Freesurfer

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18 participants
30131 discussions

MGH35 template
by Maffei, Chiara,PHD 22 Feb '23

22 Feb '23

Hi Mark, Sorry for the late reply. The population template was built using the FA images only, so there is no corresponding T1 template image. You can use the transforms stored in dmri/xfms in your TRACULA directory to map the subject’s anatomical images to this template space, or you can set the interreg variable in your dmrirc configuration file to 1 or 2 to have your TRACULA common space be the MNI152 T1 1mm space instead. I hope this helps, Chiara Dear Freesurfer developers, Hi, this message may have slipped through the cracks, hope someone can help us out on this. We're looking for the T1 image that goes along with (i.e. in same space, or at least in same participants) as the MGH35_HCP_FA_template image which is used in TRACULA? Does such a template exist, and if so, would it be possible to share? Thanks so much! Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.ed<mailto:mark.wagshul@einsteinmed.edu>

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Re: [Freesurfer] mri_easyreg tool
by Iglesias Gonzalez, Juan E. 22 Feb '23

22 Feb '23

Sorry for the late response, I went on vacation the very same day you posted your question. The floating image is the one you want to deform, and the reference image is the one you use as target for the registration /deformation. In other words: the deformed floating image should overlap with the reference image. More information here: https://surfer.nmr.mgh.harvard.edu/fswiki/EasyReg Kind regards, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Peters, Johnny Y" <jonathan-peters(a)uiowa.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, February 10, 2023 at 11:40 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_easyreg tool External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to use the mri_easyreg on the developmental version of freesurfer but I am confused about what .mgz or .nii(.gz) I am supposed to use for the reference image, floating image, and the others. I saw no previous threads on the mailing list addressing my question so I decided to email you. Would you be able to give an example command line using the subject bert in the freesurfer directory? Thank You

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Correlating and/or linear regressing surface overlays
by Finn, Quentin 22 Feb '23

22 Feb '23

External Email - Use Caution Freesurfer experts, I have some surface data that I'd like to correlate with some other data, although a linear regression would also be fine if I could get something like a t-stat out of it. This data came from two different PET tracers -- voxelwise data was resampled via vol2surf onto each subjects cortical surface: So I have, say, data like this: tracer1_subj1_lh.mgh tracer1_subj2_lh.mgh . . . . tracer1_subjn_lh.mgh And then I have another set: tracer2_subj1_lh.mgh tracer2_subj2_lh.mgh . . . . tracer2_subjn_lh.mgh I'd really like to just stack them all up with mris_preproc, something like this: mris_preproc --is tracer1_subj1_lh.mgh --is tracer1_subj2_lh.mgh [etc] --is tracer1_subjn_lh.mgh --out tracer1_lh.mgh --hemi lh --fsgd tracer1.fsgd mris_preproc --is tracer2_subj1_lh.mgh --is tracer2_subj2_lh.mgh [etc] --is tracer2_subjn_lh.mgh --out tracer2_lh.mgh --hemi lh --fsgd tracer1.fsgd The FSGD's are the same because the subjects are the same. and then run something like... mri_glmfit --glmdir tracer1_tracer2_left --y tracer1_lh.mgh --fsgd tracer1.fsgd --pvr tracer2.mgh --no-contrasts-ok --surface fsaverage lh This doesn't have an output that's really what I'm looking for as far as I can tell though, there's no fit statistics type overlay in the output folder, probably because I'm doing something wrong. Any help on this would be just wonderful! -quentin finn Houston Methodist. Leading Medicine. U.S. News & World Report has named Houston Methodist Hospital the Best Hospital in Texas for 11 years in a row. Houston Methodist is the No. 1 hospital in Texas and No. 15 in the nation. For more than 100 years, Houston Methodist has provided the best — and safest — clinical care, advanced technology and patient experience. That is our promise of leading medicine. houstonmethodist.org twitter.com/MethodistHosp facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Hole in the insula
by Aaron Tanenbaum 22 Feb '23

22 Feb '23

External Email - Use Caution I have this subject that has holes in the insula. Please see attached. I was wondering what should freesurfer have classified it as.

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Please unsubscribe me
by Manuela Dorado Novoa 22 Feb '23

22 Feb '23

External Email - Use Caution Hi, Please, unsubscribe me from your mailing list. Thank you, Manuela

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Nuisance regressors
by Marilena Wilding 22 Feb '23

22 Feb '23

External Email - Use Caution Hi Freesurfers! I would like to compare the effect of different nuisance regressors (I.e., cardiac and respiratory signal, motion) on my resting-state data. For that I’m adding the respective regressors to my first-level GLM. Now, how can I best compute a contrast between the effect of different physiological regressors and motion? Would I add them as task regressors in 1st level or rather as nuisance regressors and how can I get second-level comparison of their effect? Thanks in advance for your help! Best, Maria

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Extracting brain volume seperately
by 江一川(JIANG Yichuan) 22 Feb '23

