Re: [Freesurfer] Highlighting single atlas structures in freeview

External Email - Use Caution Hi Andrew, Thank you very much for this, I will give this a try when I next have access to that PC, which will unfortunately not be very soon. Until then, since the task I set out to do is quite straighforward, I was wondering if there is a workaround

Re: [Freesurfer] FSFAST poor registration

External Email - Use Caution Hi Douglas Thanks for the response. No, some of the registrations are fine. Some are close, but not perfect, while others are very bad. I've checked the subjectname file for some subjects with poor registration (eg 20_101), and they are correct. Tha

[Freesurfer] Double cursors when viewing inflated surfaces

External Email - Use Caution Hi, When I load my surface overlay (sig.mgh output file from GLM analysis) onto fs average lh inflated surface, I see two cursors when looking at the inner side of the brain. When i click the outer side, only one cursor shows. I have used this com

Re: [Freesurfer] FSFAST poor registration

External Email - Use Caution I meant some are nearly perfect. On Wed, Jan 23, 2019 at 11:49 AM Keri Woods wrote: > Hi Douglas > > Thanks for the response. > > No, some of the registrations are fine. Some are close, but not perfect, > while others are very bad. > > I've checked t

[Freesurfer] correction for multiple comparison: simulation vs grf vs cache

External Email - Use Caution Hi Dr Greve, I would like to correct surface based analyses of PET data for multiple comparisons. I ran group comparisons in three spaces. left and right hemispheres and subcortical. I used the method --cache in mri_glmfit-sim to correct the analyses

Re: [Freesurfer] Highlighting single atlas structures in freeview

External Email - Use Caution PS: I guess this is possible in older versions as well based on figures in older papers (such as Fig 1 in this one), that show certain ROIs on a blank fsaverage, just as I aim t

[Freesurfer] move statistical map onto the cerebellum surface

External Email - Use Caution Dear FS experts, I ran surface based PET analysis on subcortical regions. Then corrected the results for multiple comparisons using the method --grf in the command mri_glmfit-sim. I can visualize the output of multiple comparisons (i.e. the file gr

[Freesurfer] Functional connectivty walkthrough step 8 error

External Email - Use Caution Hi Dr Greve, Attached is the log file. On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Can you send the full terminal output and/or the log file? > > On 1/22/19 2:53 PM, Amrita Bedi wrote: > > > > Exte

Re: [Freesurfer] "slides" link is not working

try this one http://surfer.nmr.mgh.harvard.edu/pub/docs/GLM.pptx On 1/22/19 7:47 PM, Peters, Douglas G wrote: > > External Email - Use Caution > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples > > > Error Message: > > > Not Found > > The requested URL /pub/docs/freesurfer.group

[Freesurfer] Smoothing before or after PALM (and results conversion for Surf Ice)

External Email - Use Caution Hello FS experts and enthusiasts, Thus far, I have used mri_concat to make 4D files of subjects' lh.thickness.fwhm15.fsaverage.mgh files to be used as input for palm. The results maps are of the .mgz format. I can convert these to .nii using mri_conver