[Freesurfer] output of mri_surf2vol looks fragmented

External Email - Use Caution Hi, I'm trying to understand mri_surf2vol and mri_vol2surf but I'm not able to get the expected output when converting a surface back to volume. These are the commands I'm using: mri_vol2surf --mov lh_fusiform_pre.nii.gz --ref mri/orig.mgz --regheader

[Freesurfer] PhD Position on the Brain, Language and Multilingualism

External Email - Use Caution With the launch of a new ‘NCCR Evolving Language’ (http://www.snf.ch/SiteCollectionDocuments/nfs/Faktenblatt_NCCR_evolvinglanguage_en.pdf), which involves nearly 40 different research groups from a large variety of disciplines across Switzerland, we

Re: [Freesurfer] Label on fsaverage failure

It has to be loaded as an overlay to a surface, not a surface itself. On 7/3/2020 10:10 AM, Eleni Nikalexi wrote: External Email - Use Caution Dear Douglas, thank you very much for your help; I run the recon of MNI152_T1_1mm_brain.nii.gz (which I moved into a directory called

Re: [Freesurfer] cortical thickness

I got my answer. Thanks so much > On Jul 6, 2020, at 1:31 PM, Fischl, Bruce wrote: > > I'm not sure I understand your question. We compute the distance between > minimum distances between the white and pial in mm, then compute the minimum > between the pial and the white, then average them

Re: [Freesurfer] cortical thickness

I'm not sure I understand your question. We compute the distance between minimum distances between the white and pial in mm, then compute the minimum between the pial and the white, then average them (all in mm) -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf

Re: [Freesurfer] cortical thickness

Thanks for your response Bruce. Does FS calculate the distance between the surface and CSF border in Euclidean and then converts it into mm? Thanks Mona > On Jul 6, 2020, at 12:40 PM, Fischl, Bruce wrote: > > yes > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] cortical thickness

yes -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Nasiriavanaki, Zahra Sent: Monday, July 6, 2020 12:31 PM To: Freesurfer support list Subject: [Freesurfer] cortical thickness Hi Freesurfer experts I have a question about the way FS calculates cortical

[Freesurfer] cortical thickness

Hi Freesurfer experts I have a question about the way FS calculates cortical thickness and I appreciate if you could please respond. I calculated the cortical thickness using read_curv script in a specific ROI in parietal lobe. The mean thickness at that area was 2.4. Does this number show the

Re: [Freesurfer] Lesioned hemisphere

From the log file it got to the surface stuff and died there. You should be able to run recon-all with the -hemi [lr]h switch to just run one hemi From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Alina Rojas Sent: Monday, July 6, 2020 11:23 AM To: Freesurfer support list Subject: Re:

Re: [Freesurfer] mris_convert error

Do you mean that the inflated is not somehow in line with the pial? They are not supposed to be (and it is not clear what that would mean). The white and pial look aligned On 7/6/20 7:16 AM, Mason Wells wrote: External Email - Use Caution Hi Experts, I am using mris_convert to

Re: [Freesurfer] Destrieux atlas volume based in matlab

you can run recon-all on the MNI152 itself, though it will not reflect the average of the subjects that went into it On 7/3/20 4:42 AM, Gian Marco Duma wrote: External Email - Use Caution Dear Freesurfers experts, I need to obtain in the volume and not in the surface, in MNI space

Re: [Freesurfer] Lesioned hemisphere

What is the error? You should be able to run through to the surface generation, then only run the hemi you want Cheers Bruce -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Alina Rojas Sent: Monday, July 6, 2020 10:22 AM To: freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Lesioned hemisphere

External Email - Use Caution Hello Freesurfer experts, I’m analyzing subjects with a stroke in one hemisphere. Problem: recon-all breaks and gives an error at the white matter segmentation, what I understand. I don’t need the data from the lesioned hemisphere, I need the

Re: [Freesurfer] Fsaverage stats

External Email - Use Caution Are you sure that you want to compare their thickness with fsaverage? What is your research question? It is more common to compare to a control group with matched demographics. Tim > On July 6, 2020 at 12:57 PM Alina Rojas wrote: > > >

[Freesurfer] Fsaverage stats

External Email - Use Caution Hello Freesurfer Developers, I'm attempting to compare the cortical thickness values from the stats (?h.aparc.stats) of a stack of subjects and compare them with fsaverage. With aparcstats2table I did it for my subjects without problem, but the

Re: [Freesurfer] Freesurfer Digest, Vol 197, Issue 7 {Disarmed}

External Email - Use Caution Hi Eugenio! Thank so much for your reply. Please find attached the following files you requested: 1. A single subject processed cross sectionally - lh.hippoSfVolumes-T1.v10.txt 2. The same subject process longitudinally -