Re: [Freesurfer] Error in running make_average_subject

: Sunday, September 15, 2019 at 12:25 PM To: FS Help Subject: [Freesurfer] Error in running make_average_subject External Email - Use Caution Hello Freesurfer Developers I am trying to create an average subject for 20 subjects using the function make_average_subject. But I keep running

[Freesurfer] Error in running make_average_subject

External Email - Use Caution Hello Freesurfer Developers I am trying to create an average subject for 20 subjects using the function make_average_subject. But I keep running into a segmentation fault. I have attached the recon-all.log file. I found a few other posts about the

[Freesurfer] Error in running make_average_subject

External Email - Use Caution Hello Freesurfer Developers I am trying to create an average subject for 20 subjects using the function make_average_subject. But I keep running into a segmentation fault. I have attached the recon-all.log file. I found a few other posts about the

Re: [Freesurfer] Error in running make_average_subject

External Email - Use Caution Hello Bruce, Doug and Emanuel, I tried what you suggested (ln -s orig.mgz norm.mgz), and I also downloaded the development version and tried that, but neither procedures fixed the problem. In the meantime, my father-in-law took a week and fixed the

Re: [Freesurfer] Error in running make_average_subject

This has been fixed in our development version. I can give you a new script or you can try this: cd $SUBJECTS_DIR/*avgsubjectPRUEBAESTASI! ln -s orig.mgz norm.mgz Then re-run make_average_subject * On 12/14/18 1:43 PM, Emanuel Alvaredo wrote: > > External Email - Use Caution > >

Re: [Freesurfer] Error in running make_average_subject

External Email - Use Caution Hello Bruce, Greve and Emanuel, I have an identical problem. Have you found a solution to this issue? I'm attaching my recon-all.log, as well, in case you need it. Thank you! Marta On Fri, Dec 14, 2018 at 1:44 PM Emanuel Alvaredo wrote: >

Re: [Freesurfer] Error in running make_average_subject

can you include the full terminal output? On 12/13/18 7:45 AM, Emanuel Alvaredo wrote: External Email - Use Caution Hello Bruce, thanks for your anwer. Sure. The command is make_average_subject --out avgsubjectPRUEBAESTASI! --subjects Bartley_Recon Baez_Recon Bonilla_Recon The

Re: [Freesurfer] Error in running make_average_subject

External Email - Use Caution Hello Bruce, thanks for your anwer. Sure. The command is *make_average_subject --out avgsubjectPRUEBAESTASI! --subjects Bartley_Recon Baez_Recon Bonilla_Recon* The output is in the attached file Thanks! Emanuel On Wed, Dec 12, 2018 at 7:05 PM

Re: [Freesurfer] Error in running make_average_subject

Hi Emanuel, can you include the full command line and output? cheers Bruce On Wed, 12 Dec 2018, Emanuel Alvaredo wrote: External Email - Use Caution Thanks for your answer Douglas. I replaced the make_average_surface  file with the new one but  I have the same message

Re: [Freesurfer] Error in running make_average_subject

External Email - Use Caution Thanks for your answer Douglas. I replaced the make_average_surface file with the new one but I have the same message error. ASeg Vox2RAS: --- -1.0 0.0 0.0 128.0; 0.0 0.0 1.0 -128.0; 0.0

Re: [Freesurfer] Error in running make_average_subject

Sorry, the disk that held that patch failed and we did not have a backup so not everything was restored. I just put this file there: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface Copy it to $FREESURFER_HOME/bin. Let me know how it goes On 12/10/18

Re: [Freesurfer] Error in running make_average_subject

External Email - Use Caution Thanks Bruce. The following is the command. make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects subject1 subject2 subject3 And I made a mistake in may last mail. I use the word path instead of patch I have found this page with a

Re: [Freesurfer] Error in running make_average_subject

Hi Emanuel you need to send us the full command you ran and output of it if you want us to be able to help you cheers Bruce On Fri, 7 Dec 2018, Emanuel Alvaredo wrote: External Email - Use Caution Hello!, I am getting the following error using the command 

[Freesurfer] Error in running make_average_subject

External Email - Use Caution Hello!, I am getting the following error using the command make_average_subject mri/norm.mgz: could not load norm volume from (null) I have found this page with a path for de issue

Re: [Freesurfer] Error in running make_average_subject

Thanks, Andrew! On Tue, Feb 20, 2018 at 11:42 AM, Hoopes, Andrew wrote: > Hi Scott, > > It looks like the mri_aparc2aseg binary in that patch directory was > compiled for centos. The version at the following link was compiled on OS > X:

Re: [Freesurfer] Error in running make_average_subject

Hi Scott, It looks like the mri_aparc2aseg binary in that patch directory was compiled for centos. The version at the following link was compiled on OS X: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/OSX-ElCapitan/mri_aparc2aseg If you download this new mri_aparc2aseg

Re: [Freesurfer] Error in running make_average_subject

Thanks andrew... I will try this From: Hoopes, Andrew <ahoo...@mgh.harvard.edu> Sent: Tuesday, February 20, 2018 8:55:47 PM To: M Janani; Freesurfer support list Cc: Sasikala Sethu Subject: Re: [Freesurfer] Error in running make_average_subject Hi Janani, W

Re: [Freesurfer] Error in running make_average_subject

Hey Andrew, I am running FreeSurfer 6.0 on MacOS X and ran into the exact same issue as Janani, so I installed this patch. However, now I am getting the following error: #@# AParc-to-ASeg aparc Tue Feb 20 11:04:08 EST 2018 /Users/scottpruett/Desktop/CSMRI/Freesurfer/601_10y_av \n

Re: [Freesurfer] Error in running make_average_subject

Hi Janani, We have a patch for this bug here: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ The second part of the readme file in that directory provides instructions for resolving this. best Andrew On February 19, 2018 at 9:40:22 AM, M Janani

[Freesurfer] Error in running make_average_subject

Dear FreeSurfer Experts, I’m recently getting an error in make_average_subject and can’t find the reason. Please see the following for the error log from recon-all.log: mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz