Freesurfer June 2019

freesurfer@nmr.mgh.harvard.edu

82 participants
138 discussions

Longitudinal Masking and FDR
by Hua, Jessica 28 Jun '19

28 Jun '19

External Email - Use Caution Hi FreeSurfer Experts, I had two questions regarding the longitudinal process. 1) I am using the linear mixed effects mass-univariate approach to analyze my longitudinal data. A priori I am interested in the orbitofrontal cortex and the parahippocampal gyrus. Is there a way in FreeSurfer to mask my longitudinal analyses to these regions specifically? 2) Also is there a way to modify the FDR2? My analyses do not meet the FDR2 (q < .05) p threshold of 4.29, and I wanted to see what threshold it is meeting. Specifically, I wanted to see if it was meeting q < .1. In the lme_mass_FDR2.m, I tried to change the rate to .1, but i kept getting the same result as when it was .05. Thank you in advance for your help! Best, Jessica Hua

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[Updated announcement] Postdoc position opening at Brown University in cognitive aging and Alzheimer’s disease
by Hwamee Oh 28 Jun '19

28 Jun '19

External Email - Use Caution We are seeking a highly motivated postdoctoral researcher to study behavioral and neuroimaging markers of preclinical Alzheimer’s disease in the Warren Alpert Medical School of Brown University. The primary performance site for this postdoctoral fellowship is in the Butler Hospital Memory and Aging Program (MAP). Brown University has a strong commitment to brain science and research in neurodegenerative disorders. This commitment is united under The Carney Institute for Brain Science and the new Center for Translational Neuroscience (CTN). The mission of the Carney Institute and CTN is to promote the discovery and innovation in brain science by supporting a diverse community of experimentalists, theorists, engineers, and clinicians. The MAP, one of the leading clinical trial centers for Alzheimer’s disease (AD) in the United States, is committed to accelerating drug and biomarker development for AD and to training young investigators for careers in AD research. The successful candidate will join a team of experts in Aging, Alzheimer’s disease, and related dementia research. This postdoctoral position is primarily focused on the area of the cognitive system in aging and preclinical Alzheimer’s disease and will work on developing early behavioral and neuroimaging markers of Alzheimer’s disease and integrating structural and functional MRI, PET, cognitive, genetic, and biofluid measures from ongoing or completed projects. Fellows will have ample opportunities to explore and gain experience with multidisciplinary and clinical research in aging and Alzheimer’s disease and to interact with core faculty members in the MAP and the Carney Institute of Brain Science at Brown University. Applicants with a Ph.D. degree in cognitive neuroscience, neuropsychology, biomedical engineering, electrical engineering, computer science, physics or a relevant field are encouraged to apply. Prior experience with human neuroimaging (e.g., task fMRI, rsfMRI, MRI, DTI, ERP, PET), a strong background in cognitive neuroscience and experimental design, and familiarity with programming in relevant languages (e.g., Python, MATLAB, C) are desirable. The successful candidate is expected to demonstrate communication skills, motivation and interest in the area of cognitive and brain aging, Alzheimer’s disease, and/or neuroimaging, and the ability to independently develop research questions and work in collaboration with other team members. The MAP is part of the Department of Psychiatry and Human Behavior at the Warren Alpert Medical School of Brown University, which is located in Providence, Rhode Island. Providence is within one hour from Boston and 3 hrs from New York City by train/subway and provides an intellectually and culturally rich environment with a reasonable living cost. Please note that this postdoctoral position is research-centered and prior clinical experience is not required. Pursuing licensure for a clinical neuropsychologist is optional. The postdoctoral position is supported by the fellowship program up to 2 years, with a possibility of support in year 3 depending on funding. *The expected start date is late Summer 2019; however, it is negotiable**.* Review of applications will begin immediately and continue until the position is filled. Interested persons can find more information on the position in the websites listed below. This postdoctoral fellowship is administered though the Research Fellowship Program within *The Alpert Medical School of Brown University, Clinical Psychology Training Programs at Brown: A Consortium of the Providence VA Medical Center, Lifespan, and Care New England. * The program’s website is located here: https://www.brown.edu/academics/medical/about/departments/psychiatry-and-hu… A full description of the fellowship position can be found in the link below: https://www.brown.edu/academics/medical/about/departments/psychiatry-and-hu… Details regarding application are located here under “Application Details”: https://www.brown.edu/academics/medical/about/departments/psychiatry-and-hu… NOTE: As explained on the application page of our website, applications are submitted through the APPA CAS portal. Instructions are located on the webpage. *****Prior to APPA CAS application submission, interested applicants are strongly encouraged to send a brief description of their research background and career goals, CV, and a list of three references to Dr. Hwamee Oh via email **at hwameeoh(a)gmail.com <hwameeoh(a)gmail.com>.* For any inquiries on the research and the position, please contact Dr. Hwamee Oh, the Director of Imaging Research in the MAP, at hwameeoh(a)gmail.com.

