Re: [Freesurfer] QC Montages error

Hello, I have tried troubleshooting this problem in various ways, but I am still not able to figure out the problem. Does anyone have any idea? Thank you! I am getting an error when using a script that combines these 3 actions: preproc.sh std_map_qc_montages.bash put_tpef.bash

Re: [Freesurfer] Corrections with white matter

Good morning Bruce, Looking back to the Slice No.82 I am attaching now the brainmask for this slide. While switching between brainmask and wm.mgz my opinion is that  I shouldn't  add any vertex on the wm.mgz on the right hemisphere.  Is this correct? I am not sure about the bottom part. It

Re: [Freesurfer] Attachement for the Corrections with white matter

Hi Antonella, the surfaces look fine. As for the cerebellum, I don't think the watershed did that - it's too even. What does the orig.mgz look like? cheers Bruce On Thu, 14 Jul 2011, Antonella Kis wrote: Good morning Bruce, Looking back to the Slice No.82 I am attaching now the

[Freesurfer] Choice of input surface for mris_make_face_parcellation

Hi Bruce, I'm playing around with mris_make_face_parcellation, and I'm looking for guidance on choosing the input surface. In the usage message, the example that is given says: example: mris_make_face_parcellation lh.inflated $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot The choice of the

Re: [Freesurfer] Choice of input surface for mris_make_face_parcellation

Hi Miichael, oh, that was definitely a mistake. You want to use either ?h.sphere if you want it to be uniform in subject space or ?h.sphere.reg if you want the parcels to correspond across subjects. Sorry for the bad advice. Bruce On Thu, 14 Jul 2011, Michael Waskom wrote: Hi Bruce, I'm

[Freesurfer] Saving all the edits

Hi Bruce, I promise this is my last question for today. I finished all the wm edits and I understood from the tutorial that I have to save this work. I understood that by default tkmedit will edit on the main volume loaded, if the wm volume is loaded as your aux volume (which is my case), I

Re: [Freesurfer] Saving all the edits

yes, but you can double check by doing the save and bringing up a second instance of tkmedit with wm.mgz before exiting the first to make sure the edits are in it On Thu, 14 Jul 2011, Antonella Kis wrote: Hi Bruce, I promise this is my last question for today. I finished all the wm edits

Re: [Freesurfer] Tracula - error in pre-proc

Hi Priti, Thank you for your help. I get through the fslroi successfully by setting the nb0 variable. The lowb.nii.gz looks fine. However, when the process comes to bet, there's another error prompt for lowb.nii.gz.hdr. fslmaths

[Freesurfer] tracula pub

i thought at one time i saw a paper on the tracula methods, maybe it was the better tractography allignment paper. is there a paper specifically about the global tractography method and related, or an mit tech. report or anything thanks greg ___

Re: [Freesurfer] Tracula - error in pre-proc

Hi Phoebe - I don't have permission to access your files, but do you have FSLOUTPUTTYPE set to anything other than nifti by any chance? a.y On Thu, 14 Jul 2011, pho...@nmr.mgh.harvard.edu wrote: Hi Priti, Thank you for your help. I get through the fslroi successfully by setting the nb0

Re: [Freesurfer] tracula pub

Hi Greg - The paper has been with anonymous reviewers for the last 4 months :( a.y On Thu, 14 Jul 2011, GREGORY R KIRK wrote: i thought at one time i saw a paper on the tracula methods, maybe it was the better tractography allignment paper. is there a paper specifically about the global

Re: [Freesurfer] tracula pub

Hi Greg, I think the tracula folks might have gotten their original code from Saad Jbabdi, but then the code-bases have probably diverged. (My apologizes if this is not correct!). Here is Saad's publication on global tractography: http://www.ncbi.nlm.nih.gov/pubmed/17543543/ Peace, Matt.

Re: [Freesurfer] tracula pub

Yes, Matt is correct Bruce On Jul 14, 2011, at 10:52 PM, Matt Glasser m...@ma-tea.com wrote: Hi Greg, I think the tracula folks might have gotten their original code from Saad Jbabdi, but then the code-bases have probably diverged. (My apologizes if this is not correct!). Here is

Re: [Freesurfer] tracula pub

In fact it's a combination of Saad's likelihood term with an anatomical prior term that uses diffusion and anatomical data. On Thu, 14 Jul 2011, Matt Glasser wrote: Hi Greg, I think the tracula folks might have gotten their original code from Saad Jbabdi, but then the code-bases have

Re: [Freesurfer] retinotopy manual?

I think you can load overlays into freeview. After that it is a matter of setting the thresholds right. I think we have a fix for the sliver problem. doug On 7/14/11 10:26 PM, Babak wrote: Thanks Doug, I fixed that problem and completed the analysis process, but tksurfer doesn't work on my

Re: [Freesurfer] retinotopy manual?

I think the sliver problem means you need to update your video driver Bruce On Jul 14, 2011, at 11:08 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: I think you can load overlays into freeview. After that it is a matter of setting the thresholds right. I think we have a fix for the