Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30075 discussions

Incorporating samseg segmentation into the recon-all pipeline
by Cerri, Stefano 14 Jun '22

14 Jun '22

Hi Julian, You can use the command "samseg" with the --recon flag. See the helper function for more details (--help) Stefano External Email - Use Caution /Hello everyone,/ /We have been utilizing freesurfer for our brain morphometry and processing pipelines, and have recently tested the samseg segmentation algorithm on a clinical cohort./ /With respect to some regions, we currently prefer its results to the ones generated by the standard freesurfer segmentation algorithm. / /As SAMSEG only provides volume calculation (please correct me if I am wrong) and does not feature cortical thickness measurements,/ /I was wondering if the recon-all pipeline can be modified to utilize the samseg segmentation instead, and if so, which script(s) or chain of commands would be a good starting point to implement this./ /Looking forward to your feedback,/ /Julian / Julian McGinnis PhD Candidate TUM-Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany Department of Computer Science, Technical University of Munich, Munich, Germany Email:julian.mcgin...@tum.de _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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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mri_label2vol with fill-ribbon option
by Wu, Junjie 14 Jun '22

14 Jun '22

External Email - Use Caution Dear Freesurfer experts,, I tried to use mri_label2vol with fill-ribbon option to covert the surface-based label of perirhinal cortex into the volume (an ROI in mgz file). However, when I typed "mri_label2vol --fill-ribbon --label lh.entorhinal_exvivo.thresh.label --o lh.entorhinal_exvivo.thresh.nii --identity" in the command line, an error popped up, saying "ERROR: Option --fill-ribbon unknown". Do you have any solution in order to make it work? Thanks, Junjie

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Exciting Postdoc Position at UCLA
by Arpana Annie Gupta 13 Jun '22

13 Jun '22

External Email - Use Caution Dear Freesurfer Community, We are looking for a postdoc fr this exciting position (2-3 years)- details below https://secure-web.cisco.com/1wp5qnfMl6kH8tGZQqKIFBkrm-7MMorOxY-JjeSnDeCwRf… <https://secure-web.cisco.com/1wp5qnfMl6kH8tGZQqKIFBkrm-7MMorOxY-JjeSnDeCwRf…> Thanks Annie The Center for Neurobiology of Stress and Resilience 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 G Oppenheimer Center for Neurobiology of Stress and Resilience (CNSR) is an interdisciplinary, translational Center funded by the National Institutes of Health, and by philanthropic support. The overall research goals of the CNSR 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 “Annie” 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 https://secure-web.cisco.com/1Td84IwBPHD8C0Xja4FKyZS6G3wT_dgKSL5Vqmzs05avLQ… | 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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Trac-all error assistance
by Emmanuel Rodríguez Silva 13 Jun '22

13 Jun '22

External Email - Use Caution Hello, freesurfer developers I was running the trac-all command for infant images. But I got an error during the cst processing. I've already checked the mailbox to find similar issues, but it seems that there are several logic errors. I will appreciate any assistance on this matter. I' m attaching my trac-all.log file for reference. Thank you. This is the exact error: terminate called after throwing an instance of 'std::logic_error' what(): basic_string::_S_construct null not valid Abort (core dumped) best, Emmanuel from Mexico -- Saludos cordiales Emmanuel Rodríguez Silva Contacto: (044) 55 59 97 76 18 Licenciado en Manejo Sustentable de Zonas Costeras *UNAM*

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7z passcode
by Lindner, Thomas 13 Jun '22

