Re: [Freesurfer] Fw: error: Numerical argument out of domain; error: MRIhistogramLabelRegion: constant image\00

External Email - Use Caution Hello, I'm just checking to see if you have received the images and if you are still working on my issue? I don't think I got any more replies from you and just want to make sure if you're still working on it. Best, Adriana _

Re: [Freesurfer] Fw: error: Numerical argument out of domain; error: MRIhistogramLabelRegion: constant image\00

Hi Adriana, I don't seem to see your previous message posted. Can you share the images again, and recon-all.log too? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of adriana.jo...@unibe.ch Sent: Monday, January 30, 2023 7:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject

Re: [Freesurfer] What if FS fails

I see talairach check failed. Can you try the steps that are suggested in recon-all.log? “ #@# Talairach Failure Detection Wed Jan 4 15:13:30 IST 2023 /Volumes/Rakshathi/Freesurfer/subj55_anat/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transfo

[Freesurfer] LME design matrix for changes in 1 group

External Email - Use Caution Hi, I have 2 sessions of data acquired in the same day for each participant before and after the drug intake. I wonder how to analyse this with LME tool. I create design matrix X in 2 columns, first all ones and second the time differences(which are the

[Freesurfer] High resolution T1

External Email - Use Caution I understand that from Version 7.0, better high resolution surface reconstruction with -hires is done. My question is, if we use higher resolution T1, such as 0.8mm, will it improve the accuracy of the cortical thickness measurement? If yes, is there

Re: [Freesurfer] LME design matrix for changes in 1 group

Hi Amirhossein, - If you have two time points for all participants, - and the time difference is the same for all you can simply subtract the thickness (or volume) values per participant and run a regular GLM. LME is a little overkill here. In LME, you have one column of ones, and one of the ti

Re: [Freesurfer] LME design matrix for changes in 1 group

External Email - Use Caution Thanks a lot Martin for the information. We have actually 2 sessions of placebo for each subject. How do you suggest to do the analysis including that data? BR On Mon, 30 Jan 2023 at 16:30, Reuter, Martin,Ph.D. wrote: > Hi Amirhossein, > > - If you h

Re: [Freesurfer] LME design matrix for changes in 1 group

Hi Amirhossein, So you have session 1 , placebo , session 2 Another day session 3, drug, session 4 ? Again if this is for all subjects, easiest is to subtract session 2 from 1, and 4 from 3, to get thickness/volume differences for each condition. Then compute the difference of the differences

Re: [Freesurfer] High resolution T1

External Email - Use Caution We showed improved data (more accurate surface placement leading to more accurate myelin maps) in prior publications (Glasser et al., 2013; 2014 Neuroimage). It makes a difference for cortical thickness too (e.g., falsely too low cortical thickness

Re: [Freesurfer] High resolution T1

External Email - Use Caution Thank you so much for the information, Matt! From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Glasser, Matt Sent: Monday, January 30, 2023 1:23 PM To: Freesurfer support list Subject: [EXTERNAL] Re: [Freesurfer] High resolution T1 CAUTION

Re: [Freesurfer] High resolution T1

External Email - Use Caution Dear, Matt, What kind of issues did you have with version 7.x and the hires stream? It would help us to know what we are facing… Thanks. Sang From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Glasser, Matt Sent: Monday, January 30, 2023 1:2

Re: [Freesurfer] High resolution T1

External Email - Use Caution On Mon, Jan 30, 2023 at 12:40 PM Lee, Sang Hoon wrote: > External Email - Use Caution > > Dear, Matt, > > > > What kind of issues did you have with version 7.x and the hires stream? > > It would help us to know what we are facing… > > Thanks.

Re: [Freesurfer] High resolution T1

External Email - Use Caution Issues with surface placement in harder areas (e.g., white matter surface placement in heavily myelinated cortex; pial surface placement in lightly myelinated cortex). Matt. From: on behalf of "Lee, Sang Hoon" Reply-To: Freesurfer support list D

Re: [Freesurfer] LME design matrix for changes in 1 group

External Email - Use Caution Thanks Martin. I assume in GLM approach I should calculate change for session 1 and 2 and then 3 and 4 and then run difference of difference. We actually randomized the order so half day1 is plcebo and half drug. So I just need to be caretabout the des

[Freesurfer] mri_robust_register --minsize

Hello, I am trying to register a full volume to a single slice, and I follow example 3 of mri_robust_register's help. I get the following error: Input image is smaller than min dimension: 1 < 16 Input dimensions (after conformalizing) MOV: 64 64 64 Input dimensions (after conformalizing) DST:

Re: [Freesurfer] Skull stripping with external brainmask

Dear Narlon, I believe you can add -xmask [mask_volume_file] to your recon-all command. To generate such external mask, maybe you could use mri_synthseg with the --robust flag and binarize the output? Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: on behalf of "Boa So

Re: [Freesurfer] Skull stripping with external brainmask

External Email - Use Caution Thanks Juan! It looks like the -xmask is available only for newer distributions of FreeSurfer. I’m using v7.1.1. I appreciate the help though! Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSHR BC/PARF Postdoctoral Research