Re: [Freesurfer] trac-all -prep -c ERROR

Subject: Re: [Freesurfer] trac-all -prep -c ERROR External Email - Use Caution Hi back, Should be alright now. Please try this link: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://drive.google.com/dri

Re: [Freesurfer] trac-all -prep -c ERROR

External Email - Use Caution Hi back, Should be alright now. Please try this link: https://secure-web.cisco.com/1LYPTJn0s7YjdWTtPFS55k3z-IqjPfKIscsxsCg4qgjYm5i7hgZ47NYZ8BRHgQAtw4DZhP0bO52JhFFLI8LcEH2uXcDPnyyn6mXbi2PEZLkzub2KbFSDNMpQcj-DHyeMAdbjU8od-fcAnsd58VKB5nnYprNNUzbu4SeyZphu

Re: [Freesurfer] trac-all -prep -c ERROR

Hi Ela - Can you make the google doc accessible by all? Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh Sent: Thursday, June 30, 2022 5:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] trac-all -prep -c ERROR

Re: [Freesurfer] trac-all -prep -c ERROR

External Email - Use Caution Thank you for the reply. For some reason, when I change the DCM file to nii and look at them, in majority of our subjects, the cerebellum and lower brain stem has been cut off, but in this specific subject, I don't think the CST is truncated or out o

Re: [Freesurfer] trac-all -prep -c ERROR

Any chance that part of the left CST is truncated in this one subject? E.g., if the top part of the brain was outside the field of view? Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh Sent: Wednesday, June 29, 2022 11:3

Re: [Freesurfer] Trac-all -prep -c error

Hi Elizabeth - This was a tricky one. My guess is that there's an error in what comes right after the mri_binarize command, but the error doesn't get written into the log file and is only shown on your terminal (I'm going to fix the error logging aspect of this). If my guess is right, the error

Re: [Freesurfer] Trac-all -prep -c error

). Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh Sent: Monday, January 10, 2022 4:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] Trac-all -prep -c error External Email - Use Caution Thank you for

Re: [Freesurfer] Trac-all -prep -c error

External Email - Use Caution Thank you for constantly improving TRACULA. I believe we don't have reverse polarity scan or a field-map. We might be able to acquire the field-map though since the MRI has been acquired locally. Having that in mind, and just for clarification and m

Re: [Freesurfer] Trac-all -prep -c error

u and your instructor for bringing this to our attention! Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh Sent: Sunday, January 9, 2022 8:26 PM To: Freesurfer support list Subject: Re: [Freesurfer] Trac-all -prep -c

Re: [Freesurfer] Trac-all -prep -c error

External Email - Use Caution Dear Anastasia, I just wanted to share with you that after following up with our instructor, asking him why he recommended FLIRT rather than bbregister, he clarified that 4-5 years ago when he was using TRACULA for his project, registration using bbr

Re: [Freesurfer] Trac-all -prep -c error

rom: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh Sent: Tuesday, January 4, 2022 3:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] Trac-all -prep -c error External Email - Use Caution Dear Anastasia, Honestly, this was just based on our instructor'

Re: [Freesurfer] Trac-all -prep -c error

Hi Ela - Is there a specific reason why you are not using the default method for dMRI-to-T1 registration (bbregister, a.k.a. boundary-based registration in the config file)? Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh

Re: [Freesurfer] Trac-all -Prep -C Error

External Email - Use Caution Hello Elizabeth, To use the latest development build you can set freesurfer home to, /autofs/vast/freesurfer/centos7_x86_64/dev  or /usr/local/freesurfer/dev - R. On Dec 31, 2021, at 16:11, Kaplan, Elizabeth wrote:   

Re: [Freesurfer] Trac-all -Prep -C Error

External Email - Use Caution Thanks for your prompt response, Anastasia. How do I switch to the dev version? Would I set my FREESURFER_HOME variable to a different pathway? The one I currently use is /autofs/vast/freesurfer/centos7_x86_64/7.2.0 Thank you, again! Happy New Year!

Re: [Freesurfer] Trac-all -Prep -C Error

Hi Elizabeth - If you're using launchpad, just switch to the dev version. It has the latest bug fixes. Happy new year! Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Kaplan, Elizabeth Sent: Friday, December 31, 2021 1:56 PM To: freesurfer

Re: [Freesurfer] trac-all -prep -c error

Hi Ela - The example config file that you used is from the old version, not the new version. That's why the old version doesn't give you an error and the new one does. Take the example config file from the new version (in $FREESURFER_HOME/bin/), then adapt it accordingly for your data. This wik