[Freesurfer] Initializing FreeSurfer's recon-all with rigid registration

External Email - Use Caution Hi, How do I concatenate the resulting recon-all transform with another rigid transform to produce a single transform? I have the aseg.nii.gz (generated from the T1w image in T1w space) output label in the atlas space and I would like to transform

Re: [Freesurfer] aparc a2009s stats ROI names don't match ColorLUT for FS 6.0

Hi Don, Thanks for pointing this out. The stats labels were being taken from an older lookup table embedded in the aparc atlases. Putting together a fix for this in the development version now. If it helps, I've attached updated LUTs as well as a simple 5.3-to-6.0 label name translation table.

[Freesurfer] Neuroimaging programmer job opening at Mayo Clinic

External Email - Use Caution The Mayo Clinic Aging and Dementia Imaging Research Lab is an international leader in studies of Alzheimer's Disease and Related Dementias. IT staff from the Research Application Solutions (RAS) Unit provide data management and processing

[Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine

Hello experts, I've recently run into a case the gtmstats uptake (reference region: cerebellum) for the pericarlcarine ROI's are as low as 0.40, however computing the voxel wise mean using input.rescaled.nii.gz and mgx.ctxgm.nii.gx and aux/seg.nii.gz, the values are closer to 1, as expected: |

Re: [Freesurfer] overlay threshold in freeview

HI Rachele, You can set overlay threshold from the command-line like this: freeview -f lh.inflated:overlay=overlay_file:overlay_threshold=low,high More information about threshold setting can be found by: freeview -h Best, Ruopeng On 3/10/20 11:29 AM, Rachele Sanfelici wrote:

[Freesurfer] overlay threshold in freeview

External Email - Use Caution Dear Freesurfer experts, I created .mgh files from a dimensionality reduction analyses (similar to parcels from a known parcellation). These matrices have low values near to 0. When I overlay each of the .mgh file in freeview, it gets automatically

Re: [Freesurfer] aparc a2009s stats ROI names don't match ColorLUT for FS 6.0

External Email - Use Caution Hi, I also have code that parses the stats files and noticed this a while ago, a short thread is here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64090.html Basically just the names changed, the data is identical, so I just

[Freesurfer] Group analysis with qdec: qcache change this?

External Email - Use Caution Dear freesurfer experts, Before running group analysis in qdec is necessary run the qcache command over all subjects but, does this command change some segmentation file (eg. rh/lh Pial or white surface) or other importants file? We would also like to

Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

External Email - Use Caution Maybe Doug or Bruce should comment on that, but afaik that should not affect your analysis at all: recon-all will resample your data to 256x256x256 (as part of creating what FreeSurfer calls the 'conformed' version of the image) anyways. The error