Freesurfer March 2017

freesurfer@nmr.mgh.harvard.edu

148 participants
263 discussions

Report indicating aseg edits
by Tamara Tavares 13 Mar '17

13 Mar '17

Hello, I am currently checking and editing the aseg outputs in my longitudinal data. I was wondering whether Freesurfer offers a report indicating the edits I have made to aseg output. Thank you, Tamara

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Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding
by Daniela 13 Mar '17

13 Mar '17

I second the problem found in this thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51917.html I recently downloaded FreeSurfer v. 6 on a macOS 10.12. To work around the System Integrity Protection issue, I installed my freesurfer folder in a local "Documents" folder instead of in Applications and that seemed to allow me to keep System Integrity Protection enabled while running FreeSurfer commands. Last night I ran recon-all on the same subject simultaneously, one using the -parallel tag and the other without it. This morning I see that only the one with the -parallel tag exited with errors and it seems to be this same "lazy symbol" error (see attached for recon-all error log). dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Users/Ajay/Documents/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib I can try running with System Integrity Protection off to see if that will make the -parallel tag work... any other thoughts? Thanks, Daniela

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How to cite freeview
by Luigi Antelmi 13 Mar '17

13 Mar '17

Hello, what is the correct way to cite freeview in a papar for a manual rois segmentation task? Thanks, Luigi.

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WM/pial edits
by Octavian Lie 13 Mar '17

13 Mar '17

Dear All, A simple issue of precedence. In the recon-all pipeline, wm edits take precedence to pial edits. If there are both wm and pial defects, should one apply edits sequentially, say on brainmask.mgz (first wm edits, rerun recon-all say recon-all -autorecon2 -wm, then do pial edits, rerun recon-all say recon-all -autorecon2 -pial) or to some extent pial edits influence the final surface generation in conjunction to wm edits (understood that the latter may influence more the final form than the former -pial- edits), in that case one may do both edits, then run -autorecon2 -wm only. Please advise, Octavian

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Error recon-all program quits at mri_nu_correct
by David WALTER 13 Mar '17

13 Mar '17

Hello FreeSurfer Developers, Im trying with an engineer to launch a recon-all command but it seems to fail and I dont find any verbose logs to help me to understand what is the problem. Please find in attachment all the logs I have and we are on CentOS 6.8 Thanks for your help ------------------------------ David WALTER The computer guy david.walter(a)ens.fr <mailto:david.walter@ens.fr> 01/44/32/27/94 INSERM U960 Laboratoire de Neurosciences Cognitives Ecole Normale Supérieure 29, rue d'Ulm 75005 Paris

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Re: [Freesurfer] Freesurfer Digest, Vol 157, Issue 35
by IPL Neurosurgery 13 Mar '17

13 Mar '17

Hi, Command: sudo chmod -R 777 freesurfer I really thank you for the response.I tried the above command and its asking for sudo password. How can I able to know my sudo password. Thanking you, IPL Neurosurgery Sent from Outlook<http://aka.ms/weboutlook> ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: 11 March 2017 22:30:01 To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 157, Issue 35 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Repost: tracula stats including NAs? (Jacobs H (NP)) 2. Re: Error viewing corrected results (Antonin Skoch) 3. MRI intensity normalize (shi yao wang) 4. Re: Error mri_surf2surf FS6 (Juergen Haenggi) 5. Error while attempting Segmentation (IPL Neurosurgery) 6. Re: Error while attempting Segmentation (Juergen Haenggi) 7. How to check if FS are processing correctly. (shi yao wang) 8. Re: Intensity normalization in longitudinal processing (Bruce Fischl) 9. Re: MRI intensity normalize (Bruce Fischl) 10. -dura_thresh (Octavian Lie) ---------------------------------------------------------------------- Message: 1 Date: Fri, 10 Mar 2017 22:39:49 +0000 From: "Jacobs H (NP)" <h.jacobs(a)maastrichtuniversity.nl> Subject: [Freesurfer] Repost: tracula stats including NAs? To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <D4E8E959.31257%h.jacobs(a)maastrichtuniversity.nl> Content-Type: text/plain; charset="us-ascii" Hi FreeSurfer, I have analyzed my diffusion data using Tracula and combined the voxelwise diffusion measures across all subjects in one file (following the guidelines on the wiki). In this text file, I saw that for some of these voxels some people have NAs, so their tract is most likely shorter. I now would like to do t-tests for each voxel and plot these in freeview (as also suggested in the wiki). Would you recommend to only take those voxels that have a value in each subject to keep the number of subjects consistent at each voxel ? Look forward to your thoughts on this. Best wishes Heidi

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WM edits
by Manuel Delgado 13 Mar '17

13 Mar '17

Dear Freesurfer list, I am using Freesurfer 6.0 in Ubuntu 16.04. In the troubleshooting I have encountered a frequent problem with many of my subjects. I enclose an example. Is it necessary to edit the areas that have not been included in the wm mask? Namely, that tiny area close to the temporal horn of the left lateral ventricle (Image_1)? As you can see in the other image (Image_2) this might be affecting the pial surface that seems to include parts of wm in the vicinity of the temporal horn. How would you deal with this? Best wishes, Manuel

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Faulty alignment to standard surface
by Daan Wesselink 12 Mar '17

12 Mar '17

Dear experts, I've run the standard recon-all pipeline on a subject, for whom the log does not report any errors and the white and pial surface follow the structural nicely. However, the coregistration to the standard surface has gone wrong: it seems like the central sulcus (e.g. labels BA1, BA3a) is placed on top of the postcentral sulcus. Does someone know how to fix this problem and/or better identify the step where it went wrong? Many thanks, Daan Wesselink

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Kind Request - Unexpected Crashing of the Program
by Abhinav Kurada 12 Mar '17

12 Mar '17

I am attempting to Load a Volume into free surfer to perform WM/GM segmentation. Every time I attempt to upload a volume (even including the bert sample volumes provided with the installation), Freesurfer quickly crashes and exits. I have attached a screenshot of the crashing prompt. Do you have any suggestions on how to fix this? Thank you in advance, Abhinav Kurada https://share.polymail.io/v1/z/f/NThjMmQzNTk3OWY4/qWSFPkGW8mSq3STKSS8ylMpRj… Shot 2017-03-10 at 11.30.02 AM.png https://share.polymail.io/v1/z/f/NThjMmQzNTk3OWY4/qWSFPkGW8mSq3STKSS8ylMpRj… Shot 2017-03-10 at 11.30.02 AM.png

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How to check if FS are processing correctly.
by shi yao wang 12 Mar '17

12 Mar '17

Dear FS experts: I am using FS to analyze our MRI data. When I finished recon -all, there are following informaion: Started at Fri Mar 10 11:26:05 EST 2017 Ended at Fri Mar 10 18:26:51 EST 2017 #@#%# recon-all-run-time-hours 7.013 recon-all -s 10001 finished without error at Fri Mar 10 18:26:51 EST 2017 Does that mean every steps is correct? (although there were some error message when I checking recon -all. log file). thanks Lawrence

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Freesurfer March 2017