[Freesurfer] MeanItensities- PET

External Email - Use Caution Hi, I wonder if someone can help me to do something similar to that: " the mean intensity of each FreeSurfer region (ROI) for the 45 subcortical and the 68 cortical regions were assessed the mean intensity of each FreeSurfer region (ROI) for the 45 su

Re: [Freesurfer] using brain mask from older FreeSurfer version on a newer

External Email - Use Caution Actually, I didn't try this idea and also I don't know what's the difference between brain mask from previous versions. Le mar. 14 juin 2022 à 22:39, Aaron Tanenbaum a écrit : > External Email - Use Caution > > Great. glad I was of some help.

Re: [Freesurfer] I cannot start my first subject.

Hi Refaat, This tutorial talks about unpacking dicom files and basic recon-all options. It should help you get started - https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of refaat el-said Sent: Tuesday, June 14

Re: [Freesurfer] Ubuntu VM Error - /dev/sda1 contains a file system with errors

External Email - Use Caution Hi R, (I tried to reply in the other email thread with fsbu...@contbay.com but it said delivery failure with that email so I am responding here). Thank you very much for your response. I was able to get through the first 2 recovery steps but on step

[Freesurfer] Problem with longitudinal processing

External Email - Use Caution Dear community, I tried to process MS- patient's MRIs (mostly same scanner, same settings) Longitudinally over a long period of time. I first processed all timeponits crosssectionally and then initialised the base image by recon- all - base TP1 TP2

Re: [Freesurfer] Ubuntu VM Error - /dev/sda1 contains a file system with errors

External Email - Use Caution If you have not run fsck with the -y option from the intramfs prompt, you could try the instructions in this post - which shows the error (on a different version of Ubuntu),  https://secure-web.cisco.com/1G_OxjZo0eZ-YJ0rw8-xiLxDsmlEKgBMgmEnSsywbnbejdo

Re: [Freesurfer] FreeSurfer Passcode - Apologies!

External Email - Use Caution Hello Rachel, You should have just received the info for the Freesurfer Ubuntu VM. Replies to these requests are now being sent directly to the email of the requestor and are no longer copied to the Freesurfer list so as not to generate extra  list.

[Freesurfer] SPM to FreeSurfer

External Email - Use Caution Hello, I am trying to take my SPM images and cortically project them with free surfer (SpmPainting - Free Surfer Wiki (harvard.edu)

Re: [Freesurfer] SPM to FreeSurfer

External Email - Use Caution Apologies for repeat email – I’m getting the following error message, is there something I should add? developer@developer-VirtualBox:~$ mri_convert i.mgz i.img mri_convert i.mgz i.img reading from i.mgz... error: mghRead(/home/developer/i.mgz, -1): c

Re: [Freesurfer] SPM to FreeSurfer

External Email - Use Caution Hello Rachel, SUBJECTS_DIR is preset in the terminal window to point to the example subjects already provided with the freesurfer distribution under /usr/local/freesurfer/7.2.0/subjects.  You will see subject names under that directory like “bert”.  

[Freesurfer] Nii to Img file

External Email - Use Caution Hello, Thank you for your assistance! I am trying to convert an nii nifti file to an img file within free surfer. I’ve used the mri convert function and did create the img file, but I’m getting an error message in SPM when I try to co-register it to

[Freesurfer] FSL Password

External Email - Use Caution Hello, I am downloading FSL into ubuntu freesurfer VM, and have gotten the following prompt: developer@developer-VirtualBox:~/Downloads$ python3 fslinstaller.py --- FSL Installer - Version 3.2.3 --- [Warning] Some operations of the installer require

Re: [Freesurfer] FSL Password

External Email - Use Caution Try, $ sudo  python3  fslinstaller.py … then enter password for developer.  The sudo command will use admin privileges which may allow install to occur. - R. On Jun 15, 2022, at 20:54, Rachel Wagner wrote:External Email - Use

Re: [Freesurfer] FSL Password

External Email - Use Caution Thank you very much for the help! Upon trying that, I get this: developer@developer-VirtualBox:~$ cd ~/Downloads developer@developer-VirtualBox:~/Downloads$ $ sudo python3 fslinstaller.py $: command not found developer@developer-VirtualBox:~/Download

[Freesurfer] Freesurfer Password

External Email - Use Caution Hello! I need the password to expand the archive for Freesurfer 7.2.0 release in Ubuntu 18.04.06. Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/li

Re: [Freesurfer] Ubuntu VM Error - /dev/sda1 contains a file system with errors

External Email - Use Caution Hi R, The instructions in that link fixed the problem! Thank you very much for your help. I'll be backing up my files right away and will continue to do that. All my best, Joanna -- Joanna Eckhardt Neurosciences Graduate Program University of Cal