Re: [Freesurfer] longitudinal analysis: rate of change

Hi Shannon, it is the slope of the linear fit into the thickness values (assuming the time axis is in years, else it will be mm/month or whatever). Best, Martin On Mon, 2012-08-13 at 11:55 -1000, Shannon Kogachi wrote: > Hi, > > I had a question about the rate of change (thickening in mm/year)

[Freesurfer] Radial Distance from Tessellated Hippocampus Surface

Hi Freesurfer folks, I was wondering if anyone knew an automated or semi-automated method for calculating radial distance along the longitudinal axis of the hippocampus from a surface generated by tessellating the segmentation from aseg. I know radial distance is used to examine local changes i

[Freesurfer] longitudinal analysis: rate of change

Hi, I had a question about the rate of change (thickening in mm/year) for the longitudinal processing. How is this value calculated when there are more than two timepoints per subject? Thank you! -Shannon K. ___ Freesurfer mailing list Freesurfer@nmr.mg

Re: [Freesurfer] Edits to aparc+aseg.mgz

Hi Cyrus, this may or may not be a problem. The cortical label in aseg.mgz is not used for this reason. Usually, the surface-based method will exclude the dura in these situations. Are the surfaces accurate or are they including dura as well? BTW, you should not be editing the aparc+aseg.mgz. d

Re: [Freesurfer] Tracula: pathway #7

Hi Chris - That's probably the corpus callosum forceps major or minor. It's the highest-curvature path and that makes it harder to initialize the tractography. If it looks right visually, and it took 90 tries to do that, then it's doing its job as it's supposed to :) a.y On Mon, 13 Aug 2012,

Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 10

Hi Linda, can you send the terminal output for mri_segstats? Can you also send the summary file? doug On 08/13/2012 10:59 AM, Linda Douw wrote: > Hi Doug, > > I first parcellate fsaverage5 using ico4 (all my functional data are > morphed to fsaverage5 surface): > > mris_make_face_parcellation /fs

Re: [Freesurfer] polar angle analysis with clockwise- and counterclockwise-rotating wedges

wow, that's good to know. Sounds like I need to add another hook so that people can set that parameter. doug On 08/13/2012 08:24 AM, Thomas Janssens wrote: > Hi Doug, > > It seems that, our stimulus presentation is inconsistent with the way > freesurfer processes the retinotopy clockwise and cou

Re: [Freesurfer] memory corruption when performing mri_segstats

Hi Wenjing, I don't know what is happening either . Can you tar up the aparc+aseg.nii.gz and filtered_func_data.nii.gz file can send them to me on our file drop? www.nmr.mgh.harvard.edu/facility/filedrop/index.html thanks doug On 08/

Re: [Freesurfer] mri_annotation2label problem

Hi Matt, this means that those annotation are empty (ie, have no vertices with that label). Is this the case? Can you verify that those labels actually exist for this subject? doug On 08/10/2012 03:32 PM, mn...@nmr.mgh.harvard.edu wrote: > Hello, > > I'm attempting to use a custom parcellation

[Freesurfer] Tracula: pathway #7

Hello, When I go through trac-prep, pathway #7 always takes much much longer than any of the others. And for that pathway it always displays this: INFO: Distances between consecutive points are 34 37 34 40 WARN: Could not find satisfactory control point fit - try 90 Has anyone else had this pr

Re: [Freesurfer] 3d Gaussian filter on volume

Hi John, try mri_fwhm. This was designed to measure the FWHM, but you can use it to apply a given FWHM too. doug On 08/13/2012 10:09 AM, John Papaioannou wrote: > Hi, > > I can run a 3d Gaussian spacial filter on a T1.mgz image using matlab > functions, but I was wondering if there isn't alread

Re: [Freesurfer] Problems with ICV

Hi, Bruce, I've been using FS5.1 for segmentation analysis, after I updated the mri_segstats, the ICV does not seem to change at all, only the SupraTentorial Volume changed. If I want to use ICV and SupraTenrotial Volume for my analysis, is that OK to use FS5.1, I don't see more updated version tha

[Freesurfer] Edits to aparc+aseg.mgz

Hello FreeSurfer Users, I looked for a possible solution to my problem in the Mail Archive and found this article referring to almost the exact same problem I am having: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06314.html. Basically, pieces of the subarachnoid space/pia ma

Re: [Freesurfer] Problems with ICV

Hi Laura, what version of FS are you running? The ICV is estimated using the talairach xform, and there were some problems with it in 5.1. cheers Bruce On Mon, 13 Aug 2012, Wisse, L.E.M. wrote: Dear freesurfers,   I tried to calculate ICV with FreeSurfer, but I encountered some problems.

Re: [Freesurfer] mris_fix_topology stops with two T1-s

hmmm, maybe the nonlinearities between days are too big for the registration. Bruce On Sun, 12 Aug 2012, Garikoitz Lerma Usabiaga wrote: > Many thanks Bruce, > I will choose the best one in this case. > > The command line was: > recon-all -s B_06 -qcache -measure thickness -all > (I already had

Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 10

Hi Doug, I first parcellate fsaverage5 using ico4 (all my functional data are morphed to fsaverage5 surface): mris_make_face_parcellation /fsaverage5/rh.inflated $FREESURFER_HOME/lib/bem/ic4.tri rh.ico4.annot Then I extract the waveforms using mri_segstats mri_segstats --i rh.functional.nii.gz

Re: [Freesurfer] 3d Gaussian filter on volume

Hi John you can use mri_nlfilter to do this (although it will be slower than it needs to be since it is applying a nonlinear filter, but disabling the nonlinear component of it): mri_nlfilter -n -gaussian cheers Bruce On Mon, 13 Aug 2012, John Papaioannou wrote: Hi, I can run a 3d Gaus

Re: [Freesurfer] Displaying cortical thickness changes in volume images

Dear Venkat, I believe the most straight forward way is to use your gamma volumes. For example if your first contrast is the difference between two time-points, thickness difference could be extracted with this command line: mri_convert ~/glmdir/contrast/gamma.mgh difference_thickness.mgh --frame

[Freesurfer] 3d Gaussian filter on volume

Hi, I can run a 3d Gaussian spacial filter on a T1.mgz image using matlab functions, but I was wondering if there isn't already a freesurfer script that does the same (with a FWHM input). John ___ John Papaioannou Medical Imaging Sciences Digital Mammography, CAD Mammography Department of Rad

[Freesurfer] Displaying cortical thickness changes in volume images

Dear All, I would like to display my cortical thickness chnages from longitudinal runs on my original T1-w volume images. I am wondering whether this is possible if so can anyone tell how I can do this. Thanks in advance Venkat === Please consider the envir

Re: [Freesurfer] polar angle analysis with clockwise- and counterclockwise-rotating wedges

Hi Doug, It seems that, our stimulus presentation is inconsistent with the way freesurfer processes the retinotopy clockwise and counter clockwise data. After going through the freesurfer code I found the following. The freesurfer code assumes that the wedge starts horizontally for both clockwi

[Freesurfer] Problems with ICV

Dear freesurfers, I tried to calculate ICV with FreeSurfer, but I encountered some problems. I first ran autorecon 1, 2 and 3, but I noticed afterwards that a few ICV values were really off. The values were really high and when I looked at brain.finalsurfs.mgz, the segmentation also included sk