[Freesurfer] Extracting LME results from label regions

External Email - Use Caution Dear Freesurfer experts, I have what seems like a simple problem, and I'm sure there is a method for doing this, hoping someone can give me some guidance. We have results from an LME model run on surface data, and then run through PALM to calculate

Re: [Freesurfer] Creating Anatomical ROI with mri_volsynth

External Email - Use Caution Actually I believe that I should just use the mri_vol2surf using the volume I created. But I don't know how to proceed. I tried fslregister --s fsaverage --mov $SUBJECTS_DIR/fsaverage/mri/MNI305.cor.mgz --reg ROI.dat to have a register data to use at

Re: [Freesurfer] Creating Anatomical ROI with mri_volsynth

External Email - Use Caution Hi Douglas, I want a ROI for measuring thickness. I have the peak difference on the MNI305 and its area. So I was trying to create a spherical volume starting at the peak and then transform it to the surface. I'm able to create the surface and see it

Re: [Freesurfer] quantifyHAsubregions.sh does not work

Hi Molly, Can you please send me the listing of files in the mri directories of one of the subjects? (i.e., /media/ubuntu/cxy/FreesT1/output.long/[SOME_SUBJECT]/mri Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From:

[Freesurfer] Bug in quantifyThalamicNuclei.sh

Dear all, Haewon Roh has discovered a small bug in quantifyThalamicNuclei.sh. We’ll fix it in the development version as soon as possible. In the meantime, we will post an amended version in the wiki; please see: https://surfer.nmr.mgh.harvard.edu/fswiki/ThalamicNuclei Thanks Haewon for picking

Re: [Freesurfer] Visualizing significant clusters, monte-carlo and permutation

External Email - Use Caution Hi, following my concern that all my significant clusters (that have survived monte carlo p<0.05 correction in this case) don't appear as their appropriate colours (i.e. in yellow or blue to show positive or negative max values, respectively), my

[Freesurfer] Generating Global Thickness and Surface Area Estiamtes from .aparc variables

External Email - Use Caution Dear Freesurfer Experts, I want to generate global measures of cortical thickness and pial surface area analogous to using total cerebral volume as a global brain volume estimate. In your opinion, would it be reasonable to generate these global

Re: [Freesurfer] Error using FsPalm

External Email - Use Caution I'm using version 6.0.0. 2020년 8월 20일 (목) 오전 12:08, Douglas N. Greve 님이 작성: > what version of fs are you using? > > On 8/19/2020 9:03 AM, 정현우 wrote: > > External Email - Use Caution > Hi Douglas, > > Thank you for your response. I followed

Re: [Freesurfer] Constraining analysis to ROI

The uncorrected results will be exactly the same. The corrected results should be more significant On 8/18/2020 7:44 PM, Erin Moe wrote: > External Email - Use Caution > > Hi Doug, > Thanks for the prompt reply. I did use the label option in mri_glmfit, but it > seemed to just show the

Re: [Freesurfer] Error using FsPalm

what version of fs are you using? On 8/19/2020 9:03 AM, 정현우 wrote: External Email - Use Caution Hi Douglas, Thank you for your response. I followed your suggestions and additionally tried using Matlab instead of Octave for FsPalm analysis, but I still failed to get the results.

Re: [Freesurfer] RBV PVC

On 8/19/2020 2:42 AM, Nathalie Mertens wrote: External Email - Use Caution Dear, I am not sure if the questions below were sent correctly to you, since I did not receive any copy of it. Please find my message below. Many thanks, looking forward to your reply. Kind regards,

Re: [Freesurfer] Creating Anatomical ROI with mri_volsynth

rh.thickness is a surface overlay, not a volume (which is needed for the commands you are running). I'm a little confused by what you are trying to do. Do you want an volume ROI or a surface ROI? On 8/18/2020 8:13 PM, Mauricio Watanabe Ribeiro wrote: External Email - Use Caution

Re: [Freesurfer] " quantifyThalamicNuclei.sh" commend does not work..

Weird! Did you try providing the subject directory explicitly as third argument? Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: Haewon Roh Date: Wednesday, August 19, 2020 at 09:21 To: Freesurfer support list , "Iglesias

Re: [Freesurfer] " quantifyThalamicNuclei.sh" commend does not work..

External Email - Use Caution Cause I segmented thalamus using only T1 image, I put the this command : quantifyThalamicNuclei.sh thalamus_nuclei_output_file.txt T1 But any file was not made after this command. > On Aug 19, 2020, at 10:18 PM, Iglesias Gonzalez, Juan E. >

Re: [Freesurfer] " quantifyThalamicNuclei.sh" commend does not work..

Dear HW, What was the exact command you ran? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Haewon Roh Reply-To: Freesurfer support list Date: Wednesday, August 19, 2020 at 03:26 To:

Re: [Freesurfer] Error using FsPalm

External Email - Use Caution Hi Douglas, Thank you for your response. I followed your suggestions and additionally tried using Matlab instead of Octave for FsPalm analysis, but I still failed to get the results. Adding $FREESURFER_HOME/fsfast/toolbox to my matlab path removed the

[Freesurfer] Developer password

External Email - Use Caution Hello, Maybe you can help me. I have followed the freesurfer installation guide with virtual box and ubuntu, but i was not able to log in. Maybe you could send me the password. I saw that people were writing because of the same in the mail archive and

Re: [Freesurfer] RBV PVC

External Email - Use Caution Dear, I am not sure if the questions below were sent correctly to you, since I did not receive any copy of it. Please find my message below. Many thanks, looking forward to your reply. Kind regards, Nathalie Mertens Van: Nathalie Mertens Datum: