[Freesurfer] Pial surface does not follow the gray/csf boundary

External Email - Use Caution Dear FreeSurfers, I’m trying to create surface reconstructions for some small monkey scans (about half the size of a rhesus macaque). The white surfaces look fine, but I can’t seem to get the pial surfaces to extend properly to the edge of the gray

[Freesurfer] "Bad CPU type in executable" error - Qdec

External Email - Use Caution Dear Ladies and Gentlemen, I am trying to run „Qdec“ which worked pretty well until I installed the new version of macOS Catalina (version 10.15.1). Since then, I always receive an error called "Bad CPU type in executable“. I am working with Freesurf

Re: [Freesurfer] selxavg in native space vs fsaverage space

Hi Doug Thanks a lot for your reply. what I mean by native space, is to register each subject's functional data on their own anatomical data. yes, I was using --surf self in my preprocessing and mkanalysis, but since I was not using any smoothing, fwhm=0 in both native and fsaverage analysis, I

Re: [Freesurfer] flat maps in native space

Thanks a lot for your reply Doug. I will re-do my recon as you said. Do you think the "blurriness" might be because of inadequate inflating of the surface? My expert option file was : mris_inflate -n 15 -w 10. In addition to your recommendations, do you think I need to increase "n"? Thanks Mona

Re: [Freesurfer] (no subject)

External Email - Use Caution Thanks. unfortunately I get an error message when I use the --aseg flag for BN_Atlas_subcotex.mgz but even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg .../fs_all_subjects/xyz/mri/aseg.mgz The file BN_Atlas_subcotex.mgz was create

[Freesurfer] Creating intermediate surfaces between white and pial?

External Email - Use Caution Dear FreeSurfer experts, I know that I can sample data from a certain depth between the white and pial surfaces, but is there any way to create an intermediate surface file (i.e., mesh)? I would like to create, e.g., a surface file that is at 10% of

Re: [Freesurfer] (no subject)

Hi Boris can you send us the full command line and screen output of the commands that are failing? cheers Bruce On Thu, 12 Dec 2019, Boris Rauchmann wrote: External Email - Use Caution Thanks. unfortunately I get an error message when I use the --aseg flag for BN_Atlas_s

Re: [Freesurfer] Creating intermediate surfaces between white and pial?

Hi Tim mris_expand -thickness ... should do the trick. If you specify -thickness it will read in the ?h.thickness file and interpret the argument as a percentage of thickness, which is what you want I think cheers Bruce On Thu, 12 Dec 2019, Tim Schäfer wrote: External Email - Us

Re: [Freesurfer] Creating intermediate surfaces between white and pial?

External Email - Use Caution Hi Bruce, thanks, that's exactly what I was looking for! Best, Tim > On December 12, 2019 at 5:39 PM Bruce Fischl > wrote: > > > Hi Tim > > mris_expand -thickness ... > > should do the trick. If you specify -thickness it will read in the > ?

Re: [Freesurfer] "Bad CPU type in executable" error - Qdec

Qdec, as well as tksurfer and tkmedit, are no longer supported on mac OS 10.15+ since they are 32-bit binaries. These programs are also no longer maintained in our development distribution, so you will have to use a different OS or move to a command line analysis. Best Andrew _

Re: [Freesurfer] (no subject)

External Email - Use Caution My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/mydir subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading l

Re: [Freesurfer] flat maps in native space

Hi I was trying to run recon-all.v6.hires, but it doesn't give me permission. I am using a linux computer in Martinos center. Could you please let me know how to solve it? Thanks Mona [bee:Mona] (nmr-stable6-env) ./make_recon.sh osre_7T_all 009 ./make_recon.sh: line 7: /usr/local/freesurfer/sta

Re: [Freesurfer] Group analysis with gray matter volume in FS 6.0

When you say "gray matter volume", does it mean you are trying to do a VBM-style analysis? You can't do VBM with FS. You can do an analysis of cortical GM volume in a similar way. When you run mris_preproc, specify "volume" as the --meas On 12/12/19 12:58 PM, Marisa Cathryn Ross wrote: > >

Re: [Freesurfer] flat maps in native space

It is hard to say. The v6 hires stream does not work very well. On 12/12/19 10:38 AM, Nasiriavanaki, Zahra wrote: > Thanks a lot for your reply Doug. > I will re-do my recon as you said. > Do you think the "blurriness" might be because of inadequate inflating > of the surface? My expert option fi

Re: [Freesurfer] (no subject)

Are you running this from 1122/mri and is BN_Atlas_subcotex.mgz in that folder? On 12/12/19 12:57 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg > BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz > SUBJEC

Re: [Freesurfer] Study specific template

When you say that you looked at the labels/segmentations and that nothing looked horribly wrong, would that mean that the labels are accurate and that they are not really outliers? On 12/5/19 7:26 PM, Joshi, Nandita wrote: > External Email - Use Caution > > Hi Dr. Greve, > > Thanks so m

Re: [Freesurfer] (no subject)

External Email - Use Caution yes to both. I always get the error ERROR: cannot find aseg... On Fri, Dec 13, 2019 at 12:58 AM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Are you running this from 1122/mri and is BN_Atlas_subcotex.mgz in that > folder? > > On 12/12/1