22 Feb '23

External Email - Use Caution Dear Experts, How can I extract scalp, skull, csf, gray, and white volume, seperately. Best wishes,Yichuan Jiang

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Re: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS
by fsbuild 22 Feb '23

22 Feb '23

External Email - Use Caution The best solution (which I think was previously emailed to you) is to have an admin/IT person update your system by doing the following: 1) Copy the link for the freesurfer release install package matching your Ubuntu system, e.g., 7.3.2 freesurfer release on Ubuntu 18, 20, 22, from https://secure-web.cisco.com/1yhwT1AT1siR71m0xkciflHcVEcWiQ2tB105s7o77YZsEO… 2) Download and install it with, $ wget <link copied from the web page above> .... say wget downloaded the file freesurfer_ubuntu18-7.3.2_amd64.deb  .... $ sudo apt-get install ./freesurfer_ubuntu18-7.3.2_amd64.deb That should install libncurses and anything else that's needed automatically.   Trying to piecemeal run commands to install individual system packages like libncurses is asking for more trouble. - R. On 2/22/23 10:54, Iglesias Gonzalez, Juan E. (JIGLESIASGONZALEZ(a)mgh.harvard.edu) wrote: Thanks for the interest in our software! Could you please try running this command from the terminal? sudo apt-get install libncurses5 Cheers, /Eugenio -- Juan Eugenio Iglesias http://secure-web.cisco.com/1KWPEVNu98oFkAEfRE8iBX30sj9pfVOIOS35SyW9UbpZ5sF…   From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of behçet ayyıldız <behcetayyildizz(a)gmail.com> Reply-To: Freesurfer support list <Freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, February 15, 2023 at 05:36 To: "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS           External Email - Use Caution         Dear All,  I was using Linux Ubuntu to perform my analysis. However, they were changed with Linux ..... a couple of days ago. And while the segmentThalamicNuclei.sh command was running before the change, after the change it didn't run and I got the following message.     drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ segmentThalamicNuclei.sh con_HaJa93 Setting ITK threads to 1 #-------------------------------------------- #@# Thalamic Nuclei processing Wed 15 Feb 2023 11:09:10 AM CET ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is ..:/sw/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/sw/freesurfer/7.1.1//MCRv84//bin/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sw/freesurfer/7..1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64: /sw/freesurfer/7.1.1//bin/SegmentThalamicNuclei: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory 127 Linux causal.brain.mri.tu-muenchen.de 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux   Do you guys have any idea how to fix it ?   Thanks in advance.   -- Behçet Ayyıldız.. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1ZBVZ5ZFSgmC71czIQz4JvouTmwCxl02_s_J7s7c5bFqzK… 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/1uQh2dF_tlYNnlReyb0WMNt1TLudo-l-6mkcvTuxmwVyoc… <https://secure-web.cisco.com/12zNRlJSicLgYfTc0OYTVbWFw67p4yuUW1gCGXLvqY60EZLB05C6R2lHBY3J0Gtv4gl3IfQyBofVg0B-vYhH6QczA7kQhDa4JkGtGaFh04VLDRkrWnQtFxs02mz9f0wFGdO4EzYTqNu0tqaOT5h4pEzcJFTFrQDbc6oDpeWWMOBJqPP2uMuJaAGzjknLwZ3kBZuUs0a9FPdL12Zi6u6HM-Dxm59CUSLPCjUVNMHfAa1ty9N70G2NfQyuK_4K9cN3q18FFgIlrG6OnkVxiHBoiEMdh3dd7RmhYAt7XXP9mAOrmpxwdmGE3L31CUXdrtEXE/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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SEEKING A DYNAMIC POSTDOC TO INVESTIGATE BRAIN GUT MICROBIOME INTERACTIONS
by Arpana Annie Gupta 22 Feb '23

