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

Hi Matthieu, sorry for the delay On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote: > External Email - Use Caution > > Dear Freesurfer's experts, > > I tried to use PETSurfer to correct partial volume effect on my FDG PET > images, testing both Muller-Gartner and RBV corrections. > > I ra

Re: [Freesurfer] Beta extraction

Use something like mri_segstats --seg ocn.mgh --i beta.mgh --excludeid 0 --avgwf beta.clusters.dat See mri_glmfit-sim --help for more info on the OCN file and mri_segstats --help for info on the avgwf file On 11/29/2018 04:40 PM, Jahan, Bushra wrote: > I am wondering how to extract beta values

Re: [Freesurfer] hippocampal subfield question

External Email - Use Caution Dear Arkadiy, Technically you should do it after, but the changes will be tiny, so it’s probably fine to do it before (as long as you’re consistent across subjects). Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Im

[Freesurfer] hippocampal subfield question

Dear Experts, I was wondering if it is important to wait for the manual edits to be done on a dataset before running hippocampal subfield analyses. I believe that recon-all processing is sufficient, and edits can be done in parallel. But wanted to make sure that they will not affect the nuclei/

[Freesurfer] Beta extraction

I am wondering how to extract beta values from the clusters of task functional data, particularly output of the multiple comparisons correction? Aava Jahan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailm

Re: [Freesurfer] Pial surface error

Hi Miguel the only way to rule out a consistent error that could induce a bias it to visually inspect the results. That said, the image you show looks fine. The white arrows are pointing to hippocampal gm, which is not supposed to be captured by the surfaces. We don't include these regions in

Re: [Freesurfer] Pial surface error

External Email - Use Caution Hi Bruce, Effectively, I was referring to the big chunck of gray matter that is missing from surfaces (I attached another image). I have decided to revise the pial and white matter segmentation again because in the study that I am carrying out I found

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

External Email - Use Caution Dear Freesurfer's experts, I tried to use PETSurfer to correct partial volume effect on my FDG PET images, testing both Muller-Gartner and RBV corrections. I ran the commands specified in PETSurfer website and used the two following commands for b

[Freesurfer] Neuroimaging staff scientist position

External Email - Use Caution The Department of Psychiatry at the University of Minnesota is seeking an experienced MR Neuroimaging Analyst to join our Discovery Program initiative. The successful candidate will join a team that will use MR brain imaging and other methods to advance

Re: [Freesurfer] ?????? ?????? ?????? Triangular mesh sampling problem

Yes, it can. You can also use mris_apply_reg, which is probably easier to use. Run it with --help to get more info On 11/29/2018 12:18 PM, 1013364183 wrote: > > ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution > > Dear Bruce, > ?0?2 ?0?2I want to know if mri_surf2surf can map high res

Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

External Email - Use Caution Hi Bram, I finally did it, thank you for your help, and sorry about my noobity! ftp> put BE2.tar.xz local: BE2.tar.xz remote: BE2.tar.xz 200 PORT command successful. Consider using PASV. 150 Ok to send data. 226 Transfer complete. 61572 bytes sent in

[Freesurfer] ?????? ?????? ?????? Triangular mesh sampling problem

External Email - Use Caution Dear Bruce, I want to know if mri_surf2surf can map high resolution meshes to low resolution meshes or low resolution meshes to high resolution meshes. If so, what should be done specifically. Thanks in advance yours yujunjie

Re: [Freesurfer] longitudinal analyses after lesion segmentation

External Email - Use Caution Sorry, I was thinking that my question may not have been very clear. Baseline T1 images were rigidly registered to 1mm^3 MNI template and then all follow-up images were rigidly registered to the individual's baseline T1. My question is whether I could s

Re: [Freesurfer] ?????? ?????? Triangular mesh sampling problem

yes, sorry, I can't think of a way to do it with existing binaries (maybe someone else can?). The only alternative I can think of is to use the various fsaverage meshes instead of the subject meshes. Then the "projection" becomes trivial as the lower res meshes are just the first N vertices in

Re: [Freesurfer] ?????? Triangular mesh sampling problem

Hi yujunjie there is source code in mrishash.c and mrisurf.c for this kind of thing, e.g. MHTfindClosestVertex. We don't have any complete code that will do exactly what you want though, so you will have to poke around in the source yourself I'm afraid. cheers Bruce On Thu, 29 Nov 2018, 1

Re: [Freesurfer] Correspondence between regions of Harvard-Oxford & DKT atlases

Hi Tudor sorry, I don't think there is a direct correspondence. Is the Oxford atlas even on the surface? cheers Bruce On Thu, 29 Nov 2018, Tudor Popescu wrote: External Email - Use Caution Dear FreeSurfer experts, I have a network of interest described in terms of regions

Re: [Freesurfer] Pial surface error

Hi Miguel, not sure exactly where you mean, but the big chunk of gray that is missing from the surfaces is probably hippocampus (so not a problem, since it is not neocortex) cheers Bruce On Thu, 29 Nov 2018, Miguel Ángel Rivas Fernández wrote: External Email - Use Caution  

Re: [Freesurfer] trouble in manual editing of pial surface

Hi Kyung it's impossible to tell what is going on from a single slice. Typically the pial surface doesn't settle at the correct spot because the underlying white is also off. If you tar and gzip the entire subject dir and upload it to out ftp site together with a set of coordinates that you t

Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

I can't see any of your data. The problem is likely that you are feeding the full file path. Try using just the file name without the path. First cd to your data directory, then log on to the freesurfer FTP file exchange and follow the instructions on our wiki. Thanks for your patience! I'll be

[Freesurfer] longitudinal analyses after lesion segmentation

External Email - Use Caution Hi FreeSurfer experts: I hope you are well. I need to segment quite a few longitudinal T1 scans from patients with multiple sclerosis. A colleague has applied an automated lesion segmentation algorithm to segment and fill the lesions. During this proce

[Freesurfer] ?????? Triangular mesh sampling problem

External Email - Use Caution Dear Bruce, I want to do the following, which source code should we use, and if so, can you send me a connection? We now have high and low resolution images, we want to resample each triangular surface mesh generated from low-resolution data onto

Re: [Freesurfer] lack of convergence when analyzing tbss-data with FreeSurfer's lme code

External Email - Use Caution Dear Freesurfer Experts I am trying to analyse tbss data using the FS lme module in Matlab. I converge the data from the tbss skeleton into matlab format and estimate an lme model with FA as the dependent variable. The problem has been that the lme a

[Freesurfer] Correspondence between regions of Harvard-Oxford & DKT atlases

External Email - Use Caution Dear FreeSurfer experts, I have a network of interest described in terms of regions from the Harvard-Oxford atlas. I would next need to describe this network in terms of regions from the DKT (Desikan–Killiany–Tourville) atlas. I have not found hints o