Freesurfer

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30132 discussions

Incorrect/Negative Hippocampal subfields volumes
by Jayachandra Raghava 21 Oct '19

21 Oct '19

External Email - Use Caution Hello Freesurfer experts & Eugenio, I have been trying to extract the volumes of hippocampal subfields using the longitudinal pipeline ( https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields) on macOS Mojave using freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c. For some reason, both the lh.hippoSfVolumes-T1.long.v10.txt and rh.hippoSfVolumes-T1.long.v10.txt text files show negative volumes as shown below. Hippocampal_tail -445.418232 subiculum -339.909193 CA1 -559.134087 hippocampal-fissure -165.590803 presubiculum -263.670386 parasubiculum -55.654556 molecular_layer_HP -541.803219 GC-ML-DG -293.794963 CA3 -222.042205 CA4 -266.645751 fimbria -66.106600 HATA -53.397592 Whole_hippocampus -3107.576783 I have also tried to extract the hippocampal subfield volumes from the longitudinally processed standard MNI T1 brain template (MNI152_T1_1mm_brain.nii.gz). And i still encounter the same problem with negative volumes. I could not find the suggested solution for this problem in the freesurfer mailing list. Could you please guide us on this issue? Thank you for your time and support. Best wishes Jay

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Re: [Freesurfer] FreeSurfer transforms
by Vinny K 21 Oct '19

21 Oct '19

External Email - Use Caution Hi, FreeSurfer does a great job in registering atlas structures to patients with big ventricles. I'd like to use the calculated FreeSurfer transforms in bringing additional subcortical structures from MNI space (either MNI305 or MNI2009b) into native T1 space. Can you please advise on how to do this? Thanks, Vinny

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aseg.stats format FreeSurfer 5 versus 6
by Tim Schäfer 21 Oct '19

21 Oct '19

External Email - Use Caution Dear fs experts, I'm parsing aseg.stats files for subjects to extract global brain measures and noticed that at least 2 names changed from FreeSurfer 5.1 versus FreeSurfer 6. It seems that: * "EstimatedTotalIntraCranialVol" is in v6, but "IntraCranialVol" is in v5 * "Total cerebral white matter volume" is in v6, but "Total cortical white matter volume" is in v5 Have these just been renamed, or do they carry different information? Did I overlook anything else that changed? -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] Learning dti processing tutorial
by Renew Andrade 20 Oct '19

20 Oct '19

External Email - Use Caution I am using a database of NITRC repository https://www.nitrc.org/projects/parktdi/ <https://www.nitrc.org/projects/parktdi/> . This images have a nifti file for 1000s/mm^2 and 2500s/mm^2. I don’t know if it is MPRAGE or not. Can you help me? What is the input file that you are supplying? Often this happens when the input it a multi-echo MPRAGE. If so, you can run mri_concat multi-echo-mprage.mgz --rms --o mprage.mgz then use mprage.mgz as the input to recon-all On 10/12/2019 4:48 PM, Renew Andrade wrote: > External Email - Use Caution > > Dear freesurfer experts: > I am trying to learn dti processing. For using Tracula it appears there is a > need for running "recon-all -all -i -s” on every subject before starting to > run Tracula. But there seems to be a problem. I have a Parkinson dwi images > database and every subject gives me an error of the type “input(s) cannot > have multiple frames!”. I am a little bit stuck on this step. Is it a problem > of the file as input? Am I putting the wrong file? Can it be done a recon-all > analysis to a dwi image? With trackvis I can obtain the results without any > problem. My doubt comes from FreeSurfer only and may be my little knowledge > about it. > Thanks for your help! > Sincerely, > Andrade. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

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Re: [Freesurfer] ECC or non-ECC Memory?
by Sotiris Michos 19 Oct '19

19 Oct '19

External Email - Use Caution Dear Matt, Memtest 86+ and similar tools can test the DRAM module only for hard errors (hardware defects). Are you suggesting that the soft errors (the common spontaneous flipping of a bit state) that happen in all memories do not have a considerable effect in Freesurfer’s results? Best Regards, Sotiris

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help
by Asim Hassan 19 Oct '19

19 Oct '19

External Email - Use Caution ?Good afternoon, Is there any other way to incorporate a manually edited brain mask into the recon all process other than through the recon-mode in freeview? Thanks! Asim Hassan Research Technician II Waugh Lab Division of Pediatric Neurology University of Texas Southwestern Medical Center Phone: 214-645-9259 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Re: [Freesurfer] can´t open an image in Freeview
by fsbuild 19 Oct '19

