Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

Ubuntu VM password
by tom.liebmann＠yahoo.com 16 Sep '21

16 Sep '21

External Email - Use Caution Like a number of similar posts, I am trying to work with the Ubuntu image for running FreeSurfer on my Windows machine. Without the Administrator password, I cannot run the image. Can you please provide the password for access. Thank you very much for the service and the support. Kind regards, -Thomas

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Re: [Freesurfer] Freesurfer 7.1.0 VirtualBox password
by fsbuild 15 Sep '21

15 Sep '21

External Email - Use Caution Sending the info to your local email shortly. - R. On Sep 14, 2021, at 12:58, Camila Fernandes da Silva <camila.fernandes.silva(a)usp.br> wrote:        External Email - Use Caution        Dear admin, I instaled Freesurfer 7.1.0 using the VirtualBox in my Windows 10.It does not allow me to use it, It asks the developer password.Could you please help me?Thank you so much!-- Atenciosamente,Camila FernandesLicenciatura em Física - IFUSP_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Samseg Choroid Plexus Segmentation T1 and T2-FLAIR separate argument
by Robb, William Hudson 15 Sep '21

15 Sep '21

External Email - Use Caution Hello, I am attempting to segment the choroid plexus using T1 and T2-FLAIR images as inputs to Samseg. On our T1 images, the choroid plexus is hardly visible, but it is much more visible on T2-FLAIR. Samseg seems to be failing to segment the choroid plexus on some images, but does a good job on others. For the pallidum, there is a flag “--pallidum-separate” which seems to privilege the T2-FLAIR for pallidum segmentation. Is there a similar argument or option that could be used to separate the segmentation of the choroid plexus to privilege the T2-FLAIR, such as “--choroid-separate”? Thank you, Hudson Robb

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ERROR: mri_ca_register with non-zero status 1
by Yanyu Xiong 15 Sep '21

15 Sep '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run recond-all on multiple subjects with T2 used to help improve pial reconstruction. However, I got the following error message for many subjects: ERROR: mri_ca_register with non-zero status 1 I have attached the recon-all.log in case it's of any use.

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mri_vol2surf clarification
by Alice Giubergia 15 Sep '21

15 Sep '21

External Email - Use Caution Dear Freesurfer's experts, I am dealing with time course extraction from preprocessed (prerpoc-sess) task functional data; I was able to extract the time courses from the fsaverage sampled surfaces fmcpr.up.sm3.fsaverage.lh.nii.gz thanks to mri_segstats, but I was wondering how to handle the data sampled to the MNI space fmcpr.up.sm5.mni305.2mm.nii.gz. I think I should run mri_vol2surf to get a surface but I don't get the kind of registration option should I use. mri_vol2surf --src fmcpr.up.sm5.mni305.2mm.nii.gz I would appreciate any suggestion, many thanks, Alice

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Calculating GMV
by Brigitte Pace 15 Sep '21

15 Sep '21

External Email - Use Caution We are trying to calculate the volume of grey matter of the significant clusters within each region identified by our initial analyses. Is there a procedure already written in matlab to accomplish this calculation? Right now we've calculated the mean thickness across all subjects for each vertex, and then averaged those thickness across each region (or across each significant portion of a region). Then took the areas from the regions (calculated through Freesurfer’s mri_surfcluster program, which for the whole regions will obviously only get a single cluster, and total area of that cluster) and multiplied them by the mean thicknesses to get total area. It should be possible to do the same thing to get the significant volumes. Does the above procedure seem like the most straightforward? Or does freesurfer have a program to do this more efficiently? -- Brigitte Pace, M.A. Doctoral Student Clinical Psychology, Health Emphasis Ferkauf Graduate School of Psychology Yeshiva University Albert Einstein College of Medicine

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recon-all crash errors (fMRIPrep)
by Rubina Chandnani 15 Sep '21

15 Sep '21

External Email - Use Caution Hi there, I'm getting in touch because I'm consistently running into a repeated recon-all error. I've tried so many suggestions (from Neurostars) and I was wondering if you can maybe suggest an alternative to running the Freesurfer license. I used this code on Ubuntu 20.04 on Windows (it worked smoothly for 17 participants and failed on the remaining participants I need to run pre-processing): fmriprep-docker /mnt/c/Users/rubin/BIDS /mnt/c/Users/rubin/derivatives participant --participant-label sub-M1121053 --fs-license-file /mnt/c/Users/rubin/fs-license/license.txt --low-mem More specifically, I get these errors (please see 4 attachments). I also tried gzipping the files (with .gz at the end of the files) but even that failed. Are there any suggestions that you can offer that would help resolve these errors? I look forward to hearing from you. If there is anything you need from my end, please do get in touch with me. Thank you and best regards, Rubina Chandnani

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Update FS version and manually edited controls
by Funk, Quentin 15 Sep '21

