I have run cat ... /my-glm.wls/group.diff/cache.th13.neg.sig.cluster.summary
and I have obtained
ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 -3.595 110577 865.93 11.8 39.4 -0.1 0.00620 0.00520 0.00720 1672 rostralanteriorcingulate
after mri_segstats --seg .../my-glm.wls/group.diff/cache.th13.neg.sig. cluster.nii.gz --i Control21/rest/fc.seed.surf.rh/R_Seed/z.nii.gz -- sum summaryfile_Control
and summary file is:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 -2 1672 1672.0 Seg-002 -2.2757 2.2172 -6.4504 2.5762 9.0266 2 0 162170 162170.0 Seg0000 1.3956 1.6398 -7.0471 14.1452 21.1923
I have two raw. Which is the raw which contains the average z-score in the cluster? What's meaning, in term of location, Seg-002/0? In cluster. cache.th13.neg.sig.cluster.summary contains only rostralanteriorcingulate.
Thanks,
Stefano
----Messaggio originale---- Da: greve@nmr.mgh.harvard.edu Data: 9-nov-2015 23.59 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: average z-score of each
subject from a common cluster
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 28146.000 >> >> 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
>> >> >> >> _______________________________________________ >> 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
-- 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