19 Oct '19

External Email - Use Caution Hello Adam, See if you can run the following command, and if it reports anything is not found (you can cut and paste the command) - R. $ ldd `which freeview` | grep not Adam Rytina October 18, 2019 at 14:31         External Email - Use Caution         Hello all, I´m new to Freesurfer and I´m struggling with loading an image in FreeView. I am running the Freesurfer 6.0.0. on Ubuntu 16.04. Virtual Machine. While opening FreeView (typing "freeview" in the shell) just some empty grey windows will pop out (please see attached the screenshot). Besides this, everything is OK, I successfully tested Freesurfer installation. I haven´t found any simmilar issue on the Internet. Thus, please, could you help me to address this issue? Thanks a lot Adam Bez virů. www.avast.com _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Research Specialist Position on the MIDUS Neuroscience project's longitudinal study of aging, emotion, and well-being at the Center for Healthy Minds
by CHM Recruiting 18 Oct '19

18 Oct '19

External Email - Use Caution The Center for Healthy Minds at the University of Wisconsin-Madison is hiring a Research Specialist. The Research Specialist will be responsible for scientific integrity of data collection, data processing, and participant recruitment, screening, and scheduling for research at the University of Wisconsin-Madison's Center for Healthy Minds. This individual may work on several research projects examining the import of individual differences in the time course of emotional responses for varied domains including cognition, health, and well-being, while elucidating the critical functional and structural brain substrates underlying these relationships. One example of such a research project is the Neuroscience Project of the Midlife in the U.S. longitudinal study of health and well-being (http://midus.wisc.edu/) Please use the following link to see a full posting of the position and to apply online https://jobs.hr.wisc.edu/en-us/job/503196/research-specialist

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can´t open an image in Freeview
by Adam Rytina 18 Oct '19

18 Oct '19

External Email - Use Caution Hello all, I´m new to Freesurfer and I´m struggling with loading an image in FreeView. I am running the Freesurfer 6.0.0. on Ubuntu 16.04. Virtual Machine. While opening FreeView (typing "freeview" in the shell) just some empty grey windows will pop out (please see attached the screenshot). Besides this, everything is OK, I successfully tested Freesurfer installation. I haven´t found any simmilar issue on the Internet. Thus, please, could you help me to address this issue? Thanks a lot Adam [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-anima…]<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Bez virů. www.avast.com<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…>

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Post-doc on multi-tracer PET-MRI
by Linnman, Clas,Ph.D. 18 Oct '19

18 Oct '19

Hi everyone, My lab is looking for a post-doc. Please spread the below advertisement far and wide With my best regards Clas Linnman The Spaulding Neuroimaging Laboratory (PI Clas Linnman, assistant professor, Harvard Medical School), working closely with the Martinos Center for Biomedical Imaging, uses simultaneous PET-MRI with a focus on neuroinflammation and opioid receptors in humans and in animal models of chronic pain. The current position is part of a research project funded by the NIH to determine if intensive aerobic exercise may reduce inflammation, strengthen endogenous pain capacity, and improve rehabilitation outcomes in patients with spinal cord injury. Key Responsibilities Conduct neuroimaging research with emphasis on brain structure, network reorganization, opioid receptor expression and neuroinflammation after spinal cord injury. Evaluate the effects of intensive whole-body aerobic exercise in patients with sub-acute spinal cord injury with regards to pain inhibition capacity, spinal cord atrophy, brain function, opioid and neuroinflammation. Apply and develop MR and PET acquisition methods for longitudinal analyses Apply and develop research methodologies for integrating PET and MR data in human and animal models. Lead and assist in the writing of academic manuscripts Lead and assist in dissemination of research findings through presentations at conferences and for patient and public engagement activities. Initiate and assist grant applications for further career development Assist in mentoring of research assistants Qualifications Qualifications and Experience Education/Degree Required - A PhD degree in a field encompassing neuroscience and neuroimaging. Experience Preferred Research experience in neuroscience and neuroimaging; preferably in the fields of pain, SCI and MR data analysis, as demonstrated by at least one first-author publication for which MRI or PET methodology has been used. Candidates are expected to have considerable experience in the analysis of neuroimaging data, basic programming skills in Python or Matlab, and a solid understanding of inferential statistics. Excellent organizational, oral, and written communication skills Strong interpersonal skills and comfort interacting with research participants with spinal cord injuries English language fluency Excellent ability to work independently Familiarity with neuroimaging tools like Freesurfer, SPM, FSL Excellent attention to detail Apply online at https://partners.taleo.net/careersection/srn/jobdetail.ftl?job=3108990&tz=G…

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