Re: [Freesurfer] Turning Significant Cluster (sig.cluster.summary or sig.mgh) into binary .nii ROI

Are you trying to create a volume-based binary mask or a surface-based mask? From the commands below, it looks like surface (but why would you need it to be in nii?). In the surface case, you can just mri_binarize --i ocn.mgh --match clusterno --o clusterno.mask.nii where "ocn" is the ocn file c

Re: [Freesurfer] vertexwise correlation between the two maps and atlases in volume (MNI) to surface

On 3/17/2022 4:41 PM, std...@virgilio.it wrote: External Email - Use Caution Hi list, a) I have two maps, one's of rs-fMRI functional connectivity (by FS-FAST) and one's of receptor density (from a PET-Atlas). Both the maps are in surface space. How can I measure the vertexwise co

Re: [Freesurfer] Permission denied error from -localGI

What version of FS are you running? On 3/20/2022 8:47 PM, Billah, Tashrif wrote: It does not exist and cannot be created in a shared cluster. Is there a way to define a different folder for /scratch/tp24093955057547375.load_mgh.m.mgh? === Douglas N. Greve Wed, 09 Mar 2022 10:04:31

Re: [Freesurfer] Tkregister2 not opening GUI

Does /Volumes/RestingState/fMRI/fMRI/Freesurfer/S0010_FS/surf/lh.white exist and do you have permission to read it? If yes to both, then try running it with --debug as the first option, then send all the terminal output On 3/21/2022 5:02 PM, Isabelle Deschamps wrote: External Email

Re: [Freesurfer] Freesurfer mri_convert

please send the command line, log file, version of FS, etc On 3/22/2022 11:59 AM, Zoe O'Brien-Moran wrote: External Email - Use Caution Dear FS Experts I am having continued issues with the mri_normalize function on MPRAGE data I get an error message: 3d normalization pass 1 of 2 e

Re: [Freesurfer] Negative eTIV

Check the talairach registration (talairch.xfm). It must be badly messed up On 3/23/2022 4:47 AM, lqcheng2017 wrote: External Email - Use Caution Dear experts, I extracted the eTIV using the mri_segstats, but it showed negative value. How could I solve this problem? Thank you very

Re: [Freesurfer] qdec analysis error

Sorry, we are not supporting qdec anymore. You will need to use the command-line stream On 3/23/2022 8:02 AM, David wrote: External Email - Use Caution Hello FreeSurfer Developers, I have a problem. Can you help me freesurfer version : 6.0.0 Load qdec when I run qdec.table.dat, the

Re: [Freesurfer] repeated measures ANOVA 2x2 covariate

Probably the easiest thing to do since you have only two time points is to compute the difference between the two, then just do a simple group analysis where you include the covariates that you want. On 3/23/2022 10:00 AM, Agurne Sampedro Calvete wrote: External Email - Use Caution D

Re: [Freesurfer] mri_segment_hypothalamic_subunits error: Illegal instruction 4

You're command line is incomplete (it needs more than just --s). Run it with --help and/or visit the wiki page On 3/23/2022 2:40 PM, Alice Tao wrote: External Email - Use Caution Thank you so much for the response! Unfortunately, that is the full command line and output: $ mri_segm

Re: [Freesurfer] mri_vol2vol anatomical to functional

I'm not sure I understand what you are saying or what the problem is. Can you provide the actual command line you are using, all the terminal output, and a picture that shows what the problem is? On 3/23/2022 2:46 PM, Manenti, Giorgio wrote: > External Email - Use Caution > > Dear Frees

Re: [Freesurfer] Question about calculation of pial area in DKatlas

On 3/24/2022 2:53 AM, Dongyue Zhou wrote: External Email - Use Caution Dear FreeSurfer experts: I want to calculate mean pial surface area in DKatlas in individual space.And I know the function read_annotation.m in $FREESURFER_HOME/matlab for loading this atlas. And if I ca

Re: [Freesurfer] [External] Re: [External] Re: classes for GLM analysis

it does not suprise me that 2014 is not working as that is pretty old. I've been using 2018 and that seems to work. On 3/24/2022 9:31 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: External Email - Use Caution It is seemingly working in matlab R2021b rather than matlab R2014a

Re: [Freesurfer] lh.pial and rh.pial is 0Kb, I cannot open them by using freesurfer

On 3/24/2022 4:49 PM, Muhammed Görünen wrote: External Email - Use Caution Hi, I run recon-all process for a subject's T1 data. At the end, the pial files are 0Kb and I cannot open them from python. Did it end with an error? Did you run out of space? What version of FS? Can you sen

Re: [Freesurfer] WM error near the right putamen

This is actually a bug in version 7.[012]. This area is probably not valid anyway. We'll have a fix in 7.3 On 3/21/2022 7:31 PM, Gabor Perlaki wrote: External Email - Use Caution Dear all, fswiki suggests that " There are regions where the surfaces are not intended to be accurate th

Re: [Freesurfer] GLM analysis - volume and surface area

Hi, sorry for the late response. No, there is nothing else you have to do. Using perm is a really good idea with volume and area, so glad to hear that is what you are doing. best doug On 3/10/2022 8:21 AM, Laura Willers de Souza wrote: External Email - Use Caution Of course! To do

[Freesurfer] Pass code to expand the archive of Free surfer 7.2.0

External Email - Use Caution Dear Free Surfer expert, Would you please send me the pass code for opening the archive of FS 7.2.0? Thanks for your attention! Yours sincerely, Krystal ___ Freesurfer mailing list Freesurfer@nmr.mgh.ha