Re: [Freesurfer] Error in running make_average_subject

External Email - Use Caution Hello Bruce, Greve and Emanuel, I have an identical problem. Have you found a solution to this issue? I'm attaching my recon-all.log, as well, in case you need it. Thank you! Marta On Fri, Dec 14, 2018 at 1:44 PM Emanuel Alvaredo wrote: > E

[Freesurfer] wm and vcsf nuisance regressors

Dear Freesurfers Hi I am using white matter and CSF external nuisance regressors in my mkanalysis-sess. However, when I make these regressors, I use -mean in fcseed-config command, and so the .dat files only have one column (the mean values, I assume). I looked up in the freesurfer archive

[Freesurfer] Help with finding which functional areas house certain electrodes

External Email - Use Caution Good afternoon, We want to find the functional areas where each electrode is located in patients. At present, we are finding the electrode RAS coordinates manually using CT-MRI co-registration. We are then manually searching for these locations in Free

Re: [Freesurfer] Issues parcellating with a custom atlas

External Email - Use Caution Hi just following up on the question... .does anyone have an idea about why the same two parcellations get dropped when swapping the atlases out and making an aparc+aseg On Mon, 14 Jan. 2019, 11:17 pm Michael Sughrue Hello > > My interest is to create

Re: [Freesurfer] mris_anatomical_stats input image?

Hi Stephanie specifying "pial" directs it to use the ?h.pial surfaces for e.g. surface area measurement. What information are you hoping to extract from the orig.mgz? cheers Bruce On Thu, 17 Jan 2019, Winkelbeiner, Stephanie A wrote: External Email - Use Caution Hi Freesu

[Freesurfer] mris_anatomical_stats input image?

External Email - Use Caution Hi Freesurfers, I'm using the below command to extract GM values: mris_anatomical_stats -mgz \ -cortex label/lh.cortex.label \ -f stats/lh.250.aparc.pial.stats \ -b -a 250.aparc \ -c label/colortable.ctab

Re: [Freesurfer] Exporting mean curvature indices

External Email - Use Caution Never mind, I just got it working by replacing "white.H" with "meancurv". Thanks. On Wed, Jan 16, 2019 at 5:32 PM Martin Juneja wrote: > Hi Freesurfer experts, > > I am interested in estimating mean curvature index for each of the 7 > networks (Yeo7

Re: [Freesurfer] convert surface-based label to volumetric space...mri_label2vol?

You can extract it with mri_binarize --i aparc+aseg.mgz --match 1027 --o ctx-lh-rostralmiddlefrontal.nii.gz 1027 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt On 1/17/19 11:31 AM, Stephanie Hare wrote: > > External Email - Use Caution > > Hi Doug, > > I converted the aparc+aseg.mgz

Re: [Freesurfer] Talairach Transform failure

The first thing to do is to check your input data to make sure that something is not really wrong. Eg, a large artifact or unusual anatomy. On 1/17/19 5:35 AM, Daniel Ferreira wrote: > > External Email - Use Caution > > Thanks Greve. Yes, I mean that the moveable is completely black. How

Re: [Freesurfer] Talairach Transform failure

External Email - Use Caution Thanks Greve. Yes, I mean that the moveable is completely black. How should I continue from here? If the registration is so far off that it is out of the field of view, what should I do next? Thanks Dani El mié., 16 ene. 2019 a las 22:54, Greve, Doug