You should use mri_label2vol. If you want to do it label by label, then
you need to convert the cluster annotation (the .annot file) into labels
with mri_annotation2label. Or you can feed the annotation directly into
mri_label2vol to create a segmentation volume. You don't need to specify
a subject (but it you were, it would be fsaverage). Leave fillthresh at
0; the clusters cannot overlap.
doug
On 8/27/12 4:17 PM, Antonella Kis wrote:
Hi,
I want to overlay my QDEC clusters on the connectivity maps in FSL
on the MNI ( this is the template I use for my connectivity maps). I
am not sure how I can mention the label of my clusters, the
uncorrected clusters.
Should I use the sig.mgh as subject id, my clusters were obtained from
all my subjects or it should be the fsaverage? Should I use
mri_label2vol or mri_surf2vol?
How I can identify the label of my clusters more exactly how I can
keep only the clusters (name and size) from QDEC as in thefollowing
table or
where I can find for each QDEC's cluster the label so I can use it
under --label option ?
mri_label2vol
--label ???
--temp MNI152_T1_1mm_brain.nii.gz
--reg $FREESURFER_HOME/average/mni152.register.dat
--fillthresh .5
--subject /lh-Diff-Class1-Class2-Intercept-thickness/sig.mgh --hemi lh
--o precentral-lh.nii
Also is the 0.5 the threshold I need to use with mri_label2vol under
option --fillthresh if I want to get my uncorrected clusters? How can
I do this if as below I have two clusters in the same region?
Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69
ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation
--------- --- ------ --------- ---- ---- ---- ----- ----------
1 -3.8743 18231 944.60 -39.8 1.5 14.1 2631 precentral
2 -3.8065 47386 1445.46 -8.2 33.1 33.9 2421 superiorfrontal
3 -2.8630 158749 181.92 -12.7 -12.6 46.4 506 superiorfrontal
4 -2.7960 73670 222.37 -33.7 0.9 8.1 564 insula
5 2.7914 52279 204.80 -9.8 -98.6 4.6 248 pericalcarine
6 -2.7364 43605 173.45 -41.4 -79.2 21.8 288 inferiorparietal
7 -2.6316 17412 301.53 -38.3 5.6 -36.8 439 temporalpole
8 2.6050 150788 64.40 -24.0 -59.1 54.7 165 superiorparietal
9 -2.5570 106020 75.96 -22.8 -8.6 47.9 200 precentral
10 -2.5070 88002 66.59 -17.6 -31.2 37.8 198
posteriorcingulate
11 -2.4736 113974 181.87 -52.7 -10.3 -26.6 236 middletemporal
12 -2.4496 118370 142.88 -43.6 -18.0 -25.5 289 inferiortemporal
13 -2.3087 111885 55.43 -46.6 -36.2 -3.9 165 bankssts
14 -2.2179 153596 36.91 -11.3 3.4 42.0 103 superiorfrontal
15 -2.1861 145681 95.36 -11.3 60.1 19.1 147 superiorfrontal
16 -2.1733 29252 59.92 -42.6 37.5 -4.4 92 parstriangularis
17 -2.1689 155583 34.83 -45.3 -14.7 -11.2 87 superiortemporal
18 -2.1636 22443 27.76 -41.6 -79.0 -3.1 43 lateraloccipital
19 -2.1592 139736 21.75 -47.5 -25.1 37.0 61 postcentral
20 -2.0221 19174 4.10 -34.2 33.8 29.2 6
rostralmiddlefrontal
------------------------------------------------------------------------
*From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu>
*To:* freesurfer@nmr.mgh.harvard.edu
*Sent:* Tuesday, August 21, 2012 4:55 PM
*Subject:* Re: [Freesurfer] Convert QDEC clusters on the MNI_152_T1 space
You can use mri_label2vol and $FREESURFER_HOME/average/mni152.register.dat
doug
On 08/21/2012 11:06 AM, Antonella Kis wrote:
> Dear All,
>
> Is possible to overlap my QDEC clusters onto MNI_152_T1 _1mm_brain
> template?
>
> Thank you.
> Antonella
>
>
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--
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MGH-NMR Center
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