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 <gr...@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 <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
>>
>>
>>
_______________________________________________
>> Freesurfer
mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>--
>Douglas N. Greve,
Ph.D.
>MGH-NMR Center
>gr...@nmr.mgh.harvard.edu
>Phone Number:
617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
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