Freesurfer January 2022

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Co-Registration after recon-all
by m-maiworm＠web.de 04 Feb '22

04 Feb '22

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mri_normalize error MP2RAGE
by Dr. Cornelius Kronlage 04 Feb '22

04 Feb '22

External Email - Use Caution Dear freesurfer experts, when running recon-all (FS version 7.2.0) on skullstripped 3T MP2RAGE sequences, about 10-20% of scans from one scanner fail because of this: mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz [...] Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 error: No such file or directory error: MRInormFindControlPoints: could not find enough control points error: No such file or directory error: MRInormFindControlPoints failed Command exited with non-zero status 253 nu.mgz as the input to mri_normalize looks good to me. I am of course happy to provide full logs and some example data - please let me know. The exact same problem (also MP2RAGE data) has been described twice before, but I couldn't find a solution: https://secure-web.cisco.com/1r3_UfItk0odyQTEjL22mLAxycj89_vXfN--AkpFwUzred… https://secure-web.cisco.com/1_dIFX4W-YMl78kLd-J9E7AGEkpzUy7zCtCTsFt-L6nLdA… Thanks you in advance and best wishes Cornelius

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TRACULA Question
by Salar Dini, Elaheh 31 Jan '22

31 Jan '22

External Email - Use Caution Dear Anastasia, I have run trac -all -prep in 2 different conditions: a) prerequisite recon-all step was done using freesurfer 7.2.0 b) prerequisite recon-all step was done using freesurfer 6 The first time everything ran smoothly without an error, but when we used aparc+aseg resulted from running recon -all using version 6 of freesurfer, we got the following error for which I also attach the log file to this message: Segmentation fault (core dumped) My question is that if I'm correct to assume that we can't run trac-all -prep using structural MRI segmentation done by previous versions of freesurfer? The reason I'm asking this is that I have a data from 100 subjects with Alzheimer's Disease. We have been collecting this data over the past 4 years and have done the recon -all step using freesurfer 6 for all of them as we acquired them. If trac-all can't use those segmentation, we have to do this step again for all these 100 subjects. I appreciate your help and insight. Ela

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Survey testing experimental setup
by Lepauvre, Alex 31 Jan '22

31 Jan '22

External Email - Use Caution Dear Freesurfer community, Have you ever wondered what is the impact that the experimental setup might have on reported results in neuroscience and psychology? If yes, you are not alone! We have created a survey to better understand and identify common practices used in the field to test experimental code and experimental hardware. This survey is addressed to anyone having undertaken the programming, implementation and testing of a neuroscientific or psychophysical experiment at some point in their careers. The responses to the survey are anonymized and the data will be presented as aggregates. We aim to collect responses from a wide variety of researchers, hopefully at different career stages. Feel free to share the link with as many of your peers as possible. The survey will take no more than 5 mins to be completed. By clicking on this link, you will proceed to the survey: https://secure-web.cisco.com/1kD2sLN_HI4j9OvgcO-Cw1G1C7XZxMFNGnxI2wDDXGiJGJ… Thanks in advance for your help! Kind regards, Alex & Rony Alex Lepauvre, Max Planck institute for empirical aesthetics, Frankfurt, Germany Rony Hirschhorn Tel-Aviv University, Tel Aviv, Israel

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Re: [Freesurfer] Reading files from a hard drive (on Windows in the Fressurfer Ubuntu VM)
by fsbuild 30 Jan '22

30 Jan '22

External Email - Use Caution Please see the updated documentation in the previous announcement about how to share/mount an external hard drive at https://secure-web.cisco.com/1yjgxLva8l6O68IkaN5KFrOHCn5Y3OV8mnxI6DMsZ2kYAv… - R. krystaly (krystaly(a)hku.hk) January 27, 2022 at 19:33         External Email - Use Caution         I’m not sure if this is the correct way (please see the attached) to solve my problem. Please kindly advise. Thank you for your attention.   Best regards, Krystal   From: fsbuild Sent: Tuesday, January 25, 2022 9:57 AM To: freesurfer(a)nmr.mgh.harvard.edu Cc: ts+ml(a)rcmd.org Subject: Re: [Freesurfer] Reading files from a hard drive (on Windows in the Fressurfer Ubuntu VM)     _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1oDBI5mZnFPqTOWdVRbiAc7B-sr876yiNnvgoHpRWeSrCR…