13 Jun '22

External Email - Use Caution Hello, I try to install FreeSrufer in the Virtual Box and wanted to inquire for the passcode for the archive. I already got a license. Best, Thomas PD Dr. habil. Thomas Lindner MRT Physik Universitätsklinikum Hamburg-Eppendorf Klinik und Poliklinik für Neuroradiologische Diagnostik und Intervention Martinistraße 52 Gebäude West 14, Raum 57 20251 Hamburg Telefon: +49 (0) 1522 281-6068 Fax: +49 (0) 40 7410-40114 t.lindner(a)uke.de<https://secure-web.cisco.com/14usmkgRpvd5xxCiTPznBPbi5aCfp3GrnVcnZU54SMcMHY…> http://secure-web.cisco.com/1Y4B8P9UqEywb5Hsn3XKBb8t_-VA52lOT5OQBCjnzoSiN1X…<https://secure-web.cisco.com/1dqgYPpKWQv14jcXrVHmf0-tWFSJ2gGqxBTUErc3nmxZkU…> https://secure-web.cisco.com/13bEOcWh6AZVsZg0_1ijjkkEAEB_gyQkzxY9N99dJjuxq5…<https://secure-web.cisco.com/1OxZfQ7jcP8kvGAAVt-5Bup02Jiz-gnWgn6GD0hJW8e2Mx…> -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | http://secure-web.cisco.com/1Y4B8P9UqEywb5Hsn3XKBb8t_-VA52lOT5OQBCjnzoSiN1X… Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

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mri_vol2surf with --projopt
by Kamiya Kouhei 13 Jun '22

13 Jun '22

External Email - Use Caution Dear FreeSurfer experts, I have a question on the usage of mri_vol2surf's option, "--projopt". What I want to do is to map the diffusion scalar value (like mean diffusivity [MD]) to the cortical surface. Though mri_vol2surf with --projfrac 0.5 worked pretty well, I also tried with --projopt which I assumed to yield better dealing with the partial volume effects. However, when I run with --projopt, I encountered the following errors. ....... error: GM estimation at vno 31257 couldn't find enough samples error: GM estimation at vno 31258 couldn't find enough samples ....... It looks the code tells me there is not enough data to solve the problem. Could you please instruct me what should I do to use mri_vol2surf with --projopt ? My diffusion maps are in 1.7mm isotropic voxel and aligned with anatomical T1w with BBregister, and I used the code as below. ################ tkregister2 --mov ${SUBJECTS_DIR}/${subject}/mri/norm.mgz --s ${subject} --regheader --reg regheader.subject.dat --noedit mri_compute_volume_fractions regheader.subject.dat ${SUBJECTS_DIR}/${subject}/mri/norm.mgz pvf # this gave me pvf.wm.mgz, pvf.csf.mgz, pvf.cortex.mgz, which are in 1mm voxel mv pvf.cortex.mgz pvf.gm.mgz # rename to pvf.gm.mgz to be compatible with the file name that appears in mri_vol2surf code mri_vol2surf --mov MD.nii.gz --regheader ${subject} --hemi lh --surf white --projopt pvf --o lh.MD_pvf.GM.mgz ################ Respectfully yours, Kouhei Kamiya

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Monte Carlo for lme
by Knut J Bjuland 11 Jun '22

11 Jun '22

External Email - Use Caution Dear Freesurfer experts, I am looking into Monte Carlo simulation to control for multiple comparisons for lme in Matlab. Are there any good library that has implemented this in Matlab? Best regards Knut Jørgen Bjuland PhD

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traculina errors in -prep process
by Emmanuel Rodríguez Silva 11 Jun '22

11 Jun '22

External Email - Use Caution Hello, I'm Emmanuel from Mexico. I'm currently working with the pipeline of traculina, but during the first process (-prep) I found an error that says: "can't open orig/COR-.inf" and below that message there appears also: "ERROR: tkregister2_cmdl". I figured out that infant freesurfer does not generate such a directory, as freesurfer does. I know that inside the 'orig' directory freesurfer locates a file called t1.mgz, or something like that. Do you know how I can solve this issue? I have already tried to create manually these files, but it did not work ------------------------------------------------------------------------------- I'm using the latest version of freesurfer, My O.S. is ubuntu 20.04 I'll appreciate your help, best regards -- Saludos cordiales Emmanuel Rodríguez Silva Contacto: (044) 55 59 97 76 18 Licenciado en Manejo Sustentable de Zonas Costeras *UNAM*

