Re: [Freesurfer] Freesurfer recon-all qcache partial failure

The command should look like this 'recon-all -s subjid -qcache -all -i input-file' From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Asuka Toyofuku Sent: Monday, January 15, 2024 9:45 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure

Re: [Freesurfer] fsLR label to fsnative annotation

Freesurfer .annot saves the annotation value at each vertex . The annotation is calculated from RGB in label file. Any labels with same RGB assigned will have the same annotations. They will appear to be the same label in .annot file. Fix the label table in .gii, re-run mris_convert. If you are

Re: [Freesurfer] Midline white/pial surface

Can you try the troubleshooting methods from this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Sunniva Fenn-Moltu Sent: Monday, January 15, 2024 6:35 AM To: freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] [External] Re: extracting measurements for mean gray matter thickness/LGI

External Email - Use Caution Sorry, to be clear, there is a measurement for bilateral mean thickness offered by default? I'm able to gather the left mean thickness and the right mean thickness easily. Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- _

Re: [Freesurfer] [External] Re: extracting measurements for mean gray matter thickness/LGI

why not just average them together? Or are you hoping that FS provides this last small step? I don't think that we do ... On 1/16/2024 10:04 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: External Email - Use Caution Sorry, to be clear, there is a measurement for bilateral me

Re: [Freesurfer] Midline white/pial surface

I would also be helpful to have some pics of what you are seeing. The surface is not valid in the "medial well" -- ie all the non-cortical structures on the central sagittial plane such as thalamus an VDC. On 1/16/2024 7:50 AM, Huang, Yujing wrote: Can you try the troubleshooting methods from

Re: [Freesurfer] Sample registration question

Yes, that would be an ROI analysis On 1/13/2024 1:00 PM, Mirsol Choi wrote: External Email - Use Caution Hello, My goal is to compare the FA and MD values of hippocampal subfields (only inside the hippocampus) between cognitively normal, MCI, and AD subjects. I am unsure if this wou

Re: [Freesurfer] Freeview crashes when trying to load volumes

I would also check if the license file is installed properly. On Jan 15, 2024, at 7:06 PM, fsbuild mailto:fsbu...@contbay.com>> wrote: External Email - Use Caution It would help for us to know what your machine is running, e.g., linux or MacOS (Intel or Silicon Mac) - and what the ve

[Freesurfer] Issue with mri_brainvol_stats for only some participants

External Email - Use Caution Hi there,   I’ve come across a strange issue while running some new participants through Freesurfer 7.3.   A portion of participants (30%) are missing their stats files, although I have visually inspected the segmentation using Freeview and they look

Re: [Freesurfer] Issue with mri_brainvol_stats for only some participants

Can you attach recon-all.log of a failing subject? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Carly McIntyre-Wood Sent: Tuesday, January 16, 2024 4:37 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Issue with mri_brainvol_stats for only some participants Ext

[Freesurfer] recon-all errors (cannot execute binary file +

External Email - Use Caution Good day. When I run recon-all for my nii files I get either one of the following error messages: 1. ERROR: could not configure recon-all parameters Killed 2. ERROR: could not configure recon-all parameters /Applications/freesurfer/bin/fspython: l

Re: [Freesurfer] recon-all errors (cannot execute binary file +

External Email - Use Caution It looks like you did not use the .pkg file installer to install Freesurfer on the Mac, otherwise you would have a path like /Applications/freesurfer/7.4.1 to use as FREESURFER_HOME.  The installer should ensure the privileges should be correct to ru

Re: [Freesurfer] recon-all errors (cannot execute binary file +

External Email - Use Caution  do not wish to continue communication over unencrypted e-mail -Original Message-From: "윤혜정" To: "Freesurfer support list" ; Cc:Sent: 2024-01-17 (수) 10:49:56 (UTC+09:00)Sub

Re: [Freesurfer] recon-all errors (cannot execute binary file +

External Email - Use Caution  do not wish to continue communication over unencrypted e-mail,  -Original Message-From: "김민지" To: "Freesurfer support list" ; Cc:Sent: 2024-01-17 (수) 13:01:17 (UTC+09:00)Subje