Re: [Freesurfer] transform amygdala mask from FS to native space

External Email - Use Caution Ahh, great! Thanks so much! From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. Sent: 16 August 2022 08:58 To: Freesurfer support list Subject: Re: [Freesurfer] transform amygdala

Re: [Freesurfer] transform amygdala mask from FS to native space

It sets the output type to float and avoids rescaling of the intensities ;-) Juan Eugenio Iglesias http://www.jeiglesias.com On Aug 15, 2022, at 18:45, Elizabeth Haris mailto:e.ha...@unsw.edu.au>> wrote: External Email - Use Caution That worked - thank you! If it's not too difficult,

Re: [Freesurfer] transform amygdala mask from FS to native space

External Email - Use Caution That worked - thank you! If it's not too difficult, could you please tell me what that command does? (I had a quick google but couldn't find anything). Thanks again! Elizabeth From:

Re: [Freesurfer] transform amygdala mask from FS to native space

Uuumm can you please try adding “-odt float” to the command? Juan Eugenio Iglesias http://www.jeiglesias.com On Aug 15, 2022, at 18:23, Elizabeth Haris mailto:e.ha...@unsw.edu.au>> wrote: External Email - Use Caution Hi Eugenio, Yes, I did. This gives me a binary mask, which is why

Re: [Freesurfer] transform amygdala mask from FS to native space

External Email - Use Caution Hi Eugenio, Yes, I did. This gives me a binary mask, which is why I was confused and at a loss as to what else I could to do. Any suggestions? Thanks, Elizabeth From: on behalf of "Iglesias Gonzalez, Juan E." Reply to: Freesurfer support list

Re: [Freesurfer] Freeview quits unexpectedly on macOS Big Sur

External Email - Use Caution Hello Sara, You could try running bash shell and putting a copy of your license file as license.txt in your home directory and then set the environment variable FS_LICENSE to point to it, e.g. $ bash$ cd $HOME… copy in your license file here as

Re: [Freesurfer] Freeview quits unexpectedly on macOS Big Sur

Sara, do you have a double screen by any chance ? Reuben A. Get Outlook for iOS From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Sara Sanchez-Alonso Sent: Monday, August 15, 2022 5:07:01 PM To: freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Freeview quits unexpectedly on macOS Big Sur

External Email - Use Caution Hello, I have installed Freesurfer 7.3.2 on macOS Big Sur, Version 11.6.8. The installation was successful, but every time I need to open freeview, it quits unexpectedly. The environment seems to be set up correctly and I have also downloaded my

Re: [Freesurfer] Tracula - Preproc

External Email - Use Caution Hi King Wai - Thanks for your help. I downloaded version 2.1.0 as you suggested and installed it. But the error message keeps coming back. It is looking for this file: /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh But this file is not

Re: [Freesurfer] [External] Re: Tracula - Preproc

External Email - Use Caution Hi all, ANTSPATH needs to end with a trailing slash to use many ANTs utilities. So you'd do (for bash) export ANTSPATH=/home/afrancis/Imaging/ANTs/ export PATH=${ANTSPATH}:$PATH then try antsRegistrationSyNQuick.sh You can check version

Re: [Freesurfer] Tracula - Preproc

External Email - Use Caution Hi Alan, First find out the version of ANTs you have by running the command below antsRegistration --version If it is below 2.1.0 download the 2.1.0 binaries here, it works for me.

Re: [Freesurfer] Tracula - Preproc

External Email - Use Caution Hi King Wai - I used a script (enclosed) to install ANTs. Is there anyway this script could be modified to install the latest version? Thank you so much, Alan On Mon, Aug 15, 2022 at 11:40 AM King-Wai Chu wrote: > External Email - Use

Re: [Freesurfer] Tracula - Preproc

External Email - Use Caution Hi Alan, Do you have the latest version of ANTs? It should be 2.1.0 Older version don't have all the binaries and scripts required by trac-all. Best, King-Wai On Mon, Aug 15, 2022 at 11:49 AM Alan Francis wrote: > External Email - Use

[Freesurfer] segment_subregions failed

External Email - Use Caution Hi Freesurfer experts, I have been trying to segment thalamus using segment_subregions command available in freesurfer 7.3.2. Unfortunately, I have been encountering the following error. IN-NSCC-050385:~ mdalamin$ segment_subregions thalamus --cross

Re: [Freesurfer] Tracula - Preproc

External Email - Use Caution Hello King Wai - I used the C shell pathway just as you specified. But I got this error message right at the end of the processing: #@# Inter-subject registration Mon Aug 15 10:32:25 CDT 2022 /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh -d

Re: [Freesurfer] Tracula - Preproc

External Email - Use Caution Thank you so much King Wai, On Fri, Aug 12, 2022 at 5:12 PM King-Wai Chu wrote: > External Email - Use Caution > > For bash shell > ANTSPATH=/home/afrancis/Imaging/ANTs > > For tcsh > setenv ANTSPATH /home/afrancis/Imaging/ANTs > > On Fri,

Re: [Freesurfer] transform amygdala mask from FS to native space

Dear Elizabeth, You command looks good to me. Did you visualize lh_Amyg_native.mgz with colormap=lookup table? Cheers, /Eugenio Juan Eugenio Iglesias http://www.jeiglesias.com On Aug 14, 2022, at 18:58, Elizabeth Haris mailto:e.ha...@unsw.edu.au>> wrote: External Email - Use Caution

[Freesurfer] mri_fill error : *** Error in `mri_fill': double free or corruption (!prev): 0x00000000014aab70 ***

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to generate filled.mgz using the mri_fill -a */ponscc.cut.log -xform */talairach.lta -segementation aseg.auto_noCCseg.mgz wm.mgz filled.mgz Error : *** Error in `mri_fill': double free or corruption