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The Affective Neuroscience Project of the Midlife in the U.S. (MIDUS) study is recruiting a multimodal imaging scientist
by STACEY M SCHAEFER 11 Jun '24

11 Jun '24

External Email - Use Caution The Midlife in the U.S. (MIDUS; https://midus.wisc.edu/) Affective Neuroscience Project Team is excited to bring on an energetic and skilled Ph.D.-level scientist to join our dynamic team and ask questions within the national, longitudinal data to inform public health and wellbeing. The successful candidate will work in collaboration with members of the team to address critical scientific questions related to the factors contributing to brain mechanisms underlying emotional processes, cognitive decline, and brain aging with a goal of informing public health and social change to optimize emotional wellbeing and brain health. This position requires analytic thinking, expertise analyzing multimodal MRI data (e.g., structural MRI, task and resting state fMRI, diffusion weighted imaging, and perfusion imaging data), and the ability to apply technical innovation to neuroscience problems relevant to public health and wellbeing. The position is open to a qualified scientist with evidence of training in applying quantitative solutions to neuroscience imaging data and at least 2 years of post-doctoral experience. Please distribute this far and widely to anyone who may be interested and anywhere people might see it who have the skills and interests to work with our team. Please share with relevant neuroimaging, neuroscience, and psychology societies, departments, schools, and universities. Thanks very much! For more information on the position, please see: https://aging.wisc.edu/join-us/ https://jobs.wisc.edu/jobs/multimodal-imaging-scientist-madison-wisconsin-u… For more information on the MIDUS Affective Neuroscience team, please see: https://aging.wisc.edu/midus-affective-neuroscience-project/ Stacey M. Schaefer, Ph.D. Leader of the MIDUS Neuroscience Project & Co-Leader of the MIDUS Admin Core Institute on Aging 2245C Medical Sciences Center University of Wisconsin-Madison 1300 University Ave Madison, WI 53706 USA 608-265-3486

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Unequal size groups
by stdp82＠virgilio.it 11 Jun '24

11 Jun '24

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Fwd: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus
by Ahsan Ali 11 Jun '24

11 Jun '24

External Email - Use Caution Hello everyone, Could anyone please help me to know which Atlas is used in the segmentation of corpus callosum, hippocampus, and fornix using freeSurfer from Brian MR images. I have gone through the literature but couldn't find it. With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics (Biomedical Engineering Group) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552 ---------- Forwarded message --------- From: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu> Date: Wed, May 22, 2024, 10:52 PM Subject: RE: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus To: Ahsan Ali <ahsan889960(a)gmail.com> Can you please post to the list so that others can answer? *From:* Ahsan Ali <ahsan889960(a)gmail.com> *Sent:* Wednesday, May 22, 2024 1:04 PM *To:* Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu> *Subject:* Re: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus * External Email - Use Caution * Dear sir, It is not clear from these papers to me. With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics (Biomedical Engineering Group) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552 On Wed, May 22, 2024, 8:19 PM Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu> wrote: Mostly these: https://secure-web.cisco.com/1DKaAagv5wrZcn_HucsSWH8TG1zknHKvHLkGgJhoy1pwq5… <https://secure-web.cisco.com/1HR13_22Yz_9WpJjcigfRprjowpMV_nRs6XlxrY4Yb6j-e…> https://secure-web.cisco.com/1XuxKv5CEuHRfXAdPzciFLM-HiNv8hX8h1hN2vYlGz0J9u… <https://secure-web.cisco.com/1uYxJbJpTbAO8ILMWce1OXOAM2VlXwJ80ARMpic7_Y4CDC…> cheers Bruce *From:* Ahsan Ali <ahsan889960(a)gmail.com> *Sent:* Wednesday, May 22, 2024 4:31 AM *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>; Huang, Yujing <YHUANG43(a)mgh.harvard.edu>; Fischl, Bruce R.,PHD < BFISCHL(a)mgh.harvard.edu> *Subject:* Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus * External Email - Use Caution * Dear FreeSurfer Team, After reviewing the literature, I have a question: which atlases are used in the segmentation of the fornix, corpus callosum, and hippocampus from magnetic resonance images using FreeSurfer? This is a significant question for me, and I would appreciate a clear and concise answer. Please provide some relevant references. With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics and Biomedical Engineering (AMBE) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1OM4mcc50Qfe8k4W6OcHgaA943SBzfkdd7bNh8ZqMDtb9_… <https://secure-web.cisco.com/1N0MvKNFIBgTBpwH0_fE4Erq9GYA9l1dAIs9zS_j_cM3I1…> . 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1OM4mcc50Qfe8k4W6OcHgaA943SBzfkdd7bNh8ZqMDtb9_… .

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Intensity affected after using -c flag in mri_convert
by ERNEST KISSI 11 Jun '24

11 Jun '24

External Email - Use Caution Dear fresurfer team, Why does the use of conform flag (-c) in mri_convert affect the intensity of the image? I have an image with absolute intensity of 1000 and after using the conform flag in mri_convert, the intensity is around 98.1. why is there a different scale in the intensity after the use of the flag?

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Transformed geometry does not match
by Yasmine Salman 11 Jun '24

11 Jun '24

External Email - Use Caution Dear FreeSurfer developers, I am trying to run longitudinal recon-all -long command. For some subject the recon-all -long command does not work and the error message indicate that 'transformed geometry does not match". I checked and the initial recon-all finished without error as well as the recon-all -base. I also tried to re-run de base but it does not help. Knowing that recon-all -long command worked for the majority of my subjects, what can explain that it does not work for some of them ? And how can we solve that problem ? Thanks in advance for your help, Best, Yasmine

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Issue with cortical data extraction for mkanalysis-sess
by O'Dor, Sarah 11 Jun '24

11 Jun '24

We are trying to run resting state connectivity analyses using amygdala ROI. The left hemisphere ran fine, but for the right hemisphere, something is clearly off. When we export the results into a table, the unknown column, which should be zero, has values, and one of the regions instead has zeroes. It’s as if something is shifted, but we’ve checking the coding. Briefly, the commands we used were mri_vol2vol, fcseed-config, fcseed-sess, mkanalysis-sess, selxavg3-sess, mri_glmfit, mri_segstats. Any ideas on where/which commend we should be troubleshooting? We’ve run it twice and gotten the same results. Thanks, Sarah

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negative values converting mgz files to nifty
by Nina Rouhani 11 Jun '24

11 Jun '24

External Email - Use Caution hello! after freesurfer segmentation (through fmriprep v23), i converted the aparc+aseg.mgz file into a nifty file using the below code (freesurfer v7.4.1): -rl $fs_dir/mri/rawavg.mgz -rt nearest $fs_dir/mri/aparc+aseg.mgz $sub_dir/rois/anatomical/aparc_aseg2mprage.nii.gz however, the voxel values of the aparc_aseg2mprage.nii.gz range between 31000-32000 and -31000- -32000. consequently, the label values for particular regions no longer correspond to what’s in the freesurfer manuals (like those listed here: FsTutorial/AnatomicalROI/FreeSurferColorLUT - Free Surfer Wiki <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurf…> ). would be incredibly grateful if i could be pointed to what i’m missing or what could be going wrong! thank you!

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Bug in mri_convert reslice-like with 4D images
by Iglesias Gonzalez, Juan E. 11 Jun '24

11 Jun '24

Dear FS experts, We get a segfault when I try to resample images with the command: mri_convert input.mgz output.mgz -rl reference.mgz when reference.mgz has multiple frames (e.g., a RGB volume). Any idea of why this is happening? Cheers, /Eugenio (&Stefano & Pranav)

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INTERNATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE IN HEALTHCARE (AIiH)
by Jiaxiang ZHANG 11 Jun '24

