Re: [Freesurfer] Using a cluster as an ROI for further analysis

External Email - Use Caution For instance, if there is any way to extract spatial location of cluster X1 and use this location to extract thickness values of all the subjects from P2 and P3, that way I can perform two-sample t-test. I am not sure if that's feasible and if so, then

[Freesurfer] Using a cluster as an ROI for further analysis

External Email - Use Caution Hi experts, I found a cluster X1, which showed significant difference in cortical thickness between two groups C1 and P1, determined using mris_preproc, mri_surf2surf and mri_glmfit commands. I am interested in determining if the same cluster X1 has s

Re: [Freesurfer] coregistering with bbregister

On 08/13/2018 03:02 PM, Ben M wrote: > > External Email - Use Caution > > Hi Doug, > > Thank you very much for your response, it helped me a lot. > I checked the examples of mri_vol2vol and for functional-to-structural > registration I think I should do > > $ bbregister --t2 --lta /data/

[Freesurfer] TRACUAL eddy_correct Usage

External Email - Use Caution Hello, I notice that within TRACULA 6.0 that eddy_correct is used for the eddy current correction. This is an older tool as compared to eddy, is there a reason that eddy_correct is still used? Have you done cross comparisons between eddy_correct and ed

Re: [Freesurfer] Untar and sh files in dev version

And the downloads have finished successfully each time? Are you definitely grabbing the tarball from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-linux-centos6_x86_64-dev.tar.gz? Andrew From: on behalf of Schumman Resonance Reply-To: FS Help Date: Saturday, August 1

Re: [Freesurfer] Stats2table_bash.sh script

asegstats2table is a python2 script, and you are likely running it with python3. Try running the script with “python2” prepended to the command: python2 asegstats2table --subjects $list --meas volume --skip --statsfile wmparc.stats --all-segs --tablefile wmparc_stats.txt best, Andrew From: o

Re: [Freesurfer] coregistering with bbregister

External Email - Use Caution Hi Doug, Thank you very much for your response, it helped me a lot. I checked the examples of mri_vol2vol and for functional-to-structural registration I think I should do $ bbregister --t2 --lta /data/bbregister/reg.lta --mov /data/mean_func.nii.gz -

Re: [Freesurfer] Outlier voxels after partial volume correction using Petsurfer

External Email - Use Caution Hi Doug, it is kinetic modelling, not uptake. Thank you.  On Monday, August 13, 2018, 10:36:13 AM GMT+1, Shane Schofield wrote: Hello Petsurfers! A few of my subjects ended up with vertices that had outlier PET values after I followed the

Re: [Freesurfer] Outlier voxels after partial volume correction using Petsurfer

Is this a kinetic modeling study or just an uptake? On 08/13/2018 05:36 AM, Shane Schofield wrote: > > External Email - Use Caution > > Hello Petsurfers! > > A few of my subjects ended up with vertices that had outlier PET > values after I followed the PetSurfer steps. Most of the binding

Re: [Freesurfer] fsaverage6 ?h.cortex.flat.patch files

Thank you! On Sun, Aug 12, 2018 at 6:49 PM, Bruce Fischl wrote: > oh, maybe we never got around to writing a write_patch.m. We'll put one > together and send it to you > Bruce > > On Sun, 12 Aug 2018, Dinicola, Lauren wrote: > > Hi Dr. Fischl, >> Thank you so much for this response. This is a gr

[Freesurfer] Outlier voxels after partial volume correction using Petsurfer

External Email - Use Caution Hello Petsurfers! A few of my subjects ended up with vertices that had outlier PET values after I followed the PetSurfer steps. Most of the binding potentials are in the range of 0 - 3. Looking at the histogram though there are a couple of vertices wi