[Freesurfer] Using T2 or FLAIR data to improve pial surfaces

External Email - Use Caution Dear all I want to use T2 or FLAIR data to improve pial surfaces. I wonder, which one is better? using T2pial or FLAIRpial? Is there any difference in output? Thank you so much in advance for your time and help! Hengameh _

[Freesurfer] Help with finding which functional areas house certain electrodes

External Email - Use Caution Hey Doug, We want to find the functional areas where each electrode is located in patients. At present, we are finding the electrode RAS coordinates manually using CT-MRI co-registration. We are then manually searching for these locations in Freeview u

[Freesurfer] input segmentation masks in recon-all

External Email - Use Caution Dear Prof. Fischl, I hope to use Freesurfer to get some surface measures of brain structures. The 'recon-all' command will give the output of the surface measures when input the T1w MRI images. If my input files are the segmented binary masks (such as

Re: [Freesurfer] Hippocampus cortical layers division

sorry, I don't think we have anything that will do what you want cheers Bruce On Tue, 18 Dec 2018, Yixin Ma wrote: External Email - Use Caution Hi Freesurfer experts, I'm writing to ask if you have any suggestions on generating cortical layers for hippocampus subfield cort

Re: [Freesurfer] VBM by freesurfer

External Email - Use Caution Thank you! Il giorno mar 18 dic 2018 alle ore 11:43 Bruce Fischl < fis...@nmr.mgh.harvard.edu> ha scritto: > Hi Maurizio > > the orig.mgz has been converted to 1 byte/pixel and 256^3 1mm isotropic. > You can use mri_convert to go back to your original

Re: [Freesurfer] VBM by freesurfer

Hi Maurizio the orig.mgz has been converted to 1 byte/pixel and 256^3 1mm isotropic. You can use mri_convert to go back to your original data space via: mri_convert -rl orig/001.mgz cheers Bruce On Tue, 18 Dec 2018, Maurizio Bergamino wrote: External Email - Use Caution 

[Freesurfer] VBM by freesurfer

External Email - Use Caution Hello, I am trying to run a VBM analysis by using the white matter and the grey matter masks from Freesurfer, because, often, other tools are not able to calculate a correct white matter and grey matter masks. When I have these masks, I have to apply th

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

On 12/7/18 9:29 AM, Matthieu Vanhoutte wrote: > External Email - Use Caution > > Hi Douglas, > > Thanks for these clarifications. I added some others questions inline below. > > Best, > Matthieu > >> Le 6 déc. 2018 à 17:25, Greve, Douglas N.,Ph.D. a >> écrit : >> >> >> >> On 11/30/2018

Re: [Freesurfer] Robust PET signal projection

you can use mri_vol2surf to sample at different depths. If you want a simple average across cortex, then you can use --projfrac-avg .35 .65 .05 If you want to do more sophisticated weighting, then you will have to sample at each layer and then combine the files (eg, fscalc). Unless you have very

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

You will need to set --psf 0 and --no-tfe to fully turn off PVC. On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote: External Email - Use Caution Hi Douglas, Could you help me on this point ? Best, Matthieu Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte mailto:matthieuvanhou...@gmail.c

[Freesurfer] Hippocampus cortical layers division

External Email - Use Caution Hi Freesurfer experts, I'm writing to ask if you have any suggestions on generating cortical layers for hippocampus subfield cortical regions with the help of freesurfer. When generating cortical layers for other neocortex brain region, the surface fil

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

External Email - Use Caution > > Hi Douglas, > > Could you help me about my previous mail with questions ? > > Thanks, > Matthieu > > > Le ven. 7 déc. 2018 à 14:31, Matthieu Vanhoutte < > matthieuvanhou...@gmail.com> a écrit : > >> Hi Douglas, >> >> Thanks for these clarifications.

Re: [Freesurfer] Robust PET signal projection

External Email - Use Caution Dear experts, Is there any advice on this point ? Best, Matthieu Le mer. 12 déc. 2018 à 10:47, Matthieu Vanhoutte < matthieuvanhou...@gmail.com> a écrit : > Dear Freesurfer's experts, > > In order to have a robust PET signal projection, is it possi

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

External Email - Use Caution Hi Douglas, Could you help me on this point ? Best, Matthieu Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte < matthieuvanhou...@gmail.com> a écrit : > Dear Douglas, > > Is it possible to use mri_gtmpvc command in order to intensity normalize > PE

[Freesurfer] 1) single subject surface activation in volume space and 2) small volume correction

External Email - Use Caution Dear experts, I'm running a sensory mapping experiment, which I would like to analyse in single subject space. Everything seems to be working fine (see code excerpt below). Now I'd like to do two additional things: 1) show the surface results

Re: [Freesurfer] Link for Runtime still broken

External Email - Use Caution Unless I'm mistaken, the runtime on the FTP should be identical to the one distributed by Mathworks? Maybe someone who knows can comment on this, but you could try this link: https://www.mathworks.com/products/compiler/matlab-runtime.html Just m