Re: [Freesurfer] no aseg.stats after recon-all -all?

No, it doesn't exist (lh nor rh) Can I get it somewhere? From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: vrijdag 18 december 2015 18:28 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no aseg.stats after r

[Freesurfer] Masks on tksurfer

Hi list, I would like to make a mask of a significant cluster after FDR correction on sig.mgz (FS-FAST analysis). I'm using tksurfer and its options (custom fill, new label from marked) but I have some difficulties to save the mask. Could you suggest me a reference/guide page, please? Thanks S

[Freesurfer] R: R: Re: R: Re: FDR in FS-FAST

I have run mri_fdr --help but I obtained this warning: /Applications/freesurfer/bin/mri_fdr: Permission denied. I would also ask you if is possible to threshold the FDR map (p<0. 05), eliminating clusters < 5 voxels. Thanks Stefano >>Messaggio originale >>Da: gr...@nmr.mgh.harvar

Re: [Freesurfer] move annotations across hemispheres

That version works! I actually already was using that version since I downloaded a recent dev version of freesurfer. My difficulty ended up being specifying the correct source-target registrations. For future reference, the following command moves rh annotations in subject's xhemi directory to the

Re: [Freesurfer] Tracula: trac-all prep badly formed if error

Hi Katherine - I believe that it's because you define bvecfile and bvalfile as lists of 2 file names each. Both bvecfile and bvalfile accept a single file name. In bveclist you can enter as many gradient tables as input volumes. Best, a.y On Thu, 17 Dec 2015, Katherine Damme wrote: Here i

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

Many thanks ! Matthieu Le 18 déc. 2015 18:27, "Douglas Greve" a écrit : > You'll see several files that begin with mgx: > mgx.ctxgm.nii.gz - pvc'ed cortex gm only > mgx.subctxgm.nii.gz - pvc'ed subcortical gm only > mgx.gm.nii.gz - pvc'ed all gm > > On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:

Re: [Freesurfer] no aseg.stats after recon-all -all?

Does //usr/local/freesurfer5/average/lh.DKTatlas40.gcs exist? / On 12/17/15 5:53 PM, Schweren, LJS (med) wrote: Dear Freesurfer experts, I'm trying to get BrainSeg for 5 subjects. I'm running the following commands: /for scan in ... do cd $SUBJECTS_DIR recon-all -all -subjid $scan done/ It

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

You'll see several files that begin with mgx: mgx.ctxgm.nii.gz - pvc'ed cortex gm only mgx.subctxgm.nii.gz - pvc'ed subcortical gm only mgx.gm.nii.gz - pvc'ed all gm On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote: Hello Douglas, I have run mri_gtmpvc with static PET images using the following co

Re: [Freesurfer] move annotations across hemispheres

Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg.mac On 12/18/15 10:53 AM, Peggy Skelly wrote: I downloaded the file, but cannot get it to run. I changed permissions to make it executable, but I get -bash: ./mris_apply_reg: cannot execute binary file

Re: [Freesurfer] move annotations across hemispheres

I downloaded the file, but cannot get it to run. I changed permissions to make it executable, but I get -bash: ./mris_apply_reg: cannot execute binary file I'm using Mac OS X 10.11 Peggy On Thu, Dec 17, 2015 at 4:24 PM, Douglas N Greve wrote: > Use mris_apply_reg. You can get a copy here > >

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

Hello Douglas, I have run mri_gtmpvc with static PET images using the following command : mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg gtmseg.mgz --reg register.dof6.lta --default-seg-merge --mgx 0.01 --o gtmpvc.output In the output directory "gtmpvc.output" where is the partial vol