Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30055 discussions

Development version M1 mac error
by Jasmine Cakmak 21 Oct '24

21 Oct '24

External Email - Use Caution Hello, I recently downloaded the current development version of Freesurfer onto an M1 mac (Big Sur 11.6.6) as I had read that it better allows for certain commands to be run on M1 macs. I tried to run recon-all and received the following message: dyld: Symbol not found: __ZNKSt3__115basic_stringbufIcNS_11char_traitsIcEENS_9allocatorIcEEE3strEv Referenced from: /Applications/freesurfer/dev/bin/fs_temp_file (which was built for Mac OS X 12.0) Expected in: /usr/lib/libc++.1.dylib Abort fs-check-version --s sub001 --o ERROR: flag --o requires one argument I've run a previous development version (I believe from 2022) on this mac beforehand and didn't have this problem. If I could get any help solving this that would be greatly appreciated. Thank you so much, Jasmine

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lost volume geometry information using read_surf.m and write_surf.m
by Yujia Huang 21 Oct '24

21 Oct '24

External Email - Use Caution Hi Freesurfers, I'm attempting to create equal-distant surface layers between the ?h.pial and ?h.white surface segmentation using the MATLAB functions read_surf and write_surf. I used read_surf to get the vertex coordinates and face information out of the ?h.pial and ?h.white and saved the modified vertex coordinates for the new surface into "?h.new_surface.pial" using write_surf. After loading the new surface files into freeview the command line shows the following warning message: Did not find any volume info The surface however was showing correctly on freeview. Furthermore, when I'm attempting to calculate the surface orientation angles of the newly generated surface using mris_convert --angle, I got the following error indicating the same thing about missing volume info: ************************************* CAUTION ************************************** If you are running "mris_convert --angle" on an original surface (i.e. has not been transformed by mris_surf2surf), then you can ignore this message. However, if you need to calculate orientation angles of a TRANSFOMRED surface you will need to convert the .lta/.dat registration file first and force the original volume as the source. Otherwise important header information will be lost and the angles will be incorrect (do not be fooled, they might appear close, but they won't be exact). A detailed description and example can be found on the freesurfer wiki. ************************************************************************************ error: volume size must be greater than 0 in every dimension I see similar problems have been reported previously but I was not able to locate the solution of such matter. Does anyone know what is the cause of this and how to trouble shoot? Thanks in advance! 1. Freesurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0 2. Platform: Ubuntu 20.04.6 LTS 3. uname -a: Linux hawaii 5.15.0-91-generic #101~20.04.1-Ubuntu SMP Thu Nov 16 14:22:28 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux 4. MATLAB: 2019b Best, Yujia Huang Research Assistant I Advanced Imaging Research Center UT Southwestern Medical Center 2201 Inwood Rd. Dallas, TX, USA, 75390 Office: 214.645.5241 Pronouns: He, Him, His ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Using Freesurfer for Volume Analysis with Destrieux and aseg Atlases
by Safari, Nooshin (rvz7wf) 17 Oct '24

17 Oct '24

External Email - Use Caution Hi Freesurfer experts, I am new to using Freesurfer. My lab plans to use the Destrieux atlas (a2009s) for cortical analysis and the aseg atlas for subcortical areas, specifically focusing on the Thalamus, Caudate, Putamen, Pallidum, Hippocampus, and Amygdala. We aim to perform volume analysis at the vertex and ROI levels. Does Freesurfer provide tools for this purpose, or is such analysis only possible in SPM, specifically using the CAT12 toolbox? I've searched the list and no similar questions have been posted. Thanks! Nooshin

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white surface correction trouble-shooting
by a.cocuzza 15 Oct '24

