$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?

Yes

2) 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 info

Thanks.

Stefano

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