Freesurfer

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30068 discussions

mri_synthmorph regularisation
by Simon Jones 22 Oct '24

22 Oct '24

External Email - Use Caution Dear all I tried to use change the regularisation parameter of mri_synthmorph using -s option in Freesurfer 7.4.1 but this option does not seem implemented. Is there a way to reduce the amount of regularisation? Thanks for your help, Simon **************************************************************** Mr P Simon Jones Research Associate Department of Clinical Neurosciences University of Cambridge Herchel Smith Building, Forvie Site Robinson Way Cambridge Biomedical Campus Cambridge CB2 0SZ UK ****************************************************************

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Issue with Talairach_avi Command in FreeSurfer
by parisa sehati 22 Oct '24

22 Oct '24

External Email - Use Caution Dear FreeSurfer Support Team, I hope this message finds you well. I am encountering an issue while trying to run the talairach_avi command in FreeSurfer for data reconstruction. I receive the following error message: ERROR: mpr2mni305 failed, see transforms/talairach_avi.logCommand exited with non-zero status 1 The relevant log file is located at transforms/talairach_avi.log, but I cannot access the orig_nu.mgz file or the transforms/talairach.auto.xfm file in the expected directories. My system details are as follows: Linux ps 5.15.0-1026-intel-iotg #31-Ubuntu SMP Thu Feb 16 23:20:09 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Additionally, I executed the command: recon-all -s sub-33 and it exited with errors. Could you please assist me in resolving this issue? Thank you for your help! Best regards, Parisa Sehati

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Re: [Freesurfer] Development version M1 mac error
by fsbuild 21 Oct '24

21 Oct '24

External Email - Use Caution  Mac OS 11.X is no longer supported by Apple and so likewise, we no loner build/support freesurfer on BigSur for silicon (M1, M2, ...) Macs.  The message you listed below means that a minimum you need to upgrade you machine to Mac OS 12.X (Monterey), MacOS 13.X (Ventura) or MacOS 14.X (Sonoma).   We have not tested as much on macOS 15.X (Sequoia) which came out recently, so we do not suggest upgrading to that most recent 15.X version. - R.On Oct 21, 2024, at 15:01, Jasmine Cakmak <jasmine.cakmak(a)mail.mcgill.ca> wrote:        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 Abortfs-check-version --s sub001 --oERROR: 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 _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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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