Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30087 discussions

White matter hypointensities
by Rockers, Elijah D. 03 Apr '20

03 Apr '20

External Email - Use Caution Hello, When was the wm-hypointeisities label added to the Freesurfer segmentation? Is there any paper that explicitly mentions this, or should I just cite the 2002 paper? Thanks, -Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas and among the top 20 hospitals nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital in the state and is designated as a Magnet hospital for excellence in nursing. 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.

1 0

Freesurfer with Catalina
by Stephan 03 Apr '20

03 Apr '20

External Email - Use Caution Hi Freesurer team, I am trying to run mri_convert (and recon_all) with a Macbook Pro 2019 with Catalina. Running mri_convert always leads to the following error: //Users/neurolab/Desktop/Stephan/Programmes/freesurfer/bin/mri_convert: line 3: //Users/neurolab/Desktop/Stephan/Programmes/freesurfer/bin/mri_convert.bin: cannot execute binary file All security changes haven't helped yet. Best, Stephan

1 0

Petsurfer: Gtmstats < 1, voxel wise mean is fine
by Eckbo, Ryan 03 Apr '20

03 Apr '20

Hello experts, I've recently run into a case the gtmstats uptake (reference region: cerebellum) for the pericarlcarine ROI's are as low as 0.40, however computing the voxel wise mean using input.rescaled.nii.gz and mgx.ctxgm.nii.gx and aux/seg.nii.gz, the values are closer to 1, as expected: | vol | psf | roi | gtmstats_uptake | mean_uptake | | --------------------- | --- | -------------------- | --------------- | ----------- | | input.rescaled.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 | 1.226… | | input.rescaled.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 | 1.083… | | input.rescaled.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 | 1.197… | | input.rescaled.nii.gz | 6 | ctx-lh-pericalcarine | 0.470 | 1.058… | | mgx.ctxgm.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 | 1.007… | | mgx.ctxgm.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 | 0.888… | | mgx.ctxgm.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 | 0.915… | | mgx.ctxgm.nii.gz | 6 | ctx-lh-pericalcarine | 0.470 | 0.809… | This is using Freesurfer 6.0, and the PET to anatomical registration looks fine. Any ideas why we get such bad values from the GTM method? Thanks for any help, Ryan

2 4

HP and thalamic subfield quality with a bad aparc segmentation
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 03 Apr '20

03 Apr '20

Hi all, >From my understanding from the log files, the subfield segmentations (and in general the aparc.mgz) relies on the norm.mgz (which is based off the brainmask.mgz). What if hypothetically, you have a not so good segmentation of the cerebral cortex, but willing to individually qc the subfields for the hippo, amyg and thal to see whether they are worth including in an analysis? I don't know if you would inherently discard a subject in a subfield analysis if it has a bad cerebral cortex segmentation (e.g ring artifacts) since the subfield segmentation retrieves some sort of cerebral cortex measurement in its calculations Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 3

CORONA Research study in India - an online survey !
by Sahil Bajaj 02 Apr '20

02 Apr '20

External Email - Use Caution Dear all, Our research group is looking for participants (age 19 years or older) who are currently staying in India amid 21-days COVID-19 lock down, and can complete an online 15 min survey about human behavior related to COVID-19. If you meet these two eligibility conditions: (i) age 19 years or older, and (ii) you are/were staying in India during 21-days lock-down period due to CORONA virus, and are interested in participating in the study, please email me back at sahil.brain(a)gmail.com to get the survey link. Details about my research: https://www.boystownhospital.org/research/faculty/sahil-bajaj Given the seriousness of the disease, I would really appreciate if you can contribute to scientific research related to COVID-19. Thanks a lot ! Best, Sahil -- ------------------------------------- *Sahil** Bajaj, Ph.D.* Director, Multimodal Clinical Neuroimaging Laboratory (MCNL) Center for Neurobehavioral Research *E-mail:* sahil.bajaj(a)boystown.org | *p:* 531.355.1053 | *f:* 531.355.1213 Boys Town National *ResearchHospital* Boys Town, NE 68010 Twitter <https://twitter.com/BoysTown> | LinkedIn <https://www.linkedin.com/company/boys-town-national-research-hospital/>