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Postdoctoral Research Fellow position in Neuroimaging
by Aganj, Iman 10 Jun '22

10 Jun '22

Good afternoon, The Laboratories for Computational Neuroimaging<https://www.nmr.mgh.harvard.edu/lab/lcn> at the Athinoula A. Martinos Center for Biomedical Imaging invites applications for a Postdoctoral Research Fellow position at the Massachusetts General Hospital and Harvard Medical School. The project will consist of diffusion-MRI harmonization and brain connectivity analysis, with application in studying Parkinson's disease. The appointment is for two years with the possibility of a third year based on performance and the availability of funding. The project involves reducing inter-site variability of (a.k.a. harmonizing) diffusion-MRI datasets from multiple centers, analyzing human brain networks, and examining the relationship of brain connections with stages of Parkinson's disease. The Research Fellow will be supervised by Dr. Iman Aganj, in close collaboration with Dr. Bruce Fischl. The candidate is required to have: * a Ph.D. in engineering, neuroscience, or a related field by the start date, * strong programming skills in MATLAB, Python, or a similar environment, and * experience with diffusion MRI analysis and/or MRI data harmonization. Familiarity and experience with any of the following will be a plus: * connectomics, machine/deep learning, graph theory, neurodegenerative (esp. Parkinson's disease) studies, mathematical modeling. Interested applicants are invited to send a cover letter describing research interests and experience, an up-to-date CV, and names and contact information of three references to: iaganj(a)mgh.harvard.edu<mailto:iaganj@mgh.harvard.edu> Best regards, Iman Aganj Assistant Professor of Radiology Harvard Medical School Associate Investigator Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital

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Extracting average T1w/T2w values from surface
by Austin Boroshok 09 Jun '22

09 Jun '22

Hello, I have created surfaces that contain T1w/T2w ratios (see Glasser & van Essen, 2011; Ganzetti et al., 2014 for details). I am looking to extract the average T1w/T2w value for each of the 7 Yeo networks from the surfaces. We wish to extract intensities from the surface to avoid partial voluming effects that we have observed when extracting whole-brain T1w/T2w values from the T1w/T2w ratio maps (volumes) using a cortical gray matter mask. I have previously tried using mri_anatomical_stats and mri_segstats to do this without success. I received the following errors with each command, respectively: mri_anatomical_stats: command: mris_anatomical_stats -t lh_<T1w/T2w_ratio_surface>.mgh -a <freesurfer_path>/lh.Yeo2011_7Networks_N1000.annot -b subject lh output + error: using thickness file lh_<T1w/T2w_ratio_surface>.mgh. computing statistics for each annotation in <freesurfer_path>/lh.Yeo2011_7Networks_N1000.annot. reading volume /subject/mri/wm.mgz... reading input surface /subject/surf/lh.white... Using TH3 vertex volume calc Total face volume 306338 Total vertex volume 302976 (mask=0) reading input pial surface /subject//urf/lh.pial... reading input white surface /subject/surf/lh.white... ERROR: number of vertices in lh_<T1w/T2w_ratio_surface>.mgh does not match surface (163842,154532) (And the table column of “average cortical thickness” (in my case, T1w/T2w ratio) are all 0.000s for the 7 Yeo Networks) mri_segstats: Command: mri_segstats --i lh_MM_cbpd_brannon_age_gender_n157_glm_fwhm_src5trg5.mgh --seg ../../../../../freesurfer/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot --avgwf test.dat output + error: Loading ../../../../../freesurfer/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot mri_read(): couldn't determine type of file ../../../../../freesurfer/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot ERROR: loading ../../../../../freesurfer/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot I am running macOS Monterery 12.4, Freesurfer 6.0.0. Can anyone please advise if I am using mri_anatomical_stats or mri_segstats incorrectly, or if there is a better way to extract average T1w/T2w values from the surface directly? Thank you in advance for any help. Best, Austin External Email - Use Caution

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