Re: [Freesurfer] help mri_surf2vol

Thanks, it seems to work well. is there a way to have the good labels when looking on freeview the output volume. because with the freesurferColorLut it's not the good labels. or at least having the correspondence between values and labels on a .txt file or whatever ? Regards, Pierre On Thu, Apr

Re: [Freesurfer] help mri_surf2vol

I have tried with two lookup table, the freesurferColorLut one, and the simple_surface_labels2009. but none of them seems convincing. parcels look ok with the freesurfercolorlut, but label name is wrong. label name seems good with simple_surface_labels, but the value of the parcels doesn't seem to

[Freesurfer] mris_label2annot not creating annot file

Hi, I was using the mris_label2annot to create .annot file before but now couldn't figure out why the .annot file is not being created. The mris_label2annot is giving the below output but not creating the label files. My label file names are as node-lh-xx.label and the content of ctab file as b

[Freesurfer] REPOST: Two stage model question

Dear FreeSurfer experts, I have a longitudinal design with 3 groups and 3 time points. For one group the intervention did not work so for now I would like to look at 2 groups only. Can I do this with the Longitudinal Two Stage Model by looking at the spc from tp1 to tp2 and then looking at th

[Freesurfer] Differences in aseg volumes between FreeSurfer 5.3.0 and FreeSurfer 6.0

Dear FreeSurfer expert, I have compared the aseg volume between FreeSurfer 5.3 and FreeSurfer 6.0 with asegstatsdiff from FreeSurfer 6.0 for each subject in my data set. I have enclosed the range for some of the volume. I found the largest differences in subcortical structures, especially in

Re: [Freesurfer] REPOST: Two stage model question

Hi Clara, the SPC (or any percent change) could be problematic, as the base value (either the volume at the baseline timepoint, or the average volume) will change depending wich interval you look at. You could check if the rate (mm/time_unit) or mm^3/time_unit is changing. I am not sure how y

Re: [Freesurfer] Need help to run freesurfer

Dear ZK, I have done md5sum check. I got the following message. How to confirm it is complete or not? pc@RB:~/Downloads$ md5sum freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz 5362fc776145b06ded219f42af4a8207 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz Thanks RB On Thu, A