Freesurfer

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30132 discussions

obtaining the most recent build of FreeSurfer development version
by Antonin Skoch 14 Aug '17

14 Aug '17

Dear experts, I would like to download the most recent build of FreeSurfer development version (linux 64 bit). The origin/dev git repository contains commit up to today (14.8.17), but last change of "daily build" of dev version is 28.7.17. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Linux-c… How is the build of dev version sheduled? Antonin Skoch

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mri_binarize/mri_mask command help
by Yagmur Ozdemir 19 14 Aug '17

14 Aug '17

Dear FreeSurfer experts, I am trying to use the following command to merge the volume file of a template with original T1 orientation*, with a file like rawavg to get the full brain volume, but the following attached image gets produced and I am pretty sure, as a freesurfer novice, I am using a wrong command line. I have tried mri_mask as well but do not think it is the command to go. I also checked if two volumes are in the same orientation using mri_orient. mri_binarize --i rawavg.mgz --o scanner.template_angle.mgz --wm+vcsf * (I have the native oriented version of this volume template as well, and I attached a photo of the template as well) I would deeply appreciate if someone could help me correct my command line. Thank you all for the time and help Idil

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Developmental Neuroimaging Postdoc
by emma jane 14 Aug '17

14 Aug '17

The Program for Translational Research on Adversity and Neurodevelopment (P-TRAN) at The Pennsylvania State University is seeking a qualified postdoctoral researcher with expertise in human brain imaging, specifically magnetic resonance imaging (MRI)) with children and adolescents. This position is supported by a recently awarded NICHD Center Grant (i.e., a CAPSTONE Center for Multidisciplinary Research in Child Abuse and Neglect; PI: Dr. Jennie Noll) and will be based in the Child Maltreatment Solutions Network (http://solutionsnetwork.psu.edu/) and the Prevention Research Center (www.prevention.psu.edu) both of which are located on the University Park campus in State College, PA. The primary responsibility of this position will be to provide neuroimaging research support (e.g., experimental design, implementation and data analysis) to a longitudinal project that will consider the biological embedding of child maltreatment in multiple biologic systems (e.g., neuroendocrine, autonomic, genetic, epigenetic, immunologic) and the impact of embedding on health outcomes, including neurodevelopmental trajectories. Candidates must have a PhD in psychology, neuroscience, or an allied field, or have completed all requirements for a PhD by the time of appointment. Applicants must have expertise in human subjects MRI, preferably with developmental cohorts. Preference will be given to those candidates with experience working with children who have experienced maltreatment or other high-risk groups. The successful candidate will be expected to contribute to experimental design and co-ordination of the neuroimaging aspects of the project and data analysis. Candidates must demonstrate expertise in functional and structural MRI analysis methods using standard processing packages (e.g., SPM, AFNI, FSL, Freesurfer etc.) and experience with longitudinal and complex datasets would be advantageous. The postdoctoral researcher will also be expected to contribute to manuscript preparation and presentation of study-related outcomes at key scientific meetings. Extensive mentorship will be provided to the successful candidate in order to facilitate transition to an independent research career. This position will provide an opportunity to interact with several vibrant research communities at Penn State, including the Social Sciences Research Institute (www.ssri.psu.edu) and the Social, Life and Engineering Science Imaging Center (www.imaging.psu.edu) among others. The initial appointment will be for one year, with the possibility of renewal in subsequent years. Salary and benefits are based on NIH guidelines, commensurate with experience and qualifications. Interested candidates should upload a CV, cover letter, statement of research interests, and 2-3 relevant publications. In addition, applicants should arrange for 3 professional references to be submitted separately to Dr. Emma Jane Rose (Associate Director for P-TRAN) at emmajanerose(a)psu.edu. Review of applications will begin immediately and will continue until the position is filled. For further information about this appointment, please contact Dr. Emma Jane Rose at emmajanerose(a)psu.edu or 814-865-0114. Apply online at https://psu.jobs/job/69051 CAMPUS SECURITY CRIME STATISTICS: For more about safety at Penn State, and to review the Annual Security Report which contains information about crime statistics and other safety and security matters, please go to http://www.police.psu.edu/clery/, which will also provide you with detail on how to request a hard copy of the Annual Security Report. Penn State is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applicants without regard to race, color, religion, age, sex, sexual orientation, gender identity, national origin, disability or protected veteran status. -- *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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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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