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 a écrit : > Hi Douglas, > > Thanks for these clarifications. I added some others questions inline > below. > > B

[Freesurfer] Robust PET signal projection

External Email - Use Caution Dear Freesurfer's experts, In order to have a robust PET signal projection, is it possible compute the projected PET signal as a weighted average of the PET signal intersecting with the surfaces ranging from 35 to 65% of the cortical tickness with a st

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

External Email - Use Caution Dear Douglas, Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ? Best, Matthieu ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] Problems with GM segmentation -- How to solve it

External Email - Use Caution Hi Bruce, Thank you for your reply. I am sending now a file called 013.tar.gz via ftp. And this is not the worst...there are other with more regions that have not been considered in the segmentation process. I would like to know how could I cope with G

Re: [Freesurfer] Problems with GM segmentation -- How to solve it

External Email - Use Caution Hi Bruce, Already sent: ftp> put 013.tar.gz local: 013.tar.gz remote: 013.tar.gz 200 PORT command successful. Consider using PASV. 150 Ok to send data. 226 Transfer complete. 223104380 bytes sent in 808.49 secs (269.4852 kB/s) ftp> On Wed, Dec 12, 20

[Freesurfer] Download link for Matlab runtime broken?

External Email - Use Caution Hello! I tried to download the Matlab runtime for Linux to use FSFAST but the link is broken. https://surfer.nmr.mgh.harvard.edu/pub/dist/mcr/MCRv83_linux.tar.gz Not Found The requested URL /pub/dist/mcr/MCRv83_linux.tar.gz was not found on this serv

[Freesurfer] Beta series method in FS?

Hi, I am interested in using the beta series method (https://neuroscape.ucsf.edu/wp-content/uploads/publications/Rissman2004-Measuring-functional-connectivity-during-distinct-stages-of-a-cognitive-task.pdf) for intra-subject analysis. Is there a straightforward way to do this in FreeSurfer?  I

Re: [Freesurfer] recon-all ERROR: killed

Hi Liangjun. usually that means you ran out of RAM. cheers Bruce On Thu, 13 Dec 2018, 张亮军 wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to use "recon-all -i T1.nii.gz -s zhang -all", but there is a ERROR: saving intensity scales to aseg.

Re: [Freesurfer] recon-all ERROR: killed

p.s. if you look in the recon-all.log you will see: totalusedfree shared buff/cache available Mem:4025436 1115872 794808 54712 2114756 2510316 Swap: 0 0 0 which looks like something else was running

Re: [Freesurfer] Error in running make_average_subject

External Email - Use Caution Thanks for your answer Douglas. I replaced the make_average_surface file with the new one but I have the same message error. ASeg Vox2RAS: --- -1.0 0.0 0.0 128.0; 0.0 0.0 1.0 -128.0; 0.0 -1.00

[Freesurfer] Job ad: small animal MRI faculty position

External Email - Use Caution Associate Professor, Behavioral Neuroscience University of Delaware: College of Arts & Sciences: Psychological & Brain Sciences Location: Newark, DE The University of Delaware invites applications for a tenured associate professor (or assistant profes

Re: [Freesurfer] Power analysis

External Email - Use Caution After using MRIread from Matlab in file gamma.mgh, I obtain the following: mri = struct with fields: srcbext: '' analyzehdr: [] bhdr: [] vol: [] fspec: 'gamma.mgh' pwd: '/Users/lauraferrero/Docume

Re: [Freesurfer] Error in running make_average_subject

Hi Emanuel, can you include the full command line and output? cheers Bruce On Wed, 12 Dec 2018, Emanuel Alvaredo wrote: External Email - Use Caution Thanks for your answer Douglas. I replaced the make_average_surface  file with the new one but  I have the same message erro

Re: [Freesurfer] GPU/supercomputer adaptation of freesurfer?

External Email - Use Caution Sorry I'm coming to this a bit late I'm not sure that the CUDA implementation is supported these days. I've not done much work on em_ and ca_register since 2012; I'm not sure about the surface stream (I didn't do that port). Furthermore, I don't see

[Freesurfer] Segmentation Query

External Email - Use Caution Hi I am working in Freesurfer for subcortical segmentation of brain, I did segmentation of a volume and I got around 45 regions. Is it possible that I could customize the regions I want or number of segments that I want? Thank You Regards *Fariha Mu