Re: [Freesurfer] Version 5.3 vs. Version 6

Dear Larissa, What do you mean by " anatomical ROI Analysis "? Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On 08/11/2019, 22:21, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Larissa Bechtle" wrote:

Re: [Freesurfer] Version 5.3 vs. Version 6

Hi Larissa I think we need more details. What do you mean you used 6 for anatomical ROI analysis? On the same subjects? Did you rerun them? Sorry, I can't figure out exactly what you are doing cheers Bruce On Fri, 8 Nov 2019, Larissa Bechtle wrote: >External Email - Use Caution > >

[Freesurfer] Version 5.3 vs. Version 6

External Email - Use Caution Hey everybody, i have a question concerning version 5.3 and 6.0 of freesurfer. Originally I used 5.3 for volumes and thickness as well as for a group analysis. Later I used 6.0 for an anatomical ROI Analysis. I read online that doing so should be

Re: [Freesurfer] Inconsistent Morphology Output

or start by sending us the recon-all.log from the two runs On Fri, 8 Nov 2019, Chen, Christine wrote: External Email - Use Caution Hello,   My lab has been running T1 (MPRAGE) data through run_subject (uses recon-all, autorecon, mris_volume and mris_wm_volume) then

Re: [Freesurfer] Inconsistent Morphology Output

Hi Christine maybe you can tar and gzip a subject that has been run twice with different results and file drop it or ftp it to us? cheers Bruce On Fri, 8 Nov 2019, Chen, Christine wrote: External Email - Use Caution Hello,   My lab has been running T1 (MPRAGE) data

Re: [Freesurfer] flat maps in native space

Hi Bruce Thanks for your reply. Well, two of my subjects have this problem. I have two subjects with correct flattened maps and for 3 other subjects "the mris_flatten" is still running. I attached the directory and I would appreciate if you could please take a look. Thanks MOna Zahra (Mona)

Re: [Freesurfer] flat maps in native space

Hi Mona that is pretty strange looking. Is the data somewhere local that we can take a look at it? I would guess that one of the cuts left a connection around, but would need to look at it to tell. Have you flattened other subjects successfully? cheers Bruce On Fri, 8 Nov 2019,

[Freesurfer] Inconsistent Morphology Output

External Email - Use Caution Hello, My lab has been running T1 (MPRAGE) data through run_subject (uses recon-all, autorecon, mris_volume and mris_wm_volume) then through run.r (pulls freesurfer.r and pedbirn.r) using the Desikan-Killiany atlas to output measures of cortical

[Freesurfer] FDR for aseg

External Email - Use Caution Dear Freesurfer experts, I run the command mri_glmfit --table aseg.volume.stats.dat --fsgd GLM7.fsgd dods --C contrasts6.mtx --glmdir NFL.aseg.glmdir This gave me the output sig.table.dat. Is there a way to implement an FDR to this analysis in

[Freesurfer] Question about convert fsaverage to fsaverage5

External Email - Use Caution Dear Fs Developers Hi, I am new to freesurfer, after I ran the recon-all command, I want to align the individual surface to fsaverage5 space. and then extracted the cortical thickness of each vertex. Should I use mri_surf2surf to do it, What's the