laboratory focuses on applying pharmacologic, neuropsychological and multi-modality PET and MR imaging methods to investigate the neurobiology of late life depression, mild cognitive impairment and Parkinson's disease and of interventions, including pharmacotherapy and brain stimulation. The laboratory, based in the Division of Geriatric Psychiatry and Neuropsychiatry, has strong collaborations with the Russell H. Morgan Department of Radiology and Radiological Sciences, the F. M. Kirby Research Center for Functional Brain Imaging of the Kennedy Krieger Institute, the Departments of Pathology (Neuropathology), Neurology and Neurosurgery. The fellow will have designated responsibility for specific projects, including the planning, design, execution, image processing, and analysis and will be expected to take the lead on preparing manuscripts for publication and on presentation of the results at scientific meetings. Successful applicants will have strong academic preparation (PhD, MD or MD/PhD in a relevant discipline), high motivation and enthusiasm for research, excellent written and oral communication skills including evidence of successful manuscript writing and publication productivity, strong intellectual curiosity, and ability to work independently and as part of a collaborative interdisciplinary team. Preference will be given to candidates with experience in clinical research, as well as in MRI and/or PET imaging. Applicants who plan to develop an independent research career are especially encouraged to apply. Review of applications will begin immediately and will continue until the position is filled. Applicants should send their Curriculum Vitae, a statement of academic interests and the names and addresses of four professional references to: Gwenn S. Smith, PhD, Richman Family Professor, Director, Division of Geriatric Psychiatry and Neuropsychiatry, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine 5300 Alpha Commons Drive, Baltimore, MD 21224 (gsmith95(a)jhmi.edu) The Johns Hopkins University is an equal opportunity/affirmative action employer committed to recruiting, supporting, and fostering a diverse community of outstanding faculty, staff, and students. All applicants who share this goal are encouraged to apply.

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TRACULA trac-all speed
by Mina Fakhry 12 Aug '17

12 Aug '17

I am currently using the last stable version freesurfer 6.0 I gave TRACULA a try on one subject and it took more that 2.5 days to finish the steps, with PC specs: - Processor core i7 4 GHz - VGA Nvidia GTX 980 with 1500 CUDA cores - 16 GB RAM I tried to speed it up (trac-all command) using openmp or use-gpu, but non of them worked. Is there any way to speed the TRACULA processing??

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Matlab 2016b and localGI
by Juranek, Jenifer 11 Aug '17

11 Aug '17

Hi, Hope someone can identify my user error...I've listed below key bits of info (system info, cmdline and error message, echo $PATH, cat .bashrc, cat startup.m). Really appreciate someone taking a look and walking me through a solution to my error? Many Thanks! Jenifer 1) Running Freesurfer_v6 on RHEL Centos7.3 and matlab 2016b (with imaging processing toolbox) 2) recon-all -s <FSID> -localGI returns the following: #@# Local Gyrification Index lh Thu Aug 10 15:39:03 CDT 2017 mris_compute_lgi --i lh.pial ERROR: Matlab is required to run mris_compute_lgi! Linux localhost.localdomain 3.10.0-514.el7.x86_64 #1 SMP Wed Oct 19 11:24:13 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux 3) matlab is in my path [jjuranek@localhost subjects]$ echo $PATH /home/jjuranek/freesurfer/bin:/home/jjuranek/freesurfer/fsfast/bin:/home/jjuranek/freesurfer/tktools:/home/jjuranek/fsl/bin:/home/jjuranek/freesurfer/mni/bin:/home/jjuranek/fsl/bin:/home/jjuranek/freesurfer/bin:/home/jjuranek/freesurfer/fsfast/bin:/home/jjuranek/freesurfer/tktools:/home/jjuranek/freesurfer/mni/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/jjuranek/.local/bin:/home/jjuranek/bin:/home/jjuranek/matlab/R2016b/bin/matlab 4) my .bashrc file is as follows # .bashrc # Source global definitions if [ -f /etc/bashrc ]; then . /etc/bashrc fi # User specific aliases and functions export FREESURFER_HOME=/home/jjuranek/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh matlab=/home/jjuranek/matlab/R2016b/bin/matlab alias matlab=$matlab export PATH=$PATH:/home/jjuranek/matlab/R2016b/bin/matlab #/home/jjuranek/matlab/R2016b/bin/matlab #MATLAB is selecting SOFTWARE OPENGL rendering. 5) my startup.m file is as follows %------------ FreeSurfer -----------------------------% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) addpath(genpath(fsmatlab)); end clear fshome fsmatlab; %-----------------------------------------------------% %------------ FreeSurfer FAST ------------------------% fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; %-----------------------------------------------------% %------------ FreeSurfer LGI ------------------------% FSH = getenv('FREESURFER_HOME'); fshmatlab = sprintf('%s/matlab',FSH); path(path,fshmatlab); clear fshmatlab FSH;

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Freesurfer August 2017