Re: [Freesurfer] aseg.presurf edits are undone or incomplete when brainmask.mgz edits are involved

External Email - Use Caution Hi, Thank you for the response! I just sent a file via FTP: freesurfer_aseg_edits_issue_example.zip That zip file contains a directory structure with a deidentified example, edited files, and outputs. It's a different example than the one in the imag

Re: [Freesurfer] Command Not Found

External Email - Use Caution Oh thank you, good catch! I am now encountering the issue below: developer@developer-VirtualBox:~$ tkregister2 --s home --mov updated.mgz --regheader --reg register.dat --surf orig tkregister_tcl /usr/local/freesurfer/7.2.0/tktools/tkregister2.tcl sur

Re: [Freesurfer] Command Not Found

Hi Rachel, Are you trying to run tkregister2? Looks like you forgot the t at the start of the command. -Paul From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Rachel Wagner Sent: Tuesday, June 28, 2022 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subj

[Freesurfer] Command Not Found

External Email - Use Caution Hello, Thank you for your help! I am trying to register my spm image and am getting the following error: developer@developer-VirtualBox:~$ kregister2 --s home --mov updated.mgz --regheader --reg register.dat --surf orig kregister2: command not found

Re: [Freesurfer] Error Opening File

The brain.mgz doesn't exist in that location. How did you create it? Maybe it in a subject's dir? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Rachel Wagner Sent: Tuesday, June 28, 2022 2:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error Opening File Ex

Re: [Freesurfer] Converting File Type

mri_convert file.mgz file.nii.gz should do the trick cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Rachel Wagner Sent: Tuesday, June 28, 2022 2:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Converting File Type External Email - Use Caution He

[Freesurfer] Error Opening File

External Email - Use Caution Hello, I am getting the following error when trying to convert a file on my desktop: developer@developer-VirtualBox:~$ mri_convert home/developer/desktop/brain.mgz brain.nii mri_convert home/developer/desktop/brain.mgz brain.nii reading from home/dev

[Freesurfer] Converting File Type

External Email - Use Caution Hello, I have an img and an mgz file I would like to convert to a nii file. How can I do so? Thanks! Rachel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailma

Re: [Freesurfer] Problem with sxconcat-sess

Hi Noah, I'm not super familiar with the functional stream, but it looks like something has gone wrong during the first-level analysis for some of your subjects. Can you compare the log files in the ./scripts directory for a subject that has the dof files vs a subject that doesn't and post any

[Freesurfer] Problem with sxconcat-sess

Hello, I am trying to concatenate my functional data with the following command (Ps: I am relatively new to FreeSurfer): sxconcat-sess -sf functional_ID_jun22_allSubjects -analysis PCC_Bold_R -contrast bilateral_isthmuscingulate_bold_config -o DMN_Right. I get an error that says the dof file c

[Freesurfer] passcord for FS_7_2_0_Ubuntu_18_04_06.ova.7z

External Email - Use Caution Dear FreeSurfer developer teams, Could you send me the passcode for FS_7_2_0_Ubuntu_18_04_06.ova.7z? Cheers, Ryo. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/m