Re: [Freesurfer] ma_ca_register is not called anymore in version 7.3.2

External Email - Use Caution sorry listed wrong command line - after autrecon1 I run the following command /usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 -autorecon2 -autorecon3

[Freesurfer] 7.3.2-patch issues - thalamic segmentation

External Email - Use Caution Hi FS experts, I am attempting to implement the patch on version 7.3.2 for issues with thalamic segmentation. I followed the instructions found here:

Re: [Freesurfer] Regarding MRI Understanding.

Andy's brain book and neurostars are other great resources https://andysbrainbook.readthedocs.io/en/latest/index.html https://neurostars.org/ -Paul From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of FELICITY SIMPSON Sent: Tuesday, December 6, 2022

Re: [Freesurfer] Request for Assistance

Hi Eric, Here are some online Freesurfer tutorials TeachYourselfFreeSurfer - Free Surfer Wiki (harvard.edu) Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of MANSON ERIC NAAB Sent: Friday, December 2,

[Freesurfer] Converting Volumes from Old Format to Current FreeSurfer Format

Hello, I have several flash volumes that I am able to open using stable5 but not with the current version of freesurfer. Is there a way to convert these volumes into the current freesurfer format? Best, Nathan ___ Freesurfer mailing list

Re: [Freesurfer] ma_ca_register is not called anymore in version 7.3.2

Hi Kilian, I'm wondering what were your initial recon-all commands for FS 5.3 and FS 7.1.1 because I'm not sure '-autorecon1' is making mri_ca_register call by default. But It looks like you can use '-careg' to turn on mri_ca_register call. Here is a description of recon-all steps:

Re: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error

External Email - Use Caution Hi Yujing,  No problem at all.  I really appreciate yours, and now Martin's, help with this issue.  If you would like to start with dicoms, please let me know. Again, thank you both for your help. Andrew *Andrew Beaudin, PhD* | Research

[Freesurfer] missing values, aseg

External Email - Use Caution Dear FreeSurfer Team, I am writing because I was extracting the aseg values using Freesurfer 7.1.1 and much to my surprise, these values were 'empty', or zero: 5th-Ventricle WM-hypointensities Left-WM-hypointensities Right-WM-hypointensities

Re: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error

Hi Andrew, Sorry for the late response. I’m able to reproduce your error. I have included Martin to the communication. He is the author of the program. He is going to take a look at your data. Best, Yujing From: Andrew Beaudin Sent: Friday, November 25, 2022 3:25 PM To: Huang, Yujing ;

Re: [Freesurfer] Fusion of PET and T1 weighted

External Email - Use Caution Dear Sir, I have got the .dat files from the mri_segstats command.How to convert the those multiple dat files into one excel or csv file. regards Amar Shukla On Mon, 17 Oct 2022 at 2:56 AM, Douglas N. Greve wrote: > yes, but how are you combining

[Freesurfer] password request for file FS_7_2_0_Ubuntu_18_04_06.ova.7z

External Email - Use Caution Hello FreeSurfer, I downloaded VM from the official website: FS_7_2_0_ubuntu_18_04_06.ova.7z but I need the password to successfully open the compressed package. I hope that is the right place for this request. Thank you for your time.