Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

External Email - Use Caution Thanks for sharing, Mark. One little comment: when you resample the posteriors (which are soft segmentations), why not using linear interpolation? By doing so, you ensure that the sum of the posteriors at a given voxel is still 1 (as it should). Cheer

[Freesurfer] inherent smoothing

External Email - Use Caution Dear Doug, I'd like to determine the inherent smoothing of ?h.thickness in my sample. What is the best way to do this? Thanks, -joost ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.n

Re: [Freesurfer] Longitudinal hippocampal subfields analysis problem

External Email - Use Caution Is it possible that it ran out of memory? Andrew, what do you think? -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of

Re: [Freesurfer] problem using mri_vol2label for subcortical regions

External Email - Use Caution Thank you. However I don’t know how to open the file .dms you sent me. I have tried several ways but unsuccessfully. Could you please tell me how to open files with this extension or maybe send me the file with another extension? Best regards Lucia

Re: [Freesurfer] Longitudinal hippocampal subfields analysis problem

I’m not sure. How long do these runs usually take Eugenio? I’m noticing that the process only used 9% of the cpu, which is odd since it ran for 10+ hours Andrew From: "Iglesias Gonzalez, Eugenio" Date: Tuesday, May 8, 2018 at 4:18 AM To: FS Help Cc: "Hoopes, Andrew" Subject: Re: [Freesurfer]

Re: [Freesurfer] Longitudinal hippocampal subfields analysis problem

External Email - Use Caution It depends heavily on the number of time points… I’d say ~20 mins per time point and side. -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

Re: [Freesurfer] transforming functional volumes to MNI without resampling

External Email - Use Caution Alright thanks, mri_coreg looks a little better than bbregister. But similar to bbregister, using 6 dof results in a brain that is a little too small and using 12 dof has both scaling and translation issues. What would be the way to use CVS? I tried

Re: [Freesurfer] FSGD design for multi-centre study

External Email - Use Caution Ah, I think I understand now, thanks. I've attached my contrast and FSGD file to confirm. In the FSGD file, the format for the classes are __. Please let me know. Thanks again, Colleen On 2018-05-04 09:49, C.P.E. Rollins wrote: Hi, Sorry for comin

Re: [Freesurfer] inherent smoothing

If you run a group analysis, there will be a fwhm.dat file with the estimate of the Gaussian full width half max. The smoothess is not Gaussian, but it gives a measure. Does that work? On 05/08/2018 04:20 AM, Joost Janssen wrote: > > > Dear Doug, > > I'd like to determine the inherent smoothing

Re: [Freesurfer] FSGD design for multi-centre study

That looks right for DOSS On 05/08/2018 11:56 AM, C.P.E. Rollins wrote: > External Email - Use Caution > Ah, I think I understand now, thanks. I've attached my contrast and > FSGD file to confirm. In the FSGD file, the format for the classes are > __. > Please let me know. > > Thanks again, > C

Re: [Freesurfer] transforming functional volumes to MNI without resampling

Those CVS images look about right to me for CVS, so I don't think you've done anything wrong. You could do the reg in two parts: (1) run mni152reg to register the anatomical to the mni152, and (2) run bbregister (6dof) to register the fMRI to the anatomical. Then concatenate them into one regis

Re: [Freesurfer] -qcache in recon-all commnd

Yes, I think so On 05/07/2018 10:35 PM, Alexopoulos, Dimitrios wrote: > External Email - Use Caution > > I ran 'recon-all -all -hires -qcache' on several datasets. I made numerous > edits of the brainmansk.mgz (for dura removal) and added control points and > want to rerun with the cha

Re: [Freesurfer] problem using mri_vol2label for subcortical regions

Did I send a .dms file? It should just be a binary On 05/08/2018 04:25 AM, Lucia Billeci wrote: > > > Thank you. However I don’t know how to open the file .dms you sent me. > I have tried several ways but unsuccessfully. Could you please tell me > how to open files with this extension or maybe

Re: [Freesurfer] mri_vol2surf

External Email - Use Caution Hi, I figured that part out: I can't load surfaces as volumes in freeview, but rather i need to load them as an overlay to the subject white, or pial surfaces. I have another question for which I can't find an answer to. After registering myelin maps

Re: [Freesurfer] -cw256 flag in recon-all

External Email - Use Caution El 2018-05-07 19:54, Douglas N. Greve escribió: > It will always apply it. If your data are 256 anyway, it will not have > an effect. If your data are <256, then it will have some small effects > > > On 05/03/2018 04:30 AM, JAVIER ROJO MUÑOZ wrote: >>

[Freesurfer] recon-all(about Installation' command) error

External Email - Use Caution Hello, Freesurfer Developer when I run the 'Test your FreeSurfer Installation' command (Example1~Example3) (https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall) I got the following errors pop up like this: Sorry for I'm a beginner.. Thank