22 Feb '23

External Email - Use Caution > Dear Freesurfer Community, > > We are looking for a postdoc for this exciting position (2-3 years)- details below > > https://secure-web.cisco.com/1WHR8pdGZ0jD4fwtdRnmuQyzhK93d-z7GyJPzAcC5ZgWly… <https://secure-web.cisco.com/1WHR8pdGZ0jD4fwtdRnmuQyzhK93d-z7GyJPzAcC5ZgWly…> > > > https://secure-web.cisco.com/1hhsXFQO3_XzW7eqkp7i_t1kyJoD1KGKvCjC_NxMu-HJ2U… <https://secure-web.cisco.com/1hhsXFQO3_XzW7eqkp7i_t1kyJoD1KGKvCjC_NxMu-HJ2U…> > > The Goodman-Luskin Microbiome Center in the Division of Digestive Diseases at the University of California Los Angeles is seeking a full time Post-Doctoral Research Fellow for a U54-funded project studying sex-related differences in the brain-gut-microbiome interactions related to visceral pain. This project is focused on the sex-specific effect of gut microbial metabolites, and estrogen levels on ascending arousal pathways originating in distinct brainstem nuclei to change the activity and connectivity of brain networks involved in symptom generation in irritable bowel syndrome. > > As a part of an multidisciplinary research team the fellow will apply advanced computational, neuroimaging, biostatistical, and bioinformatics approaches to assess the interaction between various levels of biological data (e.g., microbiota, metabolites, sex hormones, multimodal brain and brainstem imaging data), clinical variables (symptom severity, widespread pain) and sex. > > There will be opportunities to develop translational and clinical neuroscience research skills (e.g., target discovery, individualized treatment development and biomarker/predictor development), in addition to state-of-the-art analytical skills to address basic and pathophysiological systems biology questions. > > The Goodman-Luskin Microbiome Center is an interdisciplinary, translational Center funded by the National Institutes of Health, and by philanthropic support. The overall research goals of the Center are to better understand the interactions between mind brain and body in health and disease, and to develop novel management strategies for optimal health and for complex chronic disorders. > > Center investigators are conducting clinical, translational and basic research with human populations, using interventions (e.g., diet, cognitive behavioral therapy) alongside deep phenotyping including neuroimaging, mutli-omics profiling (gut microbiome, metabolomics, inflammatory biomarkers, psychosocial and behavioral assessments. You will work directly with Arpana Gupta, PhD and Jennifer Labus, PhD and an array of faculty collaborators across UCLA, and beyond. > > There will be many opportunities to lead high impact publications starting on day one, working with existing rich and unique datasets in addition to creating new ones. Extensive mentorship will be provided to facilitate the transition to an independent research career. > > Duties and Responsibilities: > > The Post-Doctoral Fellow’s responsibilities will include, but are not limited to: > > Develop longitudinal multimodal MRI data analysis streams (functional connectivity, task-based fMRI, diffusion tractography and volumetrics). > Analyze complex multi-omics datasets including imaging, gut microbiome, metabolomics, behavioral and clinical data. > Prepare and submit manuscripts > Mentor graduate and undergraduate students > Be inquisitive, curious and publish! > Required Qualifications: > > Ph.D. in Neuroscience, Neuropsychology, Bioinformatics, Biostatistics, Engineering, Computer Science or a related field. > Strong proficiency and independence with various neuroimaging analysis platforms, multivariate modeling strategies and network connectivity analyses. > Established quantitative and statistical skills, including strong programming skills and comfort with diverse computing environments. Experience with R, Linux, Matlab or Python preferred. > Background in systems/cognitive neuroscience, neuroanatomy and psychological/clinical constructs. > A demonstrated capacity to drive first author publications. > Excellent communication and writing skills, motivated and driven to publish. > Preferred Qualifications: > > Connectomics network analysis and machine learning modeling confer a very significant advantage. > Management/coding of neuroimaging databases (XNAT or others). > > Arpana "Annie" Gupta, Ph.D. > Associate Professor > Director: Neuroimaging Core > G. Oppenheimer Center for Neurobiology of Stress and Resilience > Ingestive Behavior and Obesity Program > UCLA Vatche and Tamar Manoukian Division of Digestive Diseases > David Geffen School of Medicine > UCLA CHS 42-210, 10833 Le Conte Avenue | Los Angeles, CA 90095-7378 > Email: agupta(a)mednet.ucla.edu <mailto:agupta@mednet.ucla.edu> > https://secure-web.cisco.com/1hhsXFQO3_XzW7eqkp7i_t1kyJoD1KGKvCjC_NxMu-HJ2U… <https://secure-web.cisco.com/1hhsXFQO3_XzW7eqkp7i_t1kyJoD1KGKvCjC_NxMu-HJ2U…> > https://secure-web.cisco.com/1hEK-fceY0ve7vGXpNdkOtpqNx7-FslJ199inEtjRniL1s… <https://secure-web.cisco.com/1hEK-fceY0ve7vGXpNdkOtpqNx7-FslJ199inEtjRniL1s…> | Twitter: @AGuptaCNS > > This message (including any attachments) contains confidential > information intended for a specific individual and purpose, and is > protected by law. If you are not the intended recipient, you should > delete this message and any disclosure, copying, or distribution of > this message, or the taking of any action based on it, by you is > strictly prohibited. >

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segmenThalamicNuclei.sh exited with ERRORS
by behçet ayyıldız 22 Feb '23

22 Feb '23

External Email - Use Caution Dear All, I was using Linux Ubuntu to perform my analysis. However, they were changed with Linux ..... a couple of days ago. And while the segmentThalamicNuclei.sh command was running before the change, after the change it didn't run and I got the following message. drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ segmentThalamicNuclei.sh con_HaJa93 Setting ITK threads to 1 #-------------------------------------------- #@# Thalamic Nuclei processing Wed 15 Feb 2023 11:09:10 AM CET ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/sw/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/sw/freesurfer/7.1.1//MCRv84//bin/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64: /sw/freesurfer/7.1.1//bin/SegmentThalamicNuclei: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory 127 Linux causal.brain.mri.tu-muenchen.de 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux Do you guys have any idea how to fix it ? Thanks in advance. -- *Behçet Ayyıldız..*

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