1 0

PhD position, University of Oldenburg, Germany
by Peter Soros 02 Apr '20

02 Apr '20

External Email - Use Caution Dear All, The University Clinic of Neurology, University of Oldenburg, Germany, seeks a highly motivated PhD student (m/f/d) for a TV-L 13 position (65 % of full time, 3 years): Neuroimaging, behavioral, and neurochemical markers of Parkinson's disease progression This position is embedded in a larger project on healthy aging and neurodegenerative disease at the University of Oldenburg and is funded by an intramural grant from the School of Medicine and Health Sciences. The successful PhD student will investigate large neuroimaging, behavioral, and clinical data sets available to us, using sophisticated statistical and neuroimaging software installed on the High-performance Computer Cluster in Oldenburg (uol.de/en/school5/sc/high-performance-computing/hpc-facilities). The overarching aim of the project is to determine biomarkers for disease progression and cognitive decline in Parkinson's disease. This project is a close collaboration between Neurology (Dr. Peter Sörös, Prof. Dr. Karsten Witt) and Anatomy (Prof. Dr. Anja Bräuer) in Oldenburg and Biostatistics at the Helmholtz Centre for Infection Research in Braunschweig (Prof. Dr. Frank Klawonn). The successful PhD student will also analyze biochemical markers of neurodegeneration in Prof. Bräuer's lab (uol.de/anatomie), participate in the development of novel software tools based on R Shiny together with Prof. Klawonn's group (www.helmholtz-hzi.de/en/research/research-topics/bacterial-and-viral-pathog…) and acquire own MRI data sets of patients and controls in the Neuroimaging Unit, School of Medicine and Health Sciences, University of Oldenburg (uol.de/en/medicine/biomedicum/neuroimaging-unit). The Neuroimaging Unit houses a research-only Siemens Prisma MRI at 3 Tesla with 64-channel head coil. Applicants are required to have an academic university degree, such as a master's degree in the field of psychology, neuroscience, physics or a related discipline, or a medical degree. A strong research background with experience in neuroimaging analysis (e.g. FreeSurfer, FSL, SPM), statistics (R), and programming (R Shiny, Python) is highly desirable. Excellent skills in written English are important. Oldenburg is an attractive city with a population of 170.000 in the northwest of Germany, close to Bremen, Hamburg, and Groningen. In order to increase the percentage of female employees in the field of science, female candidates with equal qualification will be given preference. Applicants with disabilities will be preferentially considered in case of equal qualification. Applications including a detailed letter of motivation, a complete CV, copies of university diplomas and transcripts, a copy of the B.Sc. or M.Sc. thesis (or other written work), and contact details of two academic referees should be sent to Dr. Peter Sörös: peter.soros(a)uni-oldenburg.de or to: Dr. Peter Sörös, Neurology, School of Medicine and Health Sciences, University of Oldenburg, Heiligengeisthöfe 4, 26121 Oldenburg, Germany. Application by email (one PDF document) is preferred. Deadline for application: April 30, 2020 https://uol.de/stellen/?stelle=67239 <https://uol.de/stellen/?stelle=67239>

1 0

Help Segmentation of Hippocampal subfields
by ioana cracana 02 Apr '20

02 Apr '20

External Email - Use Caution Hello, I'm doing a study about hippocampal atrophy and I'm using the Segmentation of Hippocampal subfields tool. There were some minor errors and I edited them using Freeview, voxel edit tool. I would like to generate a new [lr]h.hippoSfVolumes-T1.v10.txt file using the edited [lr]h.hippoSfLabels-T1.v10.mgz . What command do i have to use? I'm using Freesurfer v6.0.0. Thanks, Ioana

1 0

Tkmedit gui download
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 01 Apr '20

01 Apr '20

Hi all, I am still trying to adapt to working from home, and I am forced to work with incredibly slow download speeds. I am trying to download FS6.0 for mac for the sole purpose of using tkmedit, rather than the entire toolbox, just so I can edit brains (I anticipate downloading FS6.0 for mac in my house would take like 36 hours). Can someone provide me a link to download just the necessary codes for tkmedit in macs? I would greatly appreciate this. Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

Is it possible to "fill in" the region delimited by an ROI label?
by Mohammad Rashid 01 Apr '20

01 Apr '20

External Email - Use Caution Hi all, I'm able to load in a yellow outline for the entorhinal region by loading a file named ?h.entorhinal_exvivo.label as a volume. (I first load in a brain image such as brain.mgz, and then display the outline on top of it.) Is it possible to get a solid highlight of the entorhinal region in this manner, as opposed to just an outline of the region? (Strangely enough, if I load ?h.entorhinal_exvivo.label as a label on an surface file, such as ?h.inflated, then the entorhinal region is seen filled in with a yellow color on the 3D surface. This is the effect I want, except on a 2D volume.) Any help is greatly appreciated, Mohammad

2 4

Tutorial Data Error Message
by Batra, Vinita R. 01 Apr '20

01 Apr '20

External Email - Use Caution Hello FreeSurfer Team, When I run the test_commands.sh.15 I get the following error message as shown below. dyld: Library not loaded: /usr/X11/lib/libGLU.1.dylib Referenced from: /Applications/Imaging/freesurfer/bin/mri_probedicom Reason: image not found Abort Abort dyld: Library not loaded: /usr/X11/lib/libGLU.1.dylib Referenced from: /Applications/Imaging/freesurfer/bin/mri_probedicom Reason: image not found Saving session... ...copying shared history... ...saving history...truncating history files... ...completed. Please help me with this. Thank you Vinita Batra

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