Freesurfer January 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
156 discussions

(no subject)
by Boris Rauchmann 16 Jan '20

16 Jan '20

External Email - Use Caution Dear all, my intention is to use the Brainnetome Atlas parcellation/segmentation in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I used: gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg Is this the right approach to obtain a high resolution segmentation to run PVC methods? Thanks, Boris

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`GLIBCXX_3.4.19' not found error
by Pascale Patenaude 16 Jan '20

16 Jan '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to produce an automated segmentation of the hippocampal substructures and the nuclei of the amygdala (see hippocampal module https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) When I try to run the segmentHA_T1.sh bert [SUBJECTS_DIR] command with the dev version of freesurfer, I keep getting this error: /freesurfer-dev/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.19' not found /freesurfer-dev/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.19' not found It was suggested in the archives that this is a library problem but does anyone have any suggestions on how this can be fixed? Thank you in advance, Pascale

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Segfault in mris_topo_fixer
by Christian O'Reilly, Dr 16 Jan '20

16 Jan '20

External Email - Use Caution Hi, I got the following error running mris_topo_fixer: ~$ mris_topo_fixer -mgz -warnings ANTS6-0Months3T lh INFO: assuming .mgz format verbose mode on (medium mode): printing warnings reading input surface /usr/local/freesurfer/subjects/ANTS6-0Months3T/work/ANTS6-0Months3T/surf/lh.orig... Before topology correction, eno=0 (nv=43656, nf=87312, ne=130968, g=1) Surface Diagnostics: eno=0 (nv=43656, nf=87312, ne=130968) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0 The original surface is a valid manifold Counting the number of connected components The original surface has one component The original surface does not self-intersect The surface has 1 loops (X=0) Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations identify defects... marking ambiguous vertices... 1527 ambiguous faces found in tessellation segmenting defects... analyzing defects for overlaps... reading brain volume from brain... reading wm segmentation from wm... Detecting contrast direction: right direction [ GM (129.46) < WM (134.73) ] ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 Segmentation fault (core dumped) Any idea what in the data file could cause the assert "vt->nsizeMax > 0" to be triggered? Any idea how to go around it? Thank you, Christian

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Re: [Freesurfer] Oval shape in average subject inflated
by Marina Fernández 16 Jan '20

16 Jan '20

External Email - Use Caution It works! Thank you very much Bruce!

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Lab for Computational Neuroimaging is hiring new Research Techs
by Morgan, Leah 15 Jan '20

15 Jan '20

Hi everyone, The Lab for Computational Neuroimaging is hiring new Research Assistants. The job description is included below, with instructions on how to apply through MGH. Please feel free to forward on to anyone who may be interested. Computational Neuroimaging Lab seeks Research Assistant/Technician For this position, the Research Technician (RT) will learn how to run MRI experiments on several different MRI scanners (small bore 9.4T, whole-body 3T, and/or whole-body 7T), for both in vivo and ex vivo (human) projects. Responsibilities of the RT will also include preparing the brain samples to be scanned, processing the data, presenting the data at internal meetings, troubleshooting problems that arise, and analyzing data. Our methods are unique and so all new staff will be trained in them. Candidates with skills & competencies that support their ability to learn these methods quickly will be stronger candidates. We are looking to fill 2-3 positions to replace RTs going on to graduate school. The position involves working in a fast-paced computational neuroimaging lab. The lab is comprised of faculty, postdocs, graduate students, and research assistants from different backgrounds including Neuroscience, Biomedical Engineering, Psychology, Computer Science, Math, Physics, and Biology. Using these different backgrounds, the lab develops and maintains software to analyze MRI data and performs cutting edge research in a variety of domains. Other projects/tasks the RT may be involved in: *Recruitment of research subjects for in vivo scanning projects *Management of IRB protocols *Teaching FreeSurfer, our in-house software, to users from around the globe *Performing quality assessments of data run with FreeSurfer *Troubleshooting software issues for FreeSurfer users *Beta-testing new versions of FreeSurfer or other software developed in-house *Developing or improving scripts and/or code (via C shell scripting, C++, or Python) *Performing (p)OCT acquisitions on a customized (p)OCT imaging system and associated data processing The position offers great opportunities to work with prominent scientists, people from a variety of fields, a great and fun team, opportunities to publish, as well as guidance and support for future career choices. Please see our website to learn more about the different ongoing projects: http://martinos.org/lab/lcn Education: Bachelor’s degree required. Relevant backgrounds would be Neuroscience, Psychology, Engineering, Computer Science, and/or Biology. Experience: New graduates with some lab experience (via course work, internships, etc.) or those without any prior research experience will be considered for the Research Technician I position outlined above. Those with a minimum of 1 year of directly related work experience will be considered for a Research Technician II position. Individuals with even more experience or advanced degrees should still apply as there is the potential to offer a more advanced position depending on the individual’s experience. How to Apply for the Position: Please apply for the position on the MGH job board by providing a resume and cover letter: http://www.massgeneral.org/careers/viewall.aspx Look for Research Technician I (and II), job # 3113031 Use this link to see the full job description: https://surfer.nmr.mgh.harvard.edu/fswiki/ResearchAssistant Regards, Leah Morgan

1 0

Oval shape in average subject inflated
by Marina Fernández 15 Jan '20

15 Jan '20

External Email - Use Caution Dear Freesurfer team, I created the FS average subject of the same dataset with 5th and 6th order icosahedron tesselation using the following commands: make_average_subject --fsgd fsgd.txt --ico 5 --out avg_subject_ico5 make_average_subject --fsgd fsgd.txt --ico 6 --out avg_subject_ico6 When I load the inflated surface of the avg_subject_ico5 with tksurfer , it has a oval shape while when I load the avg_subject_ico6 it seems to be a normal shape. Please, see attached image. Thank you in advance. Best wishes, Marina.

2 1

Fwd: NeuroCon 2020 - save the date
by ezgi arikan 15 Jan '20

15 Jan '20

External Email - Use Caution Dear all, We are happy to announce the first meeting of the young German Neuroscience Society (jNWG), NeuroCon 2020 (see the attached flyer). The meeting will take place in September 25-27, 2020 in Ulm, Germany, and is designed specifically for early career scientists who would like to present their projects, build academic skills and connect with other colleagues in the field. The meeting is open to any neuroscience field, so a wide array of topics will be on display. Detailed information regarding the program and registration will be soon on our website: jnwg.org Best Regards, B. Ezgi Arikan

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Email info for free surfer mailing list
by ezgi arikan 15 Jan '20

15 Jan '20

External Email - Use Caution Best Regards Ezgi Arikan

1 0

Max threshold marked as '-inf' in cluster summary file
by Bronwyn Overs 14 Jan '20

14 Jan '20

External Email - Use Caution Dear Freesurfer Mailing List, I have completed an LME analysis in matlab and have generated a number of different cluster summary files for my various contrasts. In many of resulting cluster summary files the 'Max' value for the largest cluster which encompasses most of the brain surface is reported as infinity ('-inf'). Please find an example file attached. As I was hoping to use these values to generate effect size estimates, can you please tell me what alternate value I could substitute here for 'Max'? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

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Thalamus segmentation
by sara ponticorvo 14 Jan '20

14 Jan '20

External Email - Use Caution Hi Freesurfer expert, I have a question regarding the segmentation of the thalamus. After the “standard” segmentation from the recon-all (aseg), in label thalamus-Proper is included the medial geniculate body? Thanks, Sara

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Freesurfer January 2020