Freesurfer October 2024

freesurfer@nmr.mgh.harvard.edu

44 participants
51 discussions

Re: [Freesurfer] infantFS: expected outputs
by Zoellner, Frank 24 Oct '24

24 Oct '24

External Email - Use Caution Hi Lilla, and is there a reason why ? I mean are these regions (labels) not detectable in the infants or did you just not include them ? Since the adult freesurfer pipeline could segment them I am wondering why they are not labeled in the infant atlas… Yours Frank ---------------- adj. Prof. Dr. Frank Zoellner Acting head Computer Assisted Clinical Medicine Mannheim Institute for Intelligent Systems in Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim Phone: +49 (0)621 3835117 Fax: +49 (0)621 3835123 Email: Frank.Zoellner(a)MedMa.Uni-Heidelberg.de<mailto:Frank.Zoellner@MedMa.Uni-Heidelberg.de> Web: https://secure-web.cisco.com/1RqQnv7kxvO9_w5Srsw77gD-ZtwN2XNsKEWYAXYh8x70-3… Von: <freesurfer-bounces(a)nmr.mgh.harvard.edu> im Auftrag von "Zollei, Lilla,Ph.D." <LZOLLEI(a)MGH.HARVARD.EDU> Antworten an: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Datum: Donnerstag, 24. Oktober 2024 um 03:59 An: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] infantFS: expected outputs Dear Frank, You are correct. The list of segmentation labels is not 100% the same. For the infantFS segmentation labels you can refer to Table 1 in https://secure-web.cisco.com/1vWMGdCD3mZXs2SmPbxmXci6igleKzDLTd49jV-LXb9Ovp… Best, Lilla ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Zoellner, Frank <Frank.Zoellner(a)medma.uni-heidelberg.de> Sent: Monday, September 23, 2024 4:31 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] infantFS: expected outputs External Email - Use Caution Dear Lilla, Besides the differences in the files, when looking at the segmentations we wondered why there are some labels zero in the aseg stats file. These are : Left-Inf-Lat-Vent CSF Right-Inf-Lat-Vent Brain-Stem Left-vessel Left-choroid-plexus Right-vessel Right-choroid-plexus 5th ventrikel WM-hypointensities We also did a cross check and had run the same subject with the normal freesurfer pipeline and here there have been segmentations for the above structures. Maybe you have an idea what is happening here ? or are these not included in the atlas? Thanks in advance Yours Frank ----------- adjunct Prof. Dr. Frank Zoellner Acting head Computer Assisted Clinical Medicine Mannheim Institute for Intelligent System in Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim Phone: +49 (0)621 3835121 Fax: +49 (0)621 3835123 Email: Frank.Zoellner(a)MedMa.Uni-Heidelberg.de<mailto:Frank.Zoellner@MedMa.Uni-Heidelberg.de> Web: https://secure-web.cisco.com/1RqQnv7kxvO9_w5Srsw77gD-ZtwN2XNsKEWYAXYh8x70-3… Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> Im Auftrag von Zollei, Lilla,Ph.D. Gesendet: Sonntag, 22. September 2024 16:12 An: freesurfer(a)nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] infantFS: expected outputs Hi Marlene, This is correct. Even though infant_recon_all is trying to mimic the output folder structure and follows the FreeSrufer naming convention, it does not generate all of the files that the adult version does. Lilla ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Marlene Staginnus <ms2290(a)bath.ac.uk<mailto:ms2290@bath.ac.uk>> Sent: Monday, September 16, 2024 9:57 AM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] infantFS: expected outputs External Email - Use Caution Dear FreeSurfer Team, Apologies in case I missed this elsewhere, but I was wondering whether there is any information on what the expected outputs of running infant_ recon_all are, similar to this (https://secure-web.cisco.com/1mA29bmjZg8MZLmt_5OWSzYbAcnPRT4qfP6KTFLCwUY69A…) for the adult pipeline? I am asking as after testing the pipeline using the example participant provided on openneuro (https://secure-web.cisco.com/1eG9UEoGKfhMXUoWW953Ozv01X5SscPRanNwg37dq-iV0q…, I’ve noticed that some of the output differs from the adult version and I wanted to ensure that everything is running correctly before applying it to our data. For example, there is no ‘orig’ subdirectory or orig.mgz file in the ~/mri folder. Similarly, fewer files are included in the ~/stats folder (only: brainvol.stats, lh.aparc.stats, rh.aparc.stats) although I was able to able to generate other files (e.g., aseg.stats) using mri_segstats. Overall, only the following folders are generated following recon-all without errors: label, log, mri, stats, and surf. Is this correct or might there be something going wrong on my end? 1) FreeSurfer version: infant-dev-4a14499-20210109-4a14499 2) Platform: CentOS release 7 3) uname -a: Linux fhpc-1840 6.8.0-40-generic #40~22.04.3-Ubuntu SMP PREEMPT_DYNAMIC Tue Jul 30 17:30:19 UTC 2 x86_64 x86_64 x86_64 GNU/Linux 4) infant_recon_all log: see attached Thank you in advance! Best wishes, Marlene

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infantFS: expected outputs
by Marlene Staginnus 23 Oct '24

23 Oct '24

External Email - Use Caution Dear FreeSurfer Team, Apologies in case I missed this elsewhere, but I was wondering whether there is any information on what the expected outputs of running infant_ recon_all are, similar to this (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles) for the adult pipeline? I am asking as after testing the pipeline using the example participant provided on openneuro (https://openneuro.org/datasets/ds004776/versions/1.0.0, I’ve noticed that some of the output differs from the adult version and I wanted to ensure that everything is running correctly before applying it to our data. For example, there is no ‘orig’ subdirectory or orig.mgz file in the ~/mri folder. Similarly, fewer files are included in the ~/stats folder (only: brainvol.stats, lh.aparc.stats, rh.aparc.stats) although I was able to able to generate other files (e.g., aseg.stats) using mri_segstats. Overall, only the following folders are generated following recon-all without errors: label, log, mri, stats, and surf. Is this correct or might there be something going wrong on my end? 1) FreeSurfer version: infant-dev-4a14499-20210109-4a14499 2) Platform: CentOS release 7 3) uname -a: Linux fhpc-1840 6.8.0-40-generic #40~22.04.3-Ubuntu SMP PREEMPT_DYNAMIC Tue Jul 30 17:30:19 UTC 2 x86_64 x86_64 x86_64 GNU/Linux 4) infant_recon_all log: see attached Thank you in advance! Best wishes, Marlene

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Extracting generic gradient vector
by Ashwati Vipin (Dr) 23 Oct '24

23 Oct '24

External Email - Use Caution Dear Freesurfer developers, I am trying to replicate a multi shell DTI protocol from one scanner to another. However I need the generic gradient vectors so that the protocol can be replicated. Is there a script in freesurfer that can reverse engineer the relative direction coordinates and normalisation of vector strengths so that this file can be used in the scanner console to define all the parameters of this sequence and replicate it across different scanners? Please help!! Thank you so much!! Best, Ashwati -- Ashwati Vipin (PhD) Research Fellow, Dementia Research Centre (Singapore) Clinical Sciences Building 11 Mandalay Road, Singapore 308232 T: +65 6592 3963 E: ashwati.vipin(a)ntu.edu.sg<mailto:ashwati.vipin@ntu.edu.sg> W: https://secure-web.cisco.com/1UxqE_XW7QCy7OrGxdUFafNIAzhq2UJBPlV7TRZ1Pg2bya… [A close-up of a logo Description automatically generated] ________________________________ CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. Towards a sustainable earth: Print only when necessary. Thank you.

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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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Freesurfer October 2024