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postdoctoral research scientist position at Weill Cornell Medicine in NYC
by Tracy A. Butler 30 Jan '22

30 Jan '22

External Email - Use Caution Position Summary The Brain Health Imaging Institute (BHII) in the Department of Radiology of Weill Cornell Medicine is seeking highly qualified applicants for the position of postdoctoral research scientist for duration of up to three years. This position is supervised by Dr. Tracy Butler, Associate Professor of Neurology in Radiology and Psychiatry, and BHII Medical Director. Dr. Butler’s research uses MRI and PET to study brain function in normal aging and in disease states including Alzheimer’s Disease (AD) and Traumatic Brain Injury (TBI). Current research projects include study of TBI in victims of Interpersonal Violence; a multisite clinical trial of a re-purposed medication for women with AD (LUCINDA); and human studies assessing brain glymphatic and associated clearance mechanisms and potential therapeutic interventions to boost clearance. Postdoctoral researchers will have the opportunity interact with and learn from multidisciplinary BHII faculty and have access to state of the art neuroimaging and other equipment including an on-site cyclotron and radiochemistry facilities and multiple MR (3T and 7T), PET/CT and PET/MR scanners. Weill Cornell Medical College, located in the upper east side of New York City, has a vibrant biomedical research community and strong ties to the main Cornell campus in Ithaca and the Tech campus on Roosevelt Island. Responsibilities: · Under the direct supervision of Dr. Tracy Butler, develop and apply cutting-edge research methods such as MRI, PET (to study amyloid, tau, brain clearance, inflammation and/or other biological processes) and/or complementary techniques such as statistical interrogation of existing datasets, EEG, neuropathology or biospecimen wet-lab assays to understanding brain functioning in healthy subjects and in subjects suffering from a variety of disease states both common (Alzheimer’s Disease, Traumatic Brain Injury) and under-studied (victims of Interpersonal Violence, autoimmune encephalopathy.) · Disseminate research results through publications in high-impact journals and presentations at top international conferences · Support and mentor research of other fellows and students with medical or engineering background Qualifications: · MD or PhD in Neuroscience, Neuropsychology, Electrical/Biomedical Engineering, Computer Science, Applied Mathematics, Data Science, Statistics or related field · Significant track record of research and publications in top scientific conferences and journals · Effective communication skills, both written and verbal · Track record of effectively working both independently and as part of a multidisciplinary team Highly Desired Knowledge in one or more of the following: · Brain anatomy and physiology · Neuroimaging including functional/structural MRI and PET · PET kinetic modeling · Familiarity with common neuroimage processing tools, e.g. FreeSurfer, FSL, SPM, PMOD. · Statistical or mathematical models of biological systems To apply: Please send a one-page statement of career goals and research interests and full CV to tab2006(a)med.cornell.edu with subject title: Application for postdoctoral associate position. Weill Cornell Medicine: Founded in 1898, and affiliated with what is now New York-Presbyterian Hospital (NYPH) since 1927, Weill Cornell Medicine (WCM) is among the top-ranked clinical and medical research centers in the country. In addition to offering degree sin medicine, WCM also has PhD programs in biomedical research and education at the Weill Cornell Graduate School of Medical Sciences, and with neighboring Sloan-Kettering Institute and The Rockefeller University, has established a joint MD-PhD program for students to intensify their pursuit of Weill Cornell's triple mission of education, research, and patient care. WCM is divided into 24 basic science and patient care departments that focus on the sciences underlying clinical medicine and/or encompass the study, treatment, and prevention of human diseases. The basic science and clinical departments are locatd in buildings that straddle York Ave. between 68thand 72ndstreets on Manhattan’s Upper East Side. Weill Cornell Medical College has 1781 full-time faculty (3582 total faculty) distributed across 8 basic science and 15 clinical departments. WCM maintains major affiliations with Memorial Sloan-Kettering Cancer Center, The Rockefeller University, the Hospital for Special Surgery, as well as with the metropolitan-area institutions that constitute NYP Healthcare Network. Weill Cornell Medicine is a comprehensive academic medical center that's committed to excellence in patient care, scientific discovery, and the education of future physicians in New York City and around the world. Our doctors and scientists-faculty from Weill Cornell Medical College, Weill Cornell Graduate School of Medical Sciences, and the Weill Cornell Physician Organization-are engaged in world-class clinical care and cutting-edge research that connect patients to the latest treatment innovations and prevention strategies. Located in the heart of the Upper East Side's scientific corridor, Weill Cornell Medicine's powerful network of collaborators extends to its parent university Cornell University; to Qatar, where an international campus offers a U.S. medical degree; and to programs in Tanzania, Haiti, Brazil, Austria and Turkey. Our medical practices serve communities throughout New York City, and our faculty provide comprehensive care at NewYork-Presbyterian Hospital/Weill Cornell Medical Center, NewYork-Presbyterian/Lower Manhattan Hospital, and NewYork-Presbyterian/Queens. At Weill Cornell Medicine, we work together to treat each individual, not just their conditions or illnesses, as we strive to deliver the finest possible care for our patients - the center of everything we do Diversity is one of Weill Cornell Medicine’s core values and is essential to achieving excellence in patient care, research, and education. We welcome applications from candidates who share our commitment to fostering a culture of fairness, equity, and belonging. Weill Cornell Medicine is an Equal Employment Opportunity Employer, providing equal employment opportunities to all qualified applicants without regard to race, sex, sexual orientation, gender identity, national origin, color, age, religion, protected veteran or disability status, or genetic information. Tracy Butler, MD Medical Director, Brain Health Imaging Institute Associate Professor of Neurology in Radiology and Psychiatry Weill Cornell Medicine Department of Radiology 420 East 70th Street, 427 New York, NY 10021 T 646-248-6734 tab2006(a)med.cornell.edu<mailto:tab2006@med.cornell.edu>

