Hi Doug,
Thank you very much for your reply and help. If I am not doing cluster by cluster how I can know which cluster is which when I overlay the file onto MNI152? Is the following correct I am not sure how to input (using which option) my sig.mgh from QDEC:
mri_label2vol --temp MNI152_T1_1mm_brain.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --fillthresh 0 --subject /lh-Diff-Class1-Class2-Intercept-thickness/sig.mgh--hemi lh --annot lh.aparc.annot --o sig2MNI.nii
Many thanks, Antonella
________________________________ From: Douglas Greve greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, August 27, 2012 10:23 AM Subject: Re: [Freesurfer] REPOST: How to Convert QDEC clusters to standard MNI_152_T1 space
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 greve@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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