Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Edit surface in Freeview
by Davide Momi 16 Jan '20

16 Jan '20

External Email - Use Caution Dear Freesurfer expert, I am working with bem model and I have created the outer and the inner skull. Unfortunately, for few subjects the two surfaces intersect each other (see attached). I've tried to edit it manually but I had hard time in figuring it out. Could you please help me with this? thanks Dave

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Segmentation Fault during recon-all using FLAIR Image
by Swanson,Clayton 16 Jan '20

16 Jan '20

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to perform a recon-all using a T2-FLAIR image. I have already run this particular participant through recon-all with their T1 image without error. While running the recon-all using the T2 the process exited with error stating a segmentation fault. Is there any way to run fix this problem on my end or better understand why this would be occurring? I have uploaded the recon-all.log for your convenience. Thank you, Clayton ________________________________ Clayton Swanson MS Graduate Research Assistant & PhD Student Sensorimotor Neuroimaging Laboratory Colorado State University Office: (970) 491-6160 Clayton.Swanson(a)colostate.edu<mailto:Clayton.Swanson@colostate.edu>

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Flag for recon-all to output aparc2005 labels (freesurfer 6.0)
by Grodin, Erica 16 Jan '20

16 Jan '20

External Email - Use Caution Hello, I am running recon-all on my data using freesurfer 6.0 which is working correctly. However, I need to create some VOIs which labels are only outputted from the aparc2005 set and do not appear in the aparc2009 set; specifically: 9001, 9501 ctx-lh-primary-motor, ctx-rh-primary-motor 9005, 9505 ctx-lh-prim-sec-somatosensory, ctx-rh- prim-sec-somatosensory 9002, 9502 ctx-lh-premotor, ctx-rh-premotor 9004, 9504 ctx-lh-posterior-parietal, ctx-rh-posterior-parietal Is there a flag or some other option to output the 2005 set in addition to the 2009? Thank you for your help, Erica Grodin ---------------------- Erica Grodin, Ph.D. Postdoctoral Fellow University of California, Dept. of Psychology and Psychiatry

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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 Is there something wrong? > 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.

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(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

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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.

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