Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

External Email - Use Caution Hi Dr. Greve, Thank you for your suggestion. Unfortunately, the same problem occurred when I ran the command with --no-pcc. Folders and files with the same names were created. and the following error message (identical to the previous one) appeared.

Re: [Freesurfer] SAMSEG "lesion" (Illegal instruction) ~ running VM_67

External Email - Use Caution Hello Randy, I think the expectation is for users to run “samseg” from the command line. (The samseg script is a front-end you run with command line options, e.g., —help, which calls samseg_run that in turn runs the samseg python scripts in the

Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics

External Email - Use Caution Thanks!! Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779 From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Neverending mris_fix_topology

Thanks Bruce, I'm going to try that now. From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: Thursday, February 24, 2022 1:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] Neverending mris_fix_topology Hi Noam Have you tried running it without -parallel?

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

External Email - Use Caution I would like to measure uptake exclusively in gray matter. What would you recommend to accomplish this? In my previous message, I was wondering if adding a gray matter mask would be a potential way to restrict the analysis to gray matter. Thanks!

Re: [Freesurfer] Neverending mris_fix_topology

Hi Noam Have you tried running it without -parallel? It looks like it is waiting for some other PID to finish Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Peled, Noam Sent: Thursday, February 24, 2022 12:36 PM To: Freesurfer support list Subject: [Freesurfer] Neverending

Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics

To use the commands I mentioned. You must have a single voxel volume (dim = 1 1 1). You might be able to make something from you map with something like mri_mask -bb 0 VOI.mgz VOI.mgz VOI.masked.mgz # Get the dimension of this volume with mri_info --dim VOI.masked.mgz # Now create a single

Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness

Hi Asim, I ran into some issues on my test. I think the software is doing what it is supposed to do, but I think there is something wrong with the underlying permutation method when using PVRs. This will take a while for me to figure out. In the  meantime, you can try using the more

Re: [Freesurfer] Annotation File to ROI Volume Estimate

I see it in the help:    -b     tabular output On 2/24/2022 12:23 PM, Jacoby, John wrote: Hi Doug, thanks for the pointer. That was exactly what I was looking for. When I copied the command from recon-all.log, it used a -b flag. I can't find documentation for this flag

Re: [Freesurfer] Dividing surface overlays

You can also look in pctsurfcon. This compute the percent gray/white contrast. It does so on the T1w, but you could look inside the script to see how it does it and adapt to your situation. On 2/23/2022 3:26 PM, Adam Martersteck wrote: External Email - Use Caution Hi Dylan, Give

Re: [Freesurfer] Annotation File to ROI Volume Estimate

Hi Doug, thanks for the pointer. That was exactly what I was looking for. When I copied the command from recon-all.log, it used a -b flag. I can't find documentation for this flag either in the --help or on the wiki. Could you elaborate on what it does? Thank you! Best, John

Re: [Freesurfer] recon-all outpputs for deep learning

I see. Well, you will probably want some combination of cortical thickness maps and subcortical volumes at the least, although of course other information might be important as well (connectivity, myelin content, etc…). These things have different shapes (in the python sense) so you’ll have to

Re: [Freesurfer] recon-all outpputs for deep learning

External Email - Use Caution Sorry for not making it clear you are right. Yes, I want to diagnose autism spectrum disorder from brain images using structural measurements such as the gray matter volumes of regions or at the voxel level. Then, since deep learning is a black box

Re: [Freesurfer] recon-all outpputs for deep learning

Sorry, can you explain a bit more about what you want to do. What does “demonstrate morphological variation” mean? Just quantify variability? Are there any variables that you are correlating it with (e.g. disease status, cognitive measure, etc…)? I don’t understand what you are trying to do

[Freesurfer] Mass-univariate LME - contrast for one group

External Email - Use Caution Dear experts, Sorry, for posting again - I was not able to answer on my first post, don't know why. If anyone has an idea about this, please let me know! Unfortunately, I did not make any progress. Best, Franziska External Email - Use

[Freesurfer] recon-all outpputs for deep learning

External Email - Use Caution Hello Freesurfer experts I want to apply deep learning to structural brain images processed by Recon-all. My goal is to demonstrate the morphological variation(e.g., gray matter volumes or cortical thickness) of brain regions in structural magnetic

[Freesurfer] Error sending tcl command

External Email - Use Caution To whom it may concern, How are you recently? I am trying to follow the the ENIGMA Cortical QC protocol to check my external surface result after order "recon-all". The detail of scripts is attached bolow