use --segno 10 --segno 49 These codes are from $FREESURFER_HOME/FreeSurferColorLUT.txt and correspond to left and right thalamus. Use -m volume to get the volume of thalamus (this is the default). If you're only looking at one measure, then no correction for multiple comparisons is necessary. You can test the effect of gender by loading this output into a stats program or using mri_glmfit with the --table option. doug
Knut J Bjuland wrote:
Hi Bruce
I am now responding to the list as well. I have a group with different subjects where I wish to correlate thalamus volume with gender difference. Though I have extract the data using asegstats2table. I wish to be sure that the group difference is correct. Due to this reason I wish to use multiple comparsion within Freesurfer for instant FDR. I have some trouble figuring out --iv volmeasfile or how to use an label to include thalamus but exclude everything else?
Knut J
Knut J
On 08/11/2011 08:42 PM, Bruce Fischl wrote:
Hi Knut
you should respond onlist so Doug and Nick can answer! If all you want is thalamic volume then why do you have multiple comparisons? You only have one number/subject, no? Bruce
On Thu, 11 Aug 2011, Knut J Bjuland wrote:
Hi Bruce
I wish to use a group difference analysis using gender and correlate thalamus volume with IQ, and then apply multiple comparisons using FDR or Monte Carlo simulation. Do you have any links to a good tutorial? I inted to use mris_preproc and mris_glm for voulmetirc analysis, but I have some trouble figuring out --iv volmeasfile?
Cheers Knut J
Knut J
On 08/11/2011 08:03 PM, Bruce Fischl wrote:
Hi Knut
you don't need to register it since the segmentation (aseg) is created from the same data as the surface. What kind of analysis are you thinking of doing?
cheers Bruce
On Thu, 11 Aug 2011, Knut J Bjuland wrote:
I am working to do a volumetric analysis in Freesurfer using Thalamus. I do not know if this is the correct way to go. Should I first register thalamus to a surface using tkregister? There was also another post on this list, which suggested using tkregister2? I am also search to find a tutorial on how to create a volmask and the use it to calculate statistic in Freesurfer for Thalamus.
Knut J
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