Freesurfer May 2024

freesurfer@nmr.mgh.harvard.edu

56 participants
69 discussions

Subcortical surfaces from volume features.
by Sam Maddox (CMP - Postgraduate Researcher) 10 May '24

10 May '24

External Email - Use Caution Dear Freesurfer Experts, I am looking into generating subcortical surfaces from the subcortical volumes generated from recon-all. The reason for this is I am trying to create a vertex based Morphological Similarity Network generated from both cortical and subcortical regions. Ideally I would avoid Volume Based Statistics as, from what I can see, I am limited to just thickness features. I have run recon-all for all of my participants, and ideally my set up for surface subcortical features would be done in freesurfer as well, although I am aware of other tools such as: https://secure-web.cisco.com/1Naw6TVmVSgW4iHi_BvEcAItpkOmdAs3fMgTWn1abKwPfB… https://secure-web.cisco.com/1u1Ru_EifdWYQsjg7F-GHFGBp-Vkvjk_3iHSqwgV0CTWKw… https://secure-web.cisco.com/1yhlZBs4CaRuE7OrwrGVtEsQL33d47WfL9Yu02tKHEzKqG… https://secure-web.cisco.com/1SH8G6D-66tFkOVdkMhKlZU3DoZJWFrankZvFbDjhud520… inaivu/aseg2srf at master * aestrivex/inaivu * GitHub<https://secure-web.cisco.com/1Dfh65Cci0nD0VovbWbYJTBewgjEMy6UwWY0YW-6fsinPT…> The above tools may be able to generate subcortical surfaces, but I would then need to convert them back to freesurfer formats to run mris_anatomical_stats, which I am lost with. If anyone has any advice for this, this would be great! Within freesurfer, I am aware of tools such as mri_vol2surf, as well as other such as mris_sample_parc - Free Surfer Wiki (harvard.edu)<https://secure-web.cisco.com/1zui1UwPJX5g6ACi-dDQWDrdF2r3cGq_2t5-DhB34ZuQ87…>. I am a bit lost as to how to use these tools, as the documentation is limited, and threads are more looking at generating these surfaces for visualizations rather than anatomical statistics. I am also wondering if there are any additional processing steps, perhaps normalization, that may be required before creating the MSN. If anyone has tried this before or has any advice, I would love to hear. I am relatively new to this area, using freesurfer past recon-all, so any help is appreciated! Many thanks, Sam

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Contrast files - 2 groups, 4 covariates
by Liliana Wu 10 May '24

10 May '24

External Email - Use Caution Hello! I am having trouble with creating my contrast files. I did go over FsfdExamples (https://secure-web.cisco.com/1ezcK_pFVwJfmWpdVsJeZORU_8kaDi3SfZnw3BO98zpMkJ…) However, I am unsure how should I create my contrast files if I want do a 2 group comparison while controlling 4 covariates: Class: Patients, healthy control variables are: Age,gender,episodes,residuals, Here is how I set up my contrast files: 1 -1 0 0 0 0 0 0 0 0 - Contrast1 (measure group differences) 1 -1 0.125 0.125 0.125 0.125 0.125 0.125 0.125 0.125 – Contrast 2 (measure group differences while accounting for covariates) For some reason I think I am setting up those contrast files wrong… Any help is appreciated. Best, Liliana

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mri_segment_hypothalamic_subunits 7.4.1 issue
by Antonio Di Renzo 10 May '24

10 May '24

External Email - Use Caution Dear FreeSurfer developers, I have just tested the Segmentation of hypothalamic subunits, but unfortunately it does not work. I simply wrote: mri_segment_hypothalamic_subunits --s subject_folder or mri_segment_hypothalamic_subunits --s subject_folder/T1.nii or mri_segment_hypothalamic_subunits --s recon_all_processed_folder Every time the message is: Illegal instruction (core dumped). Moreover when I asked the help option: mri_segment_hypothalamic_subunits -h I obtained again: Illegal instruction (core dumped). I installed tensorflow as answered using: fspython -m pip install tensorflow but these libraries are installed already because the messages are: Requirement already satisfied written on every row. How can I use this function? Thank you in advance, Antonio ps. I used the following softwares Freesurfer version 7.4.1 Ubuntu 22.04.4 LTS Oracle virtual box for Windows 10 pro