15 Oct '24

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to perform a correction on the reconstruction of lh.white and rh.white surfaces (in excess at baseline), but it doesn't work. I checked the method with another colleague of mine, but both of us are not able to understand why or how to solve this. The procedure I use is the following (in freeview): 1)Open volume and surface objects with: freeview --volume mri/brainmask.mgz --volume mri/orig.mgz --volume mri/wm.mgz:colormap=heat:opacity=0.4 --surface surf/lh.pial:edgecolor='255,0,0' --surface surf/rh.pial:edgecolor='255,0,0' --surface surf/lh.white:edgecolor='blue' --surface surf/rh.white:edgecolor='blue'. 2) Click on the wm row so that it's highlighted in the top left corner of freeview 3) Select recon edit and then left click + shift to erase parts of the wm volume which I consider to be in excess 4) Save the wm.mgz volume 5) Launch wm and lh or rh.white correction with: recon-all -autorecon2-wm -autorecon3 -subjid $SUBJ After the conclusion of the correction, I open again freeview and I see that the wm volume corresponds to the one I edited, but the white surfaces are not "updated" to adapt to my correction of wm (see image "before smoothing"). How can I perform a recalculation of the white surfaces from my correction of wm.mgz? I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I've attached a picture of a "not-updated white surface" to make sure I can show you my problem (again, "before smoothing"). On a side note, we tried to circumvent all this by using "Tools - Reposition Surface - Smooth" to slightly smooth the excess white surface (for its effect, see image "after smoothing"). If there is no other way to do it, do you believe this is a good method or are there better ones? Could you please explain me how can I recalculate the stats after smoothing the surfaces? 1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 2) Platform: Ubuntu 22.04.4 LTS 3) uname -a: Linux vrk-neuro.auxonet.local 5.15.0-119-generic #129-Ubuntu SMP Fri Aug 2 19:25:20 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux Thank you very much for your help. Kind regards, Alessandro

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Obtaining eTIV/ICV value after recon-any processing
by Mahir Khan 14 Oct '24

14 Oct '24

External Email - Use Caution Hi, I am trying the recon-any processing stream on some clinical imaging. I am having trouble finding the eTIV or ICV value that is typically reported as an output in the normal recon-all processing stream. I noticed in the stats/brainvol.stats file that there is a “BrainSeg” measure that is around what is expected as an eTIV value - is this the eTIV value to use in downstream analyses? Best, Mahir -- Mahir Khan PhD Student, Neuroscience Graduate Program Neural Plasticity & Neurorehabilitation Lab University of Southern California Email: mhkhan(a)usc.edu <mailto:mhkhan@usc.edu>

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Hardware selection for utmost performance of Freesurfer
by Jin Liu 14 Oct '24

14 Oct '24

External Email - Use Caution Hello Freesurfer team, Our lab is considering purchasing a new workstation, typically for running Freesurfer at the current stage. The best we can get would be a Dell model with 23 physical cores (46 logical cores) 256 Gb RAM Ubuntu Nvidia box, but we are confused if the hardware processing capacity will significantly improve Freesurfer performance or will even not support Freesurfer functions. We are aware that number of cores can lead to an exponential growth in speed using parallel processing. Is there an upper limit to this increase? We also know that having a larger RAM can improve the performance of Freeview and we also wonder if it reaches marginal effects for a 256 Gb RAM, and if having a Nvidia box would make a difference. Thanks, Jin

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[WARNING: ATTACHMENT UNSCANNED]Issue with WM surface fill
by Bronwyn Overs 14 Oct '24