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Tracula trac-all -prep error
by Powell, Jake Robert 30 Jan '22

30 Jan '22

External Email - Use Caution Hello, I am trying to run the command trac-all -prep -c dmrircmultiscan.example -jobs prep.txt using a config file made for a cross-sectional study with multiple scans. Each subjects has 2 scans. When I run the command I get this error message. length of pathway list (/proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/pathlist.txt) and endpoint label ID list ERROR: () do not match Under the hood I noticed a gmids variable could be set. I this something I need to do for this data structure? I have previously not had issues using one scan. Below is the config file text. Thank you in advance! # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 or 2 # Default: 1 (yes) # set dorotbvecs = 1 # Intra-subject (diffusion-to-T1) registration method # 1: Affine with a correlation ratio cost # 2: Affine with a mutual information cost # 3: Affine with a boundary-based cost (default) # set intrareg = 3 # Degrees of freedom for intra-subject registration # Can be 6 (rigid), 9 (rigid+scaling), or 12 (full affine) # Default: 6 for infants, 9 otherwise # set intradof = 9 # Maximum rotation angle (degrees) for intra-subject registration # Default: 3 for infants, 90 otherwise # set intrarot = 90 # Inter-subject registration method # 1: Affine T1-to-T1 with a correlation ratio cost # 2: Affine T1-to-T1 with a mutual information cost # 3: Affine T1-to-T1 with a robust cost (default for infants) # 4: Nonlinear T1-to-T1 with CVS # 5: Nonlinear FA-to-FA with SyN (default) # set interreg = 5 # Target brain for inter-subject registration # Default for affine T1-to-T1: # $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # Default for nonlinear T1-to-T1: # $FREESURFER_HOME/subjects/cvs_avg35/ # Default for nonlinear FA-to-FA: # $FREESURFER_HOME/trctrain/hcp/MGH35_HCP_FA_template.nii.gz # # I think this fixed my issue with syntax # set intertrg = /proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/MGH35_HCP_FA_template.nii.gz # Whole-brain segmentation used to extract the anatomical neighborhood priors # of the pathways of interest # Must exist in each subject's FreeSurfer recon directory, under: # $SUBJECTS_DIR/$subjid/mri/$segname.mgz # Default: aparc+aseg # set segname = aparc+aseg # Use the thalamic nuclei segmentation? # This is highly recommended to use for any pathways that terminate in # or neighbor the thalamus # When used, it is merged with the whole-brain segmentation above # Must exist in each subject's FreeSurfer recon directory, under: # $SUBJECTS_DIR/$subjid/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz # Default: 1 (yes) # set usethalnuc = 0 # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # #set thrbet = 0.5 # Paths to reconstruct # Default: All paths in $FREESURFER_HOME/trctrain/hcp/pathlist.txt # set pathlist = /proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/pathlist.txt # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist (recommended, with more points for longer paths) # Default: As in $FREESURFER_HOME/trctrain/hcp/pathlist.txt # set ncpts = /proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/pathlist.txt # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # set trainfile = /proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/trainlist.txt # Number of "sticks" (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 # Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 # set nburnin = 200 # Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 7500 # set nsample = 7500 # Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) # set nkeep = 5 # Reinitialize path reconstruction? # This is an option of last resort, to be used only if one of the reconstructed # pathway distributions looks like a single curve. This is a sign that the # initial guess for the pathway was problematic, perhaps due to poor alignment # between the individual and the atlas. Setting the reinit parameter to 1 and # rerunning "trac-all -prior" and "trac-all -path", only for the specific # subjects and pathways that had this problem, will attempt to reconstruct them # with a different initial guess. # Default: 0 (do not reinitialize) # set reinit = 0 Jake R. Powell, MS, LAT, ATC Doctoral Student - Human Movement Science Matthew Gfeller Sport-Related Traumatic Brain Injury Research Center 2207 Stallings Evans Sports Medicine Center The University of North Carolina at Chapel Hill P 919-962-0409 E jrpowell(a)unc.edu<mailto:jrpowell@unc.edu>