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Re: [Freesurfer] MCR install for parcellation
by fsbuild 09 May '24

09 May '24

External Email - Use Caution  Hello Antonio, With the 7.4.1 release, you can install R2014b or R2019b matlab runtime environment into the freesurfer tree.  Earlier freesurfer releases use R2014b.  I would setup the freesurfer environment first, and then pass in the value of FREESURFER_HOME on the command line as listed below.  Below, I have shown using R2019b with a linux install of Freesurfer 7.4.1 using bash shell. - R. - - - - -  $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1                  <--- linux install path $ source $FREESURFER_HOME/SetUpFreeSurfer.sh <... output deleted ... showing SUBJECTS_DIR and other environment variables> $ cd  $FREESURFER_HOME/bin $ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2019b I believe this sets things up (for R2019b) so the libmwm* libraries are installed under $FREESURFER_HOME/MCRv97/bin/glnxa64.  You can try adding that path (or any path the fs_install_mcr script output recommends) to the start of LD_LIBRARY_PATH.  You should remove any other entries to a different MATLAB distribution other than the one you actually install. On May 9, 2024, at 12:45, Antonio Di Renzo <antoniomp777(a)hotmail.it> wrote:        External Email - Use Caution        Messers FreeSurfer developers,I dowloaded MCR zip file for linux in /home/vboxuser/Downloads from MatLab website.I extracted files in new foldern named Matlab_Component_Runtime_R2014b in Downloads.I am trying to install Matlab Component Runtime, but the the following command: fs_install_mcr R2014b does not work.Where can I find the right step by step MCR installation guide?Thank you,Antonio_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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MCR install for parcellation
by Antonio Di Renzo 09 May '24

09 May '24

External Email - Use Caution Messers FreeSurfer developers, I dowloaded MCR zip file for linux in /home/vboxuser/Downloads from MatLab website. I extracted files in new foldern named Matlab_Component_Runtime_R2014b in Downloads. I am trying to install Matlab Component Runtime, but the the following command: fs_install_mcr R2014b does not work. Where can I find the right step by step MCR installation guide? Thank you, Antonio

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Postdoc Positions in Cognitive Neuroscience/ Neuroimaging Genomics
by X K 09 May '24

09 May '24

External Email - Use Caution Postdoc positions are available at Zhejiang University (Hangzhou, China). The successful candidates are expected to work on multi-disciplinary projects in cognitive neuroscience, neuroimaging and computational modelling related to individual differences in language/spatial navigation, relevant brain networks, aging and disorders. The Cognomics Lab is led by Dr. Xiangzhen Kong, who has extensive experience in cognitive neuroscience and the application of computational modelling and neuroimaging genetics to investigate functional architecture of the human brain and how it supports human-defining cognition. We conduct large-scale studies using a variety of data sources including in-house datasets (e.g., fMRI, SEEG), and open data from UK Biobank and ENIGMA. We seek highly motivated candidates with a Ph.D. degree in cognitive neuroscience, psychology, bioinformatics, or computer science with biomedical applications, etc. The ideal candidates should be highly motivated to publish first-author papers and present at conferences, and are expected to have strong quantitative skills and experiences in programming and machine learning. Interested applicants should submit a CV, a letter briefing current research interests, and contact information for two individuals who can provide letters of recommendation to Dr. Xiangzhen Kong (*xiangzhen.kong(a)zju.edu.cn <xiangzhen.kong(a)zju.edu.cn>*). Positions will remain open until filled.

