Thanks. But what's meaning "colheader"? In my cache.th13.neg.sig.masked.nii.gz I have only a significant ROI. In the summary file there are five column and 5 different value of "mean". Which is the correct, expressing the mean z-score of the cluster?
Stefano
----Messaggio originale---- Da: greve@nmr.mgh.harvard.edu Data: 6-nov-2015 23.07 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: average z-score of each subject
from a common cluster
under the "Mean" column
On 11/06/2015 07:46 AM, stdp82@virgilio.it wrote:
I have run mri_segstats --seg .../my-glm.wls/group.diff/cache.th13.neg.sig.
masked.
nii.gz rh parc --i subj/fc.seed.surf.rh/R_seed/z.nii.gz --sum summaryfile
and I have obtained 9 columns and 5 rows. I'm confused on results. Where is the mean z-score for cache.th13.
neg.
sig.masked.nii.gz?
# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 -4 7 7.0 Seg-004 -2.4544 0.5023 -3.2164 -1.7619 1.4545 2 -3 153 153.0 Seg-003 -2.6662 1.4724 -6.2120 1.7587 7.9707 3 -2 848 848.0 Seg-002 -2.4930 2.0088 -6.4504 2.3528 8.8032 4 -1 1518 1518.0 Seg-001 -2.1416 1.6727 -6.4227 2.5420 8.9648 5 0 161316 161316.0 Seg0000 1.4152 1.6218 -7.0471 14.1452 21.1923
Because my data are on surface mri_surfcluster should be helpful?
Thanks.
Stefano
----Messaggio originale---- Da: greve@nmr.mgh.harvard.edu Data: 3-nov-2015 19.55 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: average z-score of each subject from
a
common cluster
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 groupdifference
(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
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.
edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender
and properly
dispose of the e-mail.
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.
edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On 11/07/2015 07:29 PM, stdp82@virgilio.it wrote:
Thanks. But what's meaning "colheader"?
Column header. The title of the column
In my cache.th13.neg.sig.masked.nii.gz I have only a significant ROI. In the summary file there are five column and 5 different value of "mean". Which is the correct, expressing the mean z-score of the cluster?
The column labeled "Mean", probably the 6th column
Stefano
----Messaggio originale---- Da: greve@nmr.mgh.harvard.edu Data: 6-nov-2015 23.07 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: average z-score of each subject
from a common cluster
under the "Mean" column
On 11/06/2015 07:46 AM, stdp82@virgilio.it wrote:
I have run mri_segstats --seg .../my-glm.wls/group.diff/cache.th13.neg.sig.
masked.
nii.gz rh parc --i subj/fc.seed.surf.rh/R_seed/z.nii.gz --sum summaryfile
and I have obtained 9 columns and 5 rows. I'm confused on results. Where is the mean z-score for cache.th13.
neg.
sig.masked.nii.gz?
# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 -4 7 7.0 Seg-004 -2.4544 0.5023 -3.2164 -1.7619 1.4545 2 -3 153 153.0 Seg-003 -2.6662 1.4724 -6.2120 1.7587 7.9707 3 -2 848 848.0 Seg-002 -2.4930 2.0088 -6.4504 2.3528 8.8032 4 -1 1518 1518.0 Seg-001 -2.1416 1.6727 -6.4227 2.5420 8.9648 5 0 161316 161316.0 Seg0000 1.4152 1.6218 -7.0471 14.1452 21.1923
Because my data are on surface mri_surfcluster should be helpful?
Thanks.
Stefano
----Messaggio originale---- Da: greve@nmr.mgh.harvard.edu Data: 3-nov-2015 19.55 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: average z-score of each subject from
a
common cluster
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 28146.00010 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 groupdifference
(cache.th13.pos.sig.cluster.nii.gz) as ROI mask. Thus, Iwould
extract from it the average of the z-score which iscontained
in
each subject. How should I do?Use mri_segstats passing the z map as the input (--i) andthe
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
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.
edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender
and properly
dispose of the e-mail.
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.
edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
stdp82＠virgilio.it