On Fri, Oct 2, 2015 at 6:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

You should not use both --seg and --annot. What are you trying to accomplish?

On 10/2/15 3:34 AM, Ali Radaideh wrote:
Hi Bruce,

I have used the following command line:

mri_segstats --seg scz01/mri/aseg.mgz --annot scz01 lh lh.yeo2011_17Networks_N1000.annot --sum scz01.aseg.sum

and got the following:

# ColHeaders Index SegId NVoxels Volume_mm3 StructName

1 0 15766121 15766121.0 Seg0000

2 2 182848 182848.0 Seg0002

3 3 215011 215011.0 Seg0003

4 4 6547 6547.0 Seg0004

5 5 572 572.0 Seg0005

6 7 14053 14053.0 Seg0007

7 8 47779 47779.0 Seg0008

8 10 7151 7151.0 Seg0010

9 11 4464 4464.0 Seg0011

10 12 5264 5264.0 Seg0012

11 13 1680 1680.0 Seg0013

12 14 889 889.0 Seg0014

13 15 1731 1731.0 Seg0015

14 16 17307 17307.0 Seg0016

15 17 3842 3842.0 Seg0017

16 18 1106 1106.0 Seg0018

17 24 1228 1228.0 Seg0024

18 26 656 656.0 Seg0026

19 28 3941 3941.0 Seg0028

20 30 26 26.0 Seg0030

21 31 1222 1222.0 Seg0031

22 41 191593 191593.0 Seg0041

23 42 200955 200955.0 Seg0042

24 43 6321 6321.0 Seg0043

25 44 295 295.0 Seg0044

26 46 16106 16106.0 Seg0046

27 47 46472 46472.0 Seg0047

28 49 6684 6684.0 Seg0049

29 50 4308 4308.0 Seg0050

30 51 5099 5099.0 Seg0051

31 52 1459 1459.0 Seg0052

32 53 4005 4005.0 Seg0053

33 54 988 988.0 Seg0054

34 58 633 633.0 Seg0058

35 60 3554 3554.0 Seg0060

36 62 36 36.0 Seg0062

37 63 1518 1518.0 Seg0063

38 72 18 18.0 Seg0072

39 77 1040 1040.0 Seg0077

40 80 22 22.0 Seg0080

41 85 124 124.0 Seg0085

42 251 721 721.0 Seg0251

43 252 403 403.0 Seg0252

44 253 322 322.0 Seg0253

45 254 360 360.0 Seg0254

46 255 742 742.0 Seg0255

However,

I don't see the segmentation names (cortical parts). is my command true/ complete or not?

These are 46 segmentations although I am using 17 networks cortical parcellation, is this true?

Can I add anything to make the output more informative?. Also can I get any surface area ....etc?

Many thanks in advance.

Ali

On Thu, Oct 1, 2015 at 10:43 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

sure, you can use mri_segstats to get stats from it
Bruce
On Thu, 1 Oct 2015, Ali Radaideh wrote:

Can we get any stats from this type of parcellation? I only can see two
annotation files after running the mri_surf2surf command and these can be
loaded tksurfer as an overlay.

Thanks,
Ali

On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
that will generate a parcellation on the individual subject
surface of Thomas Yeo's 17-network clustering. It won't do
anything with the thickness though. What are you trying to do?

On Tue, 29 Sep 2015, Ali Radaideh wrote:

mri_surf2surf --srcsubject fsaverage --trgsubject
scz10 --hemi rh
--sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks
_N1000.annot
--tval
$SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot

scz10 is my subject name

On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve
<greve@nmr.mgh.harvard.edu>
wrote:
what is your surf2surf command?

On 9/28/15 5:11 PM, Ali Radaideh wrote:
Dear Douglas,

Thanks for your email. I meant to say that after
running the
recon-all, i ran the sur2surf command to get the
cortical
parcellation using Thomas Yeo Atlas.

I thought that the extracted cortical thickness
after running
the surf2surf command will be different from the one
extracted
before running the command. But, Bruce kindly
replied to my
email saying that it is the same if it is calculated
on
vertex-wise basis.

Thanks,
Ali

On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu> wrote:
I can't understand what you are asking. Can
you
elaborate?

On 09/28/2015 01:51 PM, Ali Radaideh wrote:
> Thanks alot Douglas,
>
> Yes it is there but after checking it many
time I
found it corrupted
> for some subjects due to copying them many
times
between machines.
>
> But May I ask you some thing related. I have
just
posted a question
> regarding getting the cortical thickness
after
running the surf2surf
> command (17 networks cortical parcellation).
Now I
found the stats
> file not updated after running this command
only
the annotation files
> in label folder.
[rh.Yeo2011_17Networks_N1000.annot]. We
thought that
> using Yeo Atlas will give slightly different
cortical thickness, are
> we correct?
>
> Thanks,
> Ali
>
> On Mon, Sep 28, 2015 at 8:27 PM, Douglas N
Greve
> <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> does that file exist?
>
> On 09/28/2015 01:05 PM, Ali Radaideh
wrote:
> > Dear FreeSurfer experts,
> > After finishing the recon-all, I am
trying
to extract the cortical
> > thickness for each subject and group
them
into one table but
> > unfortunately i keep getting the
following
error:
> >
> > rh.aparc.DKTatlas40.stats is not found
or is
too small to be a
> valid
> > statsfile
> > Use --skip flag to automatically skip
bad
stats files
> >
> > i tried to change the stats file (e.g
I used
aparc.a2009s) but I got
> > the same error.
> >
> > I tried each brain alone and also got
the
same error.
> >
> > Any ideas please
> > Thanks,
> > Ali
> >
> > --
> > /Ali M. Al-Radaideh. PhD
> > Head of Department of Medical Imaging
> > Vice Dean of the Faculty of Allied
Health
Sciences
> > The Hashemite University,
> > Zarqa, Jordan
> > W.phone +962 5 3903333 ext.5422, 5355,
5364
> > Email: ali.radaideh@hu.edu.jo
<mailto:ali.radaideh@hu.edu.jo>
> <mailto:ali.radaideh@hu.edu.jo
<mailto:ali.radaideh@hu.edu.jo>>
> > /
> > /webpage:

http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
> >
> >
> >
> >

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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
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> Head of Department of Medical Imaging
> Vice Dean of the Faculty of Allied Health
Sciences
> The Hashemite University,
> Zarqa, Jordan
> W.phone +962 5 3903333 ext.5422, 5355, 5364
> Email: ali.radaideh@hu.edu.jo
<mailto:ali.radaideh@hu.edu.jo>
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--
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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
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https://gate.nmr.mgh.harvard.edu/filedrop2

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--
Ali M. Al-Radaideh. PhD
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 3903333 ext.5422, 5355, 5364
Email: ali.radaideh@hu.edu.jo
webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=

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--
Ali M. Al-Radaideh. PhD
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 3903333 ext.5422, 5355, 5364
Email: ali.radaideh@hu.edu.jo
webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=

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The information in this e-mail is intended only for the person
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--
Ali M. Al-Radaideh. PhD
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 3903333 ext.5422, 5355, 5364
Email: ali.radaideh@hu.edu.jo
webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=

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The information in this e-mail is intended only for the person to whom it is
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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.

--

Ali M. Al-Radaideh. PhD
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 3903333 ext.5422, 5355, 5364
Email: ali.radaideh@hu.edu.jo

webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
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The information in this e-mail is intended only for the person to whom it is
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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.

Ali M. Al-Radaideh. PhD
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 3903333 ext.5422, 5355, 5364
Email: ali.radaideh@hu.edu.jo

webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=