Yes, that can happen when there are very few active voxels.
On 08/07/2014 06:22 AM, Sarah Whittle wrote:
Hi Doug,
I've done a surface-based analysis using qdec and want to mask my significance maps before performing an FDR correction.
So I think I've figured out that I don't need to turn my mask label into a mgh file - I think I can use my label to restrict the search space for the FDR correction in tksurfer - is this correct?
I presume that I open my sig.mgh file as an overlay on fsaverage in tksurfer, then "mask values to label" (choosing my mask label), prior to performing the FDR correction?
This seemed to work for one sig.mgh file (I assume it did because the minimum z value after FDR correction was different (i.e., lower) when applying "mask values to label" versus not masking). Using a different significance map, however, the min z value following FDR correction was exactly the same after applying the same mask. Can this be correct?
Thanks,
Sarah ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, 7 August 2014 8:16 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] label to surf (.mgh file)
Hi Sara, I'm not sure what you are trying to do. Are you doing a volume or surface-based analysis? If surface based, why do you need to convert it into the volume? doug
On 08/05/2014 11:48 PM, Sarah Whittle wrote:
Hi,
I would like to create an overlay from a number of labels from the standard 2005 aparc in order to perform an fdr correction of a significance map using a mask to restrict the search space. I would like to do this with fsaverage.
As far as I can tell, there is no label or annotation to surf function??
What I have done so far is group my labels into one larger label using mri_mergelabels. Then I have converted this label to a nifti volume using mri_label2vol (I tried using this command to create an mgh file, and it did, but I was not able to subsequently open this as an overlay in tksurfer). What I then wanted to do was convert the volume to a surface using mri_vol2surf, BUT I don't have a registration file, as this has all been done with fsaverage.
I feel like there should be a simpler way to do this though! Any advice appreciated.
Thanks,
Sarah _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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