11 Jun '24

External Email - Use Caution [apologies for cross-posting] *INTERNATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE IN HEALTHCARE (AIiH)* 4 - 6 September 2024, Swansea, UK https://aiih.cc (*2nd CALL FOR ABSTRACT*) Submission deadline: Monday 1 July (FIRM) *1. INTRODUCTION * https://aiih.cc/abstracts/ AIiH 2024 welcomes late-breaking short abstract submissions to be included as poster or short spot-light presentation at the conference. This is to both enable fast dissemination of promising preliminary findings and encourage attendance by a broader audience of early career researchers (including research students), healthcare professionals, and industrial practitioners. AIiH 2024 is a single-track conference with oral and poster presentations and will include a conference tutorial on generative DNNs and 5 keynote presentations. The conference will also feature a plenary session, which consists of 3 invited speakers who have extensive experience in related areas. AIiH aims to provide a prominent platform for researchers and practitioners who are devoted to improving healthcare using modern artificial intelligence. We recognise that healthcare applications present complex and sometimes unique challenges across a wide spectrum, from ethics to technical developments, that generic AI methods are often inadequate. By creating this dedicated forum, we encourage discussions and disseminations of efficient and effective AI solutions and technologies for healthcare, and in turn we hope to influence the research, technology adoption, and decision making in healthcare. *2. CONFERENCE TUTORIAL* Title: Deep Generative Neural Networks https://aiih.cc/tutorial-generative-dnn/ Dr. Amir Atapour-Abarghouei University of Durham *3. KEYNOTE SPEAKERS* https://aiih.cc/keynote-speakers/ Prof. Hao Ni University College London Dr. Timothy Rittman Cambridge University Dr. Konstantinos Kamnitsas Oxford University Prof. Jacques Fleuriot Edinburgh University Prof. Eiichiro Tanaka Waseda University, Japan *4. PLENARY SESSION ON TRANSLATING AI RESEARCH INTO PRACTICE* https://aiih.cc/plenary-session/ Dr. Alba Di Pardo IRCCS Istituto Neurologico Mediterraneo Neuromed Dr. Noura Al Moubayed Durham University & Evergreen Life Dr. Haoda Fu Eli Lilly and Company *5. ABSTRACT SUBMISSION* Submission instructions are available at the conference website: https://aiih.cc/abstracts/ IMPORTANT DATES Abstract deadline: Monday 1 July (FIRM) Abstract notification: Monday 8 July (FIRM) Abstract registration: Monday 15 July Late registration: Monday 12 August Main conference: Wednesday 4 – Friday 6 September 2024 *6. ORGANISERS* CONFERENCE GENERAL CHAIRS Xianghua Xie, Swansea University, UK Iain Styles, Queen’s University Belfast, UK PROGRAMME CHAIRS Gibin Powathil, Swansea University, UK Marco Ceccarelli, University of Rome Tor Vergata, Italy SPECIAL SESSION CHAIRS Jiaxiang Zhang, Swansea University, UK Rex Ying, Yale University, USA SPONSORSHIP CHAIRS Daniele Cafolla, Swansea University, UK Raoul van Loon, Swansea University, UK PUBLICITY CHAIRS Lu Zhang, Swansea University, UK Beiyu Lin, University of Nevada, USA PUBLICATION CHAIR Jingjing Deng, Durham University, UK *7. SPONSORS* Gold: - Technis Blu - Infordata Silver: - Amicus Therapeutics Bronze: - Zienkiewicz Institute for Modelling, Data and AI - IET Institution of Engineering and Technology Your Researcher Sponsor: - Elsevier Journal of Theoretical Biology Best Paper Award Sponsor: - Springer *8. CONTACT* contact(a)aiih.cc <contact(a)aiih.cc>

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Incoporating synthstrip and synthseg into recon-all
by Dan Levitas 07 Jun '24

07 Jun '24

External Email - Use Caution Hello, I am using freesurfer version 7.4.1, and would like to incorporate the recently introduced synthstrip and synthseg functions into my recon-all command, if that's possible. From this archive message ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg75148.html) it seems that adding the -synthstrip option enables synthstrip; however, I don't see this as an option in the recon-all documentation ( https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all) nor as a command line option for recon-all. Assuming that both synthstrip and synthseg can be used in recon-all, would the command need to look something like this: *recon-all -subjid sub-${sub}_ses-${ses} -i $anat_file -3T -synthstrip --no-csf -synthseg -qcache -all* I'm adding the *--no-csf* synthstrip option based on this comment ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg75172.html) I should also note that I'm performing a longitudinal analysis, so this specific recon-all pertains to the cross-sectional portion of the workflow. Thanks, Dan

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