This will take the mri_surfcluster annotation output and map it into a volume in MNI152 space. Each voxel will have an integer value indicating which cluster it belongs to. This is better than trying to work with the coordinates. Note you can also specify a label instead of an annotation.

doug

mri_label2vol --annot lh.surfcluster.annot \ --subject fsaverage --proj frac 0 1 .1 --hemi lh\ --reg $FREESURFER_HOME/average/mni152.register.dat \ --temp $FSLDIR/etc/standard/avg152T1.nii.gz \ --o lh.surfcluster.mni152.nii

Georg Homola wrote:

Hi,

I'd like to extract %BOLD-change from clusters or highly activated voxels (first level fMRI data processed in FEAT, higher level done with mri_glmfit).

Can you tell me what kind of space the cluster summary list created by mri_surfcluster refers to? Is it real Talairach space as TalX, TalY and TalZ implies it? Is there a simple method to transform those coordinates to the FSL standard space (MNI152)? That seems inevitable for me, since I use Peate (a featquery based GUI) to perform model related time series extraction. Or is it somehow possible to show the percentage signal change directly with freesurfer?

Thanks in advance Georg

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It only uses the example_func, so if that is affected, then the registration will be off. In general, you should not use freesurfer with data you have non-linearly registered with some template. The freesurfer intersubject registration itself is non-linear.

doug

Georg Homola wrote:

Hi Doug!

May be a very basic question for better understanding, but how much does reg-feat2anat care about the FSL preprocessing e.g. dewarping? And especially important for me, does it make a difference if you FNIRT or FLIRT on first level? Is it a good idea to process non-linearly registered subjects with reg-feat2anat? In other words: is anat2exf.register.dat actually affected by FEAT preprocessing output (warp field and transformation matrices), or not at all?

Many thanks in advance Georg

You only need to spec the dofs with a fixed effects analysis. If that's what you are doing, then you need to sum all the dofs from the lower level.

doug

ps. these types of questions are better to post to the freesurfer mailing list

Georg Homola wrote:

Hi Doug!

When performing surface-based group analysis with mri_glmfit, I have to specify the dofs of my feat runs. But when I correct for motion outliers on first level (by additional confound EVs identified by fsl_motion_outliers) there will be different dofs for every subject. Is a correct group analysis still possible? Which dof will be the right one then (the subject with the least dofs maybe)?

Many thanks in advance Georg

Did you supply a registration matrix when you ran mri_surf2vol? Also, try viewing the overlay on the surf2vol template. BTW, it is a lot easier for us to help you if you give us command-lines and terminal output.

doug

Nasim Maleki wrote:

Dear FreeSurfers,

I'm trying to transform and overlay the sig.mgh files on the 3D volumetric data. I use mri_surf2vol to convert sig.mgh and everything works fine up to the point that I try to view the overlay with tkmedit. There is no overlay on top of the main volume although it is successfully loaded and also when I use the 'configure functional overlay' interface in tkmedit I get the following error: Error: Error 18 in FunV-TclOISetSampleType: Invalid Parameter"

Have I missed something?

Thanks for your help in advance. Nasim

P.S. I use FreeSurfer v4.3.0

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Is this for a permutation test? Sorry, this is my fault. I've put a new version here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim that should fix the problem. Can you test it out?

thanks

doug

On Mon, 1 Jun 2009, Georg Homola wrote:

Hi All (and especially Doug, again)!

As one of the final steps I run mri_glmfit-sim for clusterwise correction (of my random effects analysis btw.). It always worked well and I also didn't change the command line recently, but since I updated Freesurfer to the latest version (4.3.1) it quits with:

ERROR: you must supply --fwhm with --sim, even if it is 0

There is no flag like --fwhm for mri_glmfit-sim and when I try --fwhm-override it won't change anything. Am I missing something?

Thanks Georg

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