Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Postdoctoral Fellowship
by Didenur Sahin 17 Jan '20

17 Jan '20

External Email - Use Caution Dear All, Brain Development And Psychosis Lab, is pleased to announce the opening of a postdoctoral fellowship position in clinical neuroscience and cognitive neuroimaging. Please take a look at the attached advertisement. Best, Didenur Sahin -- Didenur Şahin Graduate Student Neuroscience Program National Magnetic Resonance Research Center (UMRAM) Bilkent University Ankara, Turkey 06800

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Re: [Freesurfer] `GLIBCXX_3.4.19' not found error
by fsbuild 16 Jan '20

16 Jan '20

External Email - Use Caution Hello Pascale, Yes, that kind of symbol error has been posted before, and it can from the version of the standard C++ (or C) libraries being too different on the machine the binaries are running on - compared to the machine they were built on.  Generally speaking, newer versions of the OS try to be backwards compatible, e.g., such that binaries built on CentOS 6 could run on CentOS7.  However, forward compatibility may not to work, e.g., CentOS 7 binaries may not run on CentOS 5 or 6. You could let us know something more about the binaries you are using and the version of the OS you are running on in order to match them up, but using different version of the standard C libraries to run only some binaries is not recommended. - R. On Jan 16, 2020, at 12:33, Pascale Patenaude <pascalepatenaude(a)hotmail.com> wrote:        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 _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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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