14 Oct '24

External Email - Use Caution Dear Freesurfer Support, I'm reviewing a specific MRI image that I have processed with Freesurfer V5.3. I'm concerned about a potential issue with voxels missing from the WM surface. This appears to impacting the pial boundaries and lateral ventricle labels in the aseg from slices 56-99. For reference, I attached 5 images (both wm and brainmask surfaces) that are each 5 slices apart. Happy to upload the whole series of images if this would be helpful. Would you recommend filling in some of the voxels near the lateral ventricles? My concern is that I am unsure where the ventricle begins, as I suspect the gyrus at the rh pericalcarine surface is not being properly labelled and identified in the pial surface. Any advice you can provide will be greatly appreciated. Kind regards, Bronwyn Overs Senior 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://secure-web.cisco.com/1PhyqjBKyb2oDl07vqwWhBygB_5YJLdeJ41dvzkSKapr3Gu… | neura.edu.au ] [ https://secure-web.cisco.com/1Nq-N5jOYtG9ZB4Dl8PisdSUykSQS1VbMzYkTSuKxvkBDE… | Twitter ] | [ https://secure-web.cisco.com/1wYi0bZZPKh6dadEH9ixKmgt3NP7bvL1I_HLfiwg9s6h5-… | Facebook ] | [ http://secure-web.cisco.com/1yUpg4OTzIo3qIvjsCh2VZmcvRXG4uvBgKotJ3qtYmng5K2… | Subscribe ]

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Request to Post Job Position on Freesurfer listserv
by Otero Ospina, Andrea 14 Oct '24

14 Oct '24

External Email - Use Caution Hi, I hope this message finds you well. We would like to post the following job position on the Freesurfer listserv. Could you please assist us with this request? Department of Psychiatry and Behavioral Sciences Postdoctoral Associate Position in Human Neuroimaging University of Miami Miller School of Medicine, Miami, Florida, USA The Gabbay Laboratory within the Department of Psychiatry at the University of Miami Miller School of Medicine is seeking highly motivated postdoctoral scholars in the field of human neuroimaging. Available positions will focus on analyzing fMRI and proton MR spectroscopy data as well as acquiring or processing related MRI and biological measures. Candidates should either have completed or be near completing a PhD in neuroscience, psychology, cognitive neuroscience, radiology, engineering, biostatistics, or a related field, and should have a strong background in quantitative analysis. Proficiencies with at least one major neuroimaging software suite (e.g. FSL, AFNI, SPM, Freesurfer, Caret, Connectome Workbench, etc.) and Unix/Linux environment are expected. Familiarity with Matlab, Python, and/or R programming languages is a plus. The primary responsibilities for this postdoctoral fellow will be to run scans, analyze neuroimaging data from multiple ongoing and recently concluded research projects, and write manuscripts. Under the mentorship of Vilma Gabbay, MD and Benjamin Ely, PhD, postdoctoral scholars will be expected to advance clinical and methodological knowledge through their postdoctoral training. Our lab is dedicated to the study and treatment of mood, anxiety, and substance use disorders in adolescent and high-risk adult (e.g. HIV+) populations using innovative neuroimaging and immunological methodologies. The neuroimaging program features high-resolution data acquisition and analysis techniques modeled on the Human Connectome Project (HCP) and is committed to the highest standards for magnetic resonance imaging and spectroscopy. The lab is funded by four ongoing NIH R01 neuroimaging studies (R01MH120601, R01DA054885, R01MH128878, and R01MH131207) and several smaller grants, providing unparalleled funding for active and exploratory studies. Major research topics include longitudinal studies of adolescent mood and anxiety disorders; comorbidity of depression, cannabis use, and HIV infection; and an intervention study aimed at improving well-being among healthcare workers with parental responsibilities during the COVID-19 pandemic. Project abstracts with further details can be found on NIH RePORTER. Resources available on-campus and through long-standing collaborations include multiple research-dedicated 3T MRI scanners (Siemens Skyra/Vida/Prisma) with cutting-edge accelerated and multi-echo fMRI sequences, high-performance scientific computing clusters, and an extensive library of analytic and statistical software. The PIs are fully committed to fostering the trainee's research independence through publication of first-authored manuscripts in top journals and mentorship in grant applications. In addition to assisting with the PI’s proposals, the successful applicant will be highly encouraged to develop and pursue funding for their own research project through federal (e.g. NIH F32) or foundation grant programs by the end of their first year. Please send a CV, statement of interest, and contact information for three references to axo833(a)med.miami.edu<mailto:axo833@med.miami.edu>. University of Miami is an equal opportunity employer, and all qualified candidates will be given equal consideration. Priority will be given to candidates available to start sooner. Compensation will be proportional to experience and will follow standard postdoctoral fellowship rates posted by University of Miami. Best, Andrea Otero, M.D. Clinical Research Coordinator Department of Psychiatry and Behavioral Sciences University of Miami — Miller School of Medicine Email: axo833(a)med.miami.edu<mailto:njh115@med.miami.edu> Phone: 305-243-7086 [cid:97820b9a-5459-48c5-b510-70a6fc22a6b5] [cid:a06cc866-1bdb-4959-a3ec-4c95e614aaf9]<https://secure-web.cisco.com/1NtHyStrjuOSWOO5EbcV14g1jIPuoLRF1sxsbaI79RQ5Jg…> Book time to meet with me<https://secure-web.cisco.com/1NtHyStrjuOSWOO5EbcV14g1jIPuoLRF1sxsbaI79RQ5Jg…>