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Incorporating hi-res T2w image in longitudinal pipeline
by Raikes, Adam C - (adamraikes) 08 May '24

08 May '24

External Email - Use Caution Good afternoon, We are collecting hi-resolution T1w and T2w images (0.8mm3) in a pre-/post- design. I am using Freesurfer 7.4.1 to process the data and have been successful in ingressing the T2w images in the cross-sectional recon-all runs with -T2 <path> and -T2pial. Two questions: 1. When creating the base image, is there any value to using the T2s and, if so, is there a way to do that? 2. When running the -long step, I know that -T2pial is an option but do I need to pass -T2 <path> with it? If I need the path, should it point to the original image or something from the cross/mri folder? Thanks Adam C. Raikes, PhD Imaging Projects Manager Center for Innovation in Brain Science University of Arizona

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outcome directions of longitudinal two stage model
by L 08 May '24

08 May '24

External Email - Use Caution Dear exports, I am wondering whether the outcomes of the longitudinal two stage model is tp1 - tp2 or tp2 - tp1. Thank you, Lihong Wang -- - Lihong

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surface and cortical thickness normalization
by yunus soleymani 08 May '24

08 May '24

External Email - Use Caution Hello, I hope you are doing well. Yesterday, I had some questions regarding normalization in Freesurfer. Thanks to Dr. Douglas N. Greve, I received answers for all of them. However, I still have one more question. When I normalize brain surfaces to eTIV, they appear to be in two different units (mm2 and mm3). Will this be a problem? Additionally, I would like to know your thoughts on normalizing cortical thicknesses. Do you think they should be normalized to eTIV, or would it be better to normalize them to the mean cortical thickness of each subject? I would greatly appreciate your response. Thank you, Yunus --------------------------------------------------------------------------------Yunus Soleymani Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences soleymani.yunus(a)yahoo.com+98 914 526 9298--------------------------------------------------------------------------------

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Difference between 2 ways to set up fsgd file and contrasts
by Lydia Chung 08 May '24

08 May '24

External Email - Use Caution Hi FS support team, I am going to be using mri_glmfit to test 1) main effects (which regions show differences in cortical thickness between group 1 and group 2) and 2) interaction effects (does the relationship between IV and DV depend on moderator). Depending on the model, the IV is sometimes a binary categorical variable and sometimes a continuous variable. The moderator is always continuous. So, interaction effects are either continuous x continuous OR categorical x continuous. One thing I'm trying to understand is whether the two examples below are basically two different approaches that answer the SAME question: Do people in Group 1 differ from Group 2 on cortical thickness? Version 1 is the one provided by FS and Version 2 is an analog of another setup I have been provided by colleagues. Are these models answering the same or different questions? The freesurfer link below also shows an example of how to do an interaction (Group x Age) using Version 1 setup; for Version 2 setup of an interaction, I know I would multiply the IV and Moderator before this step so that I would have an additional "interaction variable" column to add as one of the 'Variables' listed in the fsgd code. So, I'm also curious if the two different methods of testing an interaction (in addition to the first question about the main effect) will get you the identical answer OR if there is something conceptually different? Do the nuances of this setup have to do with the difference between using DODS or DOSS? *Main effect of Group on cortical thickness Version 1 (copied from FS example. link here <https://secure-web.cisco.com/1cgzre8FgLw0c17s9QNhmU_14vQ714XlLV20U4K14P96Af…>)* GroupDescriptorFile 1 Title OSGM Class Group1 Class Group2 Variables Age Weight Input subject1 Group1 30 100 Input subject2 Group2 40 120 Contrasts: 1 -1 0 0 0 0 (to test main effect of group; this feels like an anova approach?) *Main effect of Group on cortical thickness Version 2* GroupDescriptorFile 1 Title OSGM Class Subjects Variables Group Age Weight Input subject1 Subjects 0.5 30 100 Input subject2 Subjects -.5 40 120 contrasts: 0 1 0 0 (to test main effect of group; this feels like a linear regression approach?) Thank you in advance for your help! Lydia -- Lydia Wu-Chung, M.A. Doctoral candidate BMED Lab Department of Psychological Sciences Rice University 6500 Main St - MS201 Houston, TX 77030 Lab Phone: 713-348-8126 Email: lydia.wu(a)rice.edu <lw50(a)rice.edu> *Confidentiality Text:* The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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