look in the summaryfile. Also, don't use --seg z.nii.gz. In the command below, it works because you have --annot afterwards, but in general it is not correct
On 10/30/2015 04:22 PM, stdp82@virgilio.it wrote:
Thanks. I have obtained:
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --seg z.nii.gz --annot Control21_FS rh aparc --i z.nii.gz --sum summaryfile
sysname Darwin
hostname iMac-di-Stefano.local
machine x86_64
user Stefano
UseRobust 0
Loading z.nii.gz
Loading z.nii.gz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 22 segmentations
Computing statistics for each segmentation
0 -7 2 2.000
1 -6 110 110.000
2 -5 255 255.000
3 -4 518 518.000
4 -3 1190 1190.000
5 -2 1692 1692.000
6 -1 4104 4104.000
7 0 61577 61577.000
8 1 42598 42598.000
9 2 28146 28146.000
10 3 14859 14859.000
11 4 5845 5845.000
12 5 1899 1899.000
13 6 485 485.000
14 7 116 116.000
15 8 75 75.000
16 9 74 74.000
17 10 78 78.000
18 11 65 65.000
19 12 104 104.000
20 13 45 45.000
21 14 5 5.000
How I can know the meaning of this number? Where is z?
I have tried also with:
mri_segstats --seg z.nii.gz --annot Control_21 rh aparc --i z.nii.gz --sum summaryfile --mask .../fc.ramgseed.surf.rh/R_Amygdala/my-glm.wls/group.diff/cache.th13.neg.sig.masked.nii.gz --avgwfvol mrivol
but I have problem with interpretation.
Stefano
----Messaggio originale---- Da: greve@nmr.mgh.harvard.edu Data: 30-ott-2015 16.17 A: <freesurfer@nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] average z-score of each subject from a common cluster On 10/30/15 7:16 AM, stdp82@virgilio.it wrote:Hi list, I have two queries, please. I'd like to have the z-score from my rsfMRI data (seed-analyis). 1) I have extract the z-score from the Vtx Max In details, after groups comparison analysis, I have opened the cache.th13.pos.sig.cluster.summary contained in group.diff folder and I have read the Vtx Max coordinates. Next, I have open the z.nii.gz of each subject and I have expected the z-score from the vertex which have the Vtx Max coordinates. Is this procedure corrected?Yes2) z-score of each subject from a common cluster I would like to use the cluster which shows the group difference (cache.th13.pos.sig.cluster.nii.gz) as ROI mask. Thus, I would extract from it the average of the z-score which is contained in each subject. How should I do?Use mri_segstats passing the z map as the input (--i) and the cluster map as the seg. The output will be --sum. Run with --help for more infoThanks. Stefano _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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