Freesurfer

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30084 discussions

BrainStem & HippoAmyg segmentation
by Meena M. Makary 23 Dec '19

23 Dec '19

External Email - Use Caution Hi, I am using Freesurfer stable6_0_0 (/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin) and I used it for all my subjects, so far. Now I would like to do BrainStem and HippocampalSubfieldsAndNucleiOfAmygdala segmentation which needs me to switch to dev versions. Should I switch to the dev version for getting this segmentations only and switch back Version 6 for future reconall or is it okay to switch to the dev version for good? In other words is there any differences in the reconall between the two versions? Thank you! Meena -- — *Meena M. Makary, Ph.D.* Assistant Professor | Cairo University <http://bmes.cufe.edu.eg/> Postdoctoral Fellow | Radiology, Harvard Medical School <https://connects.catalyst.harvard.edu/Profiles/display/Person/176550> Postdoctoral Fellow | Athinoula A. Martinos Center, MGH <https://www.nmr.mgh.harvard.edu/user/4550386> Career Development and Mentoring Manager | OHBM Student and Postdoc SIG <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449>

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Re: [Freesurfer] Qdec support {Disarmed}
by fsbuild 23 Dec '19

23 Dec '19

External Email - Use Caution Hello Leona, What is the error that you are seeing? Qdec is a 32 bit program (*not* 64 bit), so even Mac OS 10.14 (Mojave) may put up a warning that it is not optimized and needs to be re-compiled, but it should still run.  It will not however run if you upgrade to Catalina (Mac OS 10.15).  Mac OS 10.14 is the last version of the OS that will run any 32 bit applications. - R. On Dec 23, 2019, at 08:34, Leona.Salewski(a)med.uni-duesseldorf.de wrote:        External Email - Use Caution        Dear experts,i was trying to run Qdec on macOS Mojave, in the past it always worked well.But now I am not able to generate stats data any more, an error message pops up every time I try running it. Is there a general problem running Qdec or is it just a problem of mine? Kind regards L. SalewskiUniklinikum DüsseldorfGermany_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Qdec support
by Leona.Salewski＠med.uni-duesseldorf.de 23 Dec '19

23 Dec '19

External Email - Use Caution Dear experts, i was trying to run Qdec on macOS Mojave, in the past it always worked well. But now I am not able to generate stats data any more, an error message pops up every time I try running it. Is there a general problem running Qdec or is it just a problem of mine? Kind regards L. Salewski Uniklinikum Düsseldorf Germany

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postdoc positions in Weill Cornell Radiology in NYC
by Tracy A. Butler 21 Dec '19

21 Dec '19

External Email - Use Caution Multiple Postdoctoral Research Scientist Positions Position Summary The newly formed Brain Health Imaging Institute (BHII) in the Department of Radiology of Weill Cornell Medicine is seeking highly qualified applicants for multiple postdoctoral research scientist positions for duration of up to three years. The BHII, a multidisciplinary research group headed by Dr. Mony de Leon, designs and implements cutting edge MRI and PET neuroimaging methods to study brain function in normal aging, and in disease states including Alzheimer’s Disease and Traumatic Brain Injury. In addition to neuroimaging, the BHII has expertise in fluid (blood and CSF) biomarkers, detailed cognitive and neurologic assessment and neuropathological examination. Postdoctoral researchers will 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 domestic 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, 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, especially of functional/structural MRI and PET * PET kinetic modeling * Familiarity with common neuroimage processing tools, e.g. FreeSurfer, FSL, AFNI, 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 research scientist 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 degrees in 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 located in buildings that straddle York Ave. between 68th and 72nd streets 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 Weill Cornell Medicine is an Equal Employment Opportunity Employer. Weill Cornell Medicine provides 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.

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Error running "Test your FreeSurfer Installation"
by Rafael Espericueta 21 Dec '19

21 Dec '19

External Email - Use Caution I was trying to run the command: recon-all -s bert -all It ran for hours, but finally output the following: writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H ln: failed to create symbolic link 'lh.white.H': Function not implemented Linux hypatia 4.15.0-66-generic #75-Ubuntu SMP Tue Oct 1 05:24:09 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Wed Dec 18 16:18:43 PST 2019 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 18.04.3 3) recon-all.log: see attached

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Re: [Freesurfer] Thickness problem
by Gwang-Won Kim 20 Dec '19

20 Dec '19

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Manual segmentation to volume
by Benjamin Ineichen 20 Dec '19

20 Dec '19

External Email - Use Caution Dear Freesurfer experts, I have a manual segmentation of a certain brain feature done in Freeview. I want to pool these segmentations from different subjects to create some kind of a heat map/probability map. In order to do this, I assume I need to convert my segmentation to a volume first (In my case the Talairach space); hence, I tried: mri_label2vol --seg example.mgz --temp talairach.xfm --o seg_talairach --reg example_orig.mgz the example_orig.mgz would correspond to the original T1 which I used to do the segmentation. But this gives me the error message: ERROR: could not determine type of talairach.xfm ERROR: reading talairach.xfm header Where is the problem? Many thanks! /Ben

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Creating a label from overlapping cluster results
by cody samth 20 Dec '19

20 Dec '19

External Email - Use Caution Hi, I was wondering if there is any automated command/method to create a new label that consists of the overlap of two labels? I've run two whole brain analyses with different predictors and have regions where the clusters from each analysis overlap. I'm interested in creating a label for visualization purposes and to extract cortical data in these regions of overlap. Thanks, Cody

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Re: [Freesurfer] Conversion fMRI volumes to surface
by Marina Fernández 19 Dec '19

19 Dec '19

External Email - Use Caution Thanks Doug. I created the surface with the command line that I sent you (mri_vol2surf ...) and then, I run that command that you sent me (tkregisterfv...) but I have the following error when freeview is trying to load the file: 'Failed to load MRI /.../4d_inputBOLD.nii'. I discard that the problem is not with the EPI file because when I load only the 4d_inputBOLD.nii there is no problem. I guess that the problem is the register.dat. What do you think I should do? Best regards, Marina.

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Pial surface does not follow the gray/csf boundary
by Ardesch, D.J. 19 Dec '19

19 Dec '19

External Email - Use Caution Dear FreeSurfers, I’m trying to create surface reconstructions for some small monkey scans (about half the size of a rhesus macaque). The white surfaces look fine, but I can’t seem to get the pial surfaces to extend properly to the edge of the gray matter. Is there a way to ‘force’ the mris_make_surfaces command to place the pial surface along a certain voxel intensity or intensity gradient? As I understand it, mris_make_surfaces takes the ?h.orig surface and extends it into the gray matter until it finds the gray matter/csf boundary. I’ve therefore tried to edit the brain.finalsurfs.mgz and brainmask.mgz volumes such that all white matter voxels have an intensity of 110 and all other brain voxels have an intensity of 80, and added some smoothing to create an intensity gradient, but this did not make a difference. The gray matter surface is still placed about 1/5th of the way between the gray/white boundary and the gray/csf boundary. Adding a T2 scan did not help either. My setup is the following: * FreeSurfer v6.0.0 * MacOS 10.14.6 * Running FreeSurfer with the -hires flag (voxel size is 0.25 mm isotropic) With some manual editing I’ve been able to complete all pipeline steps until the surface reconstruction, except the topology fixing because it created large inaccuracies in the occipital lobe (including the topology fixing step did not solve the problem either). Any help would be greatly appreciated! With kind regards, Dirk Jan

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