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Area information on certain views
by Kim, Jisoo,M.D. 28 Jun '19

28 Jun '19

Dear freesurfer team, I searched the archives, but couldn't find this kind of question. I've used the brainstem segmentation tool to get the volume of each brainstem structures, but now I am trying to get the area (mm^2) of midbrian and pons on mid-sagittal view. Do you know of an easy way to do this on FreeSurfer? Thank you. Best, Jisoo

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converting correlation coefficient file into a table
by Wenzhen Zhao 27 Jun '19

27 Jun '19

External Email - Use Caution Dear List, I finished first level analysis of functional connectivity of all subjects with respect to Left hippocampus, and have several files (ces.nii.gz, pcc.nii.gz). Is there any command that I can convert this particle correlation coefficient (which I assume contain correlation coefficient of each voxel to Left hippocampus, please correct me if I am wrong) into a table showing functional correlation between left hippocampus and other ROIs ? Thanks, Wenzhen

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recon-all multiple subjects 'for' loop?
by Benjamin Stott 27 Jun '19

27 Jun '19

External Email - Use Caution Hello, I would like to run recon-all on multiple subjects. I have 650 subjects, so running them in separate terminals isn't an option. Each subject has their own folder (e.g. sub-CC121428) containing a single T1w.nii.gz file. Unfortunately, I have very little experience coding. I appreciate any advice you can offer. Benjamin

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mri_glmfit will not use mask or label
by Jennifer Legault 27 Jun '19

27 Jun '19

External Email - Use Caution Hi Freesurfer experts, I'm trying to constrain my sMRI analysis to only search for brain regions (GMV) that are correlated with a behavioral measure within a mask (made from a functional contrast of interest, so that I'm only searching for regions that were shown to be active during a language localizer task) using mri_glmfit. I've followed recommended steps to transforming my fMRI contrast into a surface mask, and then later even tried making it into a surface label, however whenever I run the analysis, I get the same results regardless of whether I use the --mask or --label option, meaning that the summary file (cache.th40.pos.sig.cluster.summary) includes regions that are outside the mask. How can I ensure that mri_glmfit actually uses the mask? I've included below the commands I have run. I previously ran mri_glmfit to search the whole brain for regions significantly correlated with behavioral measures using the following command: mri_glmfit --y fsgd_VSL_std_age_gender_TIV.volume.00B.mgh --fsgd fsgd_VSL_std_age_gender_TIV.txt --C Contrast_VSL_std_a_g_TIV.txt --surf fsaverage lh --cortex --glmdir lh.VSL_std_age_gender_TIV.glmdir Now, when I try to use the mask, I get the same results as above (significant result in regions outside of mask), using the following command: mri_glmfit --y fsgd_VSL_std_age_gender_TIV.volume.00B.mgh --mask localizer_mask.mgh --fsgd fsgd_VSL_std_age_gender_TIV.txt --C Contrast_VSL_std_a_g_TIV.txt --surf fsaverage lh --cortex --glmdir lh.VSL_std_age_gender_TIV_localizer_mask.glmdir I also converted the mask into a label just in case, and used the following command: mri_glmfit --y fsgd_VSL_std_age_gender_TIV.volume.00B.mgh --label <path>/freesurfer/fsaverage/label/LeftMidAntTemp_surf.label --fsgd fsgd_VSL_std_age_gender_TIV.txt --C Contrast_VSL_std_a_g_TIV.txt --surf fsaverage lh --cortex --glmdir lh.VSL_std_age_gender_TIV_localizer_label.glmdir Across all these conditions, I always get the same results (even if the significant region is outside of the mask). Are there any recommendations for steps I should take to make sure I'm only searching for regions inside the mask? Best, Jen -- Jennifer Legault PhD, Neuroscience Postdoctoral Scholar Language Acquisition and Brain Lab University of Delaware

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BA label questions
by Zeng,Victor (BIDMC - Psychiatry) 27 Jun '19

27 Jun '19

?Hi All, I'm revisiting an old dataset that was previously run using FS 5.1, and now we upgraded it to FS 6.0. I seem to notice there are different set of BA.labels, ones that are called ?h.BA.label, and ones (generated from 6.0) called ?h.BA_exvivo.label. Is ?h.BA.label deprecated by ?h.BA_exvivo.label? If not, what are the differences and how can we make ?h.BA.label in FS6.0? Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab ph: 617 754 1237 -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

Labelling SurfStat p-value surface map
by Loïc Daumail 27 Jun '19

27 Jun '19

External Email - Use Caution Dear Freesurfer community, I obtained score matrices of surfaces after performing diffusion embedding map on fMRI data. I am now using the SurfStat toolbox(Matlab) in order to obtain p-value maps to compare between two groups. After obtaining the p-value map, I would like to label the surface in order to identify the regions of significant difference between both groups. Would it be possible to use Freview in order to do it? If so, which format should I use for my SurfStatP output p-value map? How would you do it, (tools to convert into a specific format, surfaces and atlas to load on Freeview, which format for those ones)? I would be very grateful if you could detail a bit, as I am new to these tools! Thanks in advance, Loïc Daumail

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Help for smoothing the pial surface
by Nillo, Ryan Michael R 27 Jun '19

27 Jun '19

Hello FreeSurfer users/developers, I want to generate a smooth pial surface similar to the one displayed on the LGI page (https://surfer.nmr.mgh.harvard.edu/fswiki/LGI <https://surfer.nmr.mgh.harvard.edu/fswiki/LGI>) without having to run the entire recon-all process. Additionally, I want to map this surface to the white surface. Is there an easy way to do this? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging External Email - Use Caution

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Viewing clusters regardless of significance
by Amrita Bedi 26 Jun '19

26 Jun '19

External Email - Use Caution Hi Freesurfer developers, I’m using the glmfit tutorial to see clusters for my data. I’m trying to view the uncorrected clusters on tksuefer using the command line tksurfer fsaverage lh inflated -overlay /path to data/cache.th13.abs.sig.ocn.annot but don’t see any clusters. According to the cluster summary file there should be 2 clusters on the left hemisphere and 9 on the right. Thank you for your help.

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Freesurfer June 2019