Re: [Freesurfer] TIV should be considered as a covariant for thickness, volume and area analyses

External Email - Use Caution Thank you so much! Ting > On Jun 29, 2018, at 2:10 PM, Douglas Greve wrote: > > Yes, for area and volume, no for thickness > > On 6/29/18 3:06 PM, Ting Li wrote: >> External Email - Use Caution >> >> Hi FreeSurfer Experts, >> >> I would li

[Freesurfer] After v.5.3 to v.6.0 update octave set up doesn't work

External Email - Use Caution Hi all, I just switched from FS 5.3 to 6.0 on Gentoo Linux. Previously Freesurfer worked fine under octave setup (as specified here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html), but after the update, when I tried te

[Freesurfer] Eddy correct command not found

External Email - Use Caution Dear community: I have a problem with trac-all processing with the tutorial data. sh-3.2# trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial INFO: SUBJECTS_DIR is /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesur

Re: [Freesurfer] TIV should be considered as a covariant for thickness, volume and area analyses

Yes, for area and volume, no for thickness On 6/29/18 3:06 PM, Ting Li wrote: > External Email - Use Caution > > Hi FreeSurfer Experts, > > I would like to do the surface analysis among two groups, like the thickness, > volume and area. When I run the GLM, do I have to consider the eTIV

[Freesurfer] TIV should be considered as a covariant for thickness, volume and area analyses

External Email - Use Caution Hi FreeSurfer Experts, I would like to do the surface analysis among two groups, like the thickness, volume and area. When I run the GLM, do I have to consider the eTIV as a covariant or not? Thanks a lot! Best wishes, Ting

Re: [Freesurfer] mri_glmfit question

You can create a surface overlay in matlab and display it using freeview.  See https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m To read it into matlab, you can run pcc = MRIread('pcc.mgh'); You can convert it to text with mri_convert --ascii pcc.mgh outputtextfile On 6/2

Re: [Freesurfer] Freeview not showing images

External Email - Use Caution Yes, that shows up fine. Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wags...@einstein.yu.edu

Re: [Freesurfer] Freeview not showing images

What if you run 'glxgears'? Does it render properly? Ruopeng On 06/29/2018 09:50 AM, Mark Wagshul wrote: Yes, I’m running it with Xming on Windows. Same thing shows up if I load a volume. Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Cen

Re: [Freesurfer] Proposed addition for Freesurfer - automated control points

Hi Chris can you elaborate a bit? Our intensity normalization is almost entirely an automated control point finding tool. cheers Bruce On Fri, 29 Jun 2018, Chris Adamson wrote: External Email - Use Caution Freesurfer devs,   I presented an automated control point addi

Re: [Freesurfer] 3T Intensity Normalization (Re-Submission)

Hi David the -3T flag changes the target atlas to one built from 3T data, and also modifies some of the parameters that are passed to nu_correct, I believe to make it a bit more aggressive. I think the parameters we use are the ones suggested here: https://www.ncbi.nlm.nih.gov/pubmed/19732839

[Freesurfer] 3T Intensity Normalization (Re-Submission)

External Email - Use Caution Hello Experts, I believe -3T Flag can be used with "recon-all" on scans collected by 3T scanners. I believe it performs intensity normalization to set white matter intensity threshold at 110. I am hoping to learn more about the flag option as it produc

Re: [Freesurfer] Freeview not showing images

External Email - Use Caution Yes, I’m running it with Xming on Windows. Same thing shows up if I load a volume. Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-

Re: [Freesurfer] Freeview not showing images

This looks like a display artifact. Are you running freeview via some kind of X Terminal Emulator on Windows? What if you load a volume? Ruopeng > On Jun 28, 2018, at 7:33 PM, Mark Wagshul > wrote: > > Hi. > > I’m a newbie to Freeview, hoping that this is a simple problem. When I open >