[Freesurfer] Matlab R2014b exits while executing segmentThalamicNuclei.sh in FS v7.1.1 under OS Big Sur

External Email - Use Caution As mentioned, recon-all function with T1 MRI data works well with no problem at all.  With results from recon-all, while trying to run segmentThalamicNuclei.sh, MATLAB quit with message as follows:

Re: [Freesurfer] memory allocation error

External Email - Use Caution dear Andrew, I was allowing 8, 16, ~36GB of memory in different runs, so I would exclude that this was the problem. bests fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences h

Re: [Freesurfer] Hippocampus ROI

Hi Jessica, There’s no direct way of doing this, since the atlas lives it its own space and there’s no intensity volume you can deform to MNI, only probabilities. Having said that, you could 1. segment all your subjects with the hippocampal module, 2. register the subjects to MNI, 3. Deform the

Re: [Freesurfer] mask error in glm_fit

External Email - Use Caution Thanks for your response! It was in the fsaverage folder when I installed Freesurfer. I also have an .nii file. Could I turn it into an .mgz file and maybe it will have the same dimensions? Could it also be because I am looking at volume and fsaverage i

Re: [Freesurfer] blurring average label files

External Email - Use Caution Hi again! On second thought, we are wondering if this averaged .label file was already blurred during the mris_spherical_average command. If this is the case, do you know what smoothing has been done and by how much? We are interested in seeing the

Re: [Freesurfer] blurring average label files

Hi Kristi I don't think it does any blurring unless you tell it to. The output should reflect the actual alignment of those labels Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Kristi Drudik Sent: Thursday, May 20, 2021 12:48 PM To: Freesurfer support list Subject: R

Re: [Freesurfer] blurring average label files

External Email - Use Caution Hi Bruce, In that case, how would I tell the command “mris_spherical_average” to blur the output? Also, how can I display the probability values in a colour scale? Thank you very much! Best, Kristi From: mailto:freesurfer-boun...@nmr.mgh.harvard.e

Re: [Freesurfer] blurring average label files

Hi Kristi You can change the display in freeview to show the p-vals instead of just the binary label. Actually you can blur and write the output in mris_spherical_average (undocumented) with: mris_spherical_average -prior <# of iterative averages> cheers Bruce From: freesurfer-boun...@nmr.mg

[Freesurfer] Issue Pertinent To Freesurfer Usage

External Email - Use Caution Dear Freesurfer, I have downloaded the application but I am unable to run it. Can you please help me in resolving this issue? Regards, Noyan Jawed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.ed

Re: [Freesurfer] blurring average label files

External Email - Use Caution Hi Bruce, Thank you very much! Apologies for my simple questions but just to clarify: In Freeview, where do I select to show the p-vals instead of the binary level? Also, how would the entire command be listed with the required flags? Would it be som

Re: [Freesurfer] Issue Pertinent To Freesurfer Usage

External Email - Use Caution > On 20-May-2021, at 10:59 PM, Noyan Jawed wrote: > > Dear Freesurfer, > > I have downloaded the application but I am unable to run it. Can you please > help me in resolving this issue? > > Regards, > > Noyan Jawed __

Re: [Freesurfer] blurring average label files

Almost. -prior takes two parameters. The second is the file name to write the results to. In freeview near the label panel there is a “color” pull down menu. You can change that from solid color to heat scale Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Kristi Drudi

Re: [Freesurfer] blurring average label files

I defer to Ruopeng for the 2nd question. And for the first Doug knows the exact formula to go from iterations of nearest neighbor smoothing to fwhm. It goes as the sqrt, so fwhm ~ sqrt(niters) I believe. From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Kristi Drudik Sent: Thursday, Ma

Re: [Freesurfer] blurring average label files

Hi Kristi, I think the color scale bar only sync with overlays, not labels. I will change that. Best Ruopeng On May 20, 2021, at 3:22 PM, Fischl, Bruce mailto:bfis...@mgh.harvard.edu>> wrote: I defer to Ruopeng for the 2nd question. And for the first Doug knows the exact formula to go from i

Re: [Freesurfer] blurring average label files

Did you load the output file from -prior (not the overall output of mris_spherical_average)? Also, 9 is a pretty small amount of smoothing. Probably like a fwhm of 1-2 mm or something From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Kristi Drudik Sent: Thursday, May 20, 2021 3:53 PM T

Re: [Freesurfer] blurring average label files

Oh boy, a w file! What if you give it the extension .mgz? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Kristi Drudik Sent: Thursday, May 20, 2021 7:06 PM To: Freesurfer support list Subject: Re: [Freesurfer] blurring average label files External Email - Use Caution

Re: [Freesurfer] Issue Pertinent To Freesurfer Usage

External Email - Use Caution Hi Noyan, I am new user too. You may run command under bash. First, type bash, enter; then type in command. Best Joe On Thursday, May 20, 2021, 10:59:45 AM PDT, Noyan Jawed wrote:         External Email - Use Caution        Dear Freesurfer