15 Sep '21

External Email - Use Caution Freesurfer experts, I have a collection of older controls that I have reconstructed with FS 5.3. Due to age, many of these controls have hypointensities in the white matter that led to some errors in reconstruction that needed to be manually fixed. Our new pipeline involves FS 6 (and soon 7, probably), and I'd like to be able to use this same group of controls aginst subjects who will be processed with newer versions of FS. Is there a way to do this that doesn't involve manually correcting the WM masks for each subject again? My naive idea would be to copy over the (edited) wm.mgz files from the old reconstructions into the new reconstruction folders, then re-do the new reconstructions, but I wanted to make sure that wouldn't break anything / wasn't unwise for reasons that I am sure to be not seeing. Thank you for any insight! Quentin Funk, PhD Houston Methodist Academic Institute 713-363-9003<tel:713-363-9003> Houston Methodist. Leading Medicine. U.S. News & World Report has named Houston Methodist Hospital the Best Hospital in Texas for 10 years in a row. Houston Methodist is the No. 1 hospital in Texas and No. 16 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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Postdoctoral Fellow Position in Simultaneous Spinal Cord-Brain fMRI
by Abdou Thiam 15 Sep '21

15 Sep '21

External Email - Use Caution DESCRIPTION The Systems Neuroscience & Pain Laboratory at Stanford University (SNAPL) is actively recruiting a postdoctoral fellow who will join our research project on chronic pain. Funded by the National Institute of Health and directed by neuroscience professors Sean Mackey and Gary Glover, our goal is to investigate mechanisms of chronic pain using methods we developed to image the entire CNS via simultaneous spinal cord/brain fMRI. Our plan is to characterize neurobiological mechanisms underlying chronic pain and use this information to develop objective biomarkers of pain, ultimately, to derive new personalized interventions. Given abundant findings that fMRI of the brain can act as biomarker for chronic pain conditions, we propose utilization of our simultaneous spinal cord/brain fMRI to develop biomarkers of pain severity. Our research can be categorized as follows: 1. CNS mechanisms of chronic pain and pain modulation, 2. central sensitization and descending modulation, 3. corticospinal biomarkers of chronic pain conditions, 4. predictive models of pain resilience. When you join, you will have opportunity to collaborate with top neuroscientists, psychologists, machine learning experts and pain specialists at Stanford. Additionally, you will have access to cutting-edge fMRI technology; to invent and develop your own related research. Multidisciplinary aspects of this project will allow you to explore diverse chronic pain topics ranging from biomarker design for degenerative conditions to heart rate variability as a simple biomarker for psychological disorders. We have a strong track record for successfully transitioning postdoctoral fellows to independent grant funding and faculty positions. We can offer NIH T32 training to select candidates. The ideal candidate is a motivated problem solver and innovator who has a neuroscience background, enjoys challenging the paradigms of contemporary research and experimentation, is proficient with computer-aided analysis, and is enthusiastic and passionate about fMRI acquisition. RESEARCH AREA * fMRI and behavioral data from Healthy Control and Fibromyalgia, * Novel analysis techniques for multiecho cardiac-gated fMRI, spinal cord/brain task/resting-state fMRI, * Experiment design for * temporal summation & central sensitization of pain, * conditioned pain modulation, * descending pain modulation & emotional reappraisal of pain, * Multivariate pattern analysis of spinal cord/brain data for corticospinal biomarker, * Simultaneous spinal cord/brain fMRI for multiple sclerosis, spinal cord injury & trauma, motor neuron disease. QUALIFICATION Applicants must have received, as of the beginning date of the appointment, an MD/PhD, MD or PhD or comparable doctoral degree from an accredited domestic or foreign institution. Experience in neuroimaging analysis is a must. Additional experience in any of these is a plus: 1. Cognitive / Affective Neuroscience 2. Computational modeling / Machine Learning / Neural Networks / ICA 3. Chronic pain 4. MATLAB / Python / R / Linux / C 5. SPM / AFNI / FSL / fMRIPrep APPLICATION MATERIALS Submit (1) CV, (2) NIH Biosketch, (3) Letter of Research Intent Find instructions, blank format pages, and sample biosketches here:<https://secure-web.cisco.com/1Gw3cKdrJJ5YO-Xix239BEzVR8sGJvGRaGxNslDo_fwSoT…> https://secure-web.cisco.com/1Gw3cKdrJJ5YO-Xix239BEzVR8sGJvGRaGxNslDo_fwSoT…. Applicants follow non-fellowship templates. Letter of Intent template is available<http://secure-web.cisco.com/1GyGUEJlHt71LAew-d0oQUp36d1ghRzSTzWAC4ce5DG0qQc…>here: http://secure-web.cisco.com/1GyGUEJlHt71LAew-d0oQUp36d1ghRzSTzWAC4ce5DG0qQc…. For more information, visit http://secure-web.cisco.com/1v2JVB1UtaPVopImV9dKbvKiLzxrwzYcPbEQKLn3KchLpMj… Address Letter of Research Intent to Christine Sze Wan Law: cslaw(a)stanford.edu<mailto:cslaw@stanford.edu>

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running freeview on MacOS Big Sur, version 11.5.2
by Jingyi Wang 14 Sep '21

14 Sep '21

External Email - Use Caution Dear freesurfer experts, I have a MacOS Big Sur, version 11.5.2 with an Intel chip. I successfully installed freesurfer on my computer. Unfortunately, the freeview quit unexpectedly every time I tried to open any file. Is the MacOS version 11.5.2 not supporting freeview? How can I solve this problem? Any insights can help! Thanks! Ps: I have attached the error message below, if needed.

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