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mri_cor2label --surf "dim mismatch between surface"
by Zeng, Qi 29 Jan '22

29 Jan '22

External Email - Use Caution Hi, I saw the same question has been asked and no answer was provided: I run ---- "mri_cor2label --c fsaverage/mri/aseg.mgz --id 4 --l fsaverage/label/Left-Lateral-Ventricle.label --surf fsaverage lh" ----- to hopefully extract lateral ventricles volume into a overlay of surface base. however, gave me error: "dim mismatch between surface (100515) and input (16777216)". What should I change? BTW, Also have questions for the following steps and hope you can answer that too: 1. convert surface-based label to volume, "mri_label2vol --label fsaverage/label/Left-Lateral-Ventricle.label --subject fsaverage --hemi lh --identify --temp fsaverage/mri/T1.mgz --o fsaverage/mri/lh.Left-Lateral-Ventricle.nii --proj frac 0 1 0.01 2. Better ROI with mri_binarize "mri_binarize" --dilate 1 -erode 1 --i fsaverage/mri/h.Left-Lateral-Ventricle.nii --o fsaverage/mri/h.Left-Lateral-Ventricle.nii --min 1 3. constrain the thick ROI "mris_calc -o fsaverage/mri/h.Left-Lateral-Ventricle.nii fsaverage/mri/h.Left-Lateral-Ventricle.nii mul fsaverage/mri/h.Left-Lateral-Ventricle.ribbon.mgz 4. Questions: Are the aforementioned steps correct? In the end, if I have a couple of ROIs, what should I use to combine them. or just load them separately with lh.white and lh.pial. Best, Qi

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Password ubuntu
by Dan Emanuel Antonesa 29 Jan '22

29 Jan '22

External Email - Use Caution Hello, I'm trying to setup freesurfer in VirtualBox and it asked me to email you for the password. Best Regards, -- *Dr. Dănuț Emanuel Antonesă* Medic rezident Radiologie-Imagistică Medicală emanuelantonesa(a)gmail.com

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Transform a surface (e.g., lh.white) with a register.dat (12 dof)
by Yixin Ma 28 Jan '22

28 Jan '22

External Email - Use Caution Hi FreeSurfer developer, I want to transform surfaces files (lh.white, lh.pial, rh.white, and rh.pial) with a registration matrix that has 12 degrees of freedom. Is there a function in FreeSurfer that can do so? Very best, Yixin Ma

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Freesurfer January 2022