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mri_segstats for lobar intensity values
by Julie Ottoy 11 Oct '24

11 Oct '24

External Email - Use Caution Hi Freesurfer team, I want to calculate the average PET intensity values per lobe. I want to use the lobar annotations as outlined here in 'lobe mapping': https://secure-web.cisco.com/1Opn2TyIP5_MF5tP6PRtaju8QtoITdCtzrmIlxZvYGO1bU… My PET images are volumetric in T1w MRI space. I have successfully created my lobes following this command: mri_annotation2label --subject $session --hemi lh --lobesStrict lobes However I'm getting an error with my next command: mri_segstats --annot $session/label/lh.lobes.annot --i $session/pet_surf/SUVR/SUVR_T1space.nii.gz --sum lh.pet_lobar.sum It is reading in the white surface, because I get this error: error: MRISread($path/$session/label/rh.lobes.annot/surf/--i.white): could not open file How should I run this command when reading from the volumetric PET image? Thank you, Julie

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Re: [Freesurfer] Error while opening Freeview on Linux
by fsbuild 11 Oct '24

11 Oct '24

External Email - Use Caution Try downloading and installing the freesurfer .deb or.rpm linux package installer that matches your OS .. from,https://secure-web.cisco.com/1Me3-1hl0gfMcAF2vBsI1JUBKuzDpNWmT5AWDIQZn… For example, on Rocky8 linux (uses RedHat lkie .rpm files),  install the .rpm file from where you downloaded it with, e.g., $ sudo yum install ./freesurfer-Rocky8-7.0.0-dev.x86_64.rpm On Ubuntu22 linux, i,e, uses debian like .pkg files), install the .deb file from where you downloaded it with,$ sudo apt install ./freesurfer_ubuntu22-7-dev_amd64.deb Those package installers should automatically install any missing libraries on you system like libpng12.so.  Downloading and expanding one of the freesurfer *.tar.gz archives will not do an actual install, i.e. won’t check for or try to install missing libraries on your system needed to run freesurfer. Then setup the freesurfer environment as listed here,https://secure-web.cisco.com/1BELDi9cDpanBzm2iGuNdHAswzIduLFc5gddCoywt… - R. On Oct 11, 2024, at 14:00, Harsh Srivastava <harsh.sriv(a)iitb.ac.in> wrote:        External Email - Use Caution        Dear Freesurfer team,I have Freesurfer installed on Linux. All Freesurfer commands work well, however, I am not able to open freeview. I get this error:freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directoryPlease let me know how it can be resolved.Warm regards,--  Harsh Srivastava (he/him), 23M0132 (2nd year), MTech Biomedical Engineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India._______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1Nteb0siX3-eisiJSbMFVKuyiiW1wlCIU90j5qryoeAjXJ…

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