[Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps

2015-08-10 Thread Elijah Mak 
Hi Freesurfer Experts,

For the purpose of defining nodes in a graph theory analysis, I would like
to generate a list of X Y Z coordinates in MNI space for all the labels in
the Destrieux atlas. I came across a previous post with the following steps:

Step 1:

mri_annotation2label --subject fsaverage --hemi lh --annotation
aparc.a2009s --outdir /Users/ElijahMak

Step 2:

mri_surfcluster --in
/Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel
lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin
--centroid --thmin 0 --hemi lh --subject fsaverage
Everything went smoothly, but I would like to check my steps with you
before I proceed to generate the coordinates individually for each ROI
per hemisphere.



The output from #2 is sum.lh.G_and_S_frontomargin. When I load it, I see


dhcp-172-17-218-173:~ ElijahMak$ cat sum.lh.G_and_S_frontomargin

# Cluster Growing Summary (mri_surfcluster)

# $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $

# $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $

# CreationTime 2015/08/10-12:29:31-GMT

# cmdline mri_surfcluster --in
/Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel
lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin
--centroid --thmin 0 --hemi lh --subject fsaverage

# cwd /Users/ElijahMak

# sysname  Darwin

# hostname dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk

# machine  x86_64

# FixVertexAreaFlag 1

# FixSurfClusterArea 1

#

# Input  /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness

# Frame Number  0

# srcsubj fsaverage

# hemi lh

# surface white

# SUBJECTS_DIR /Applications/freesurfer/subjects

# SearchSpace_mm2 65416.6

# SearchSpace_vtx 932

# Bonferroni 0

# Minimum Threshold 0

# Maximum Threshold infinity

# Threshold Signabs

# AdjustThreshWhenOneTail 1

# Area Threshold0 mm^2

# clabelfile lh.G_and_S_frontomargin.label

# clabelinv  0

# Overall max 3.33248 at vertex 83949

# Overall min 0 at vertex 0

# NClusters  1

# Total Cortical Surface Area 65416.6 (mm^2)

# FixMNI = 1

#

# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZNVtxs

   13.332   83949  82219.39-29.4  -22.0   17.4  163842


 Are those TalX TalY TalZ the values I'm looking for?



Many thanks for your time.



Best Wishes,

Elijah




-- 

Elijah Mak,

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps

2015-08-12 Thread Douglas N Greve 
Those are more-or-less talairach coords, not MNI. If you add --nofixmni, 
the results will be reported in mni305 coords.

On 08/10/2015 08:39 AM, Elijah Mak wrote:
> Hi Freesurfer Experts,
>
> For the purpose of defining nodes in a graph theory analysis, I would 
> like to generate a list of X Y Z coordinates in MNI space for all the 
> labels in the Destrieux atlas. I came across a previous post with the 
> following steps:
>
> Step 1:
>
> mri_annotation2label --subject fsaverage --hemi lh --annotation 
> aparc.a2009s --outdir /Users/ElijahMak
>
> Step 2:
>
> mri_surfcluster --in 
> /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel 
> lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin 
> --centroid --thmin 0 --hemi lh --subject fsaverage
>
>
> Everything went smoothly, but I would like to check my steps with you before 
> I proceed to generate the coordinates individually for each ROI per 
> hemisphere.
>
>
> The output from #2 issum.lh.G_and_S_frontomargin. When I load it, I see
>
> dhcp-172-17-218-173:~ ElijahMak$ cat sum.lh.G_and_S_frontomargin
>
>
> # Cluster Growing Summary (mri_surfcluster)
>
>
> # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
>
>
> # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
>
>
> # CreationTime 2015/08/10-12:29:31-GMT
>
>
> # cmdline mri_surfcluster --in 
> /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel 
> lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin 
> --centroid --thmin 0 --hemi lh --subject fsaverage
>
>
> # cwd /Users/ElijahMak
>
>
> # sysname  Darwin
>
>
> # hostname dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk 
> 
>
>
> # machine  x86_64
>
>
> # FixVertexAreaFlag 1
>
>
> # FixSurfClusterArea 1
>
>
> #
>
>
> # Input  /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness
>
>
> # Frame Number  0
>
>
> # srcsubj fsaverage
>
>
> # hemi lh
>
>
> # surface white
>
>
> # SUBJECTS_DIR /Applications/freesurfer/subjects
>
>
> # SearchSpace_mm2 65416.6
>
>
> # SearchSpace_vtx 932
>
>
> # Bonferroni 0
>
>
> # Minimum Threshold 0
>
>
> # Maximum Threshold infinity
>
>
> # Threshold Signabs
>
>
> # AdjustThreshWhenOneTail 1
>
>
> # Area Threshold0 mm^2
>
>
> # clabelfile lh.G_and_S_frontomargin.label
>
>
> # clabelinv  0
>
>
> # Overall max 3.33248 at vertex 83949
>
>
> # Overall min 0 at vertex 0
>
>
> # NClusters  1
>
>
> # Total Cortical Surface Area 65416.6 (mm^2)
>
>
> # FixMNI = 1
>
>
> #
>
>
> # ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZNVtxs
>
>13.332   83949  82219.39-29.4  -22.0   17.4  163842
>
>
>
>
> Are those TalX TalY TalZ the values I'm looking for?
>
>
> Many thanks for your time.
>
>
> Best Wishes,
> Elijah
>
>
> -- 
>
> Elijah Mak,
>
> PhD Candidate *|* Psychiatry
>
> University of Cambridge
>
> Trinity College, Cambridge, CB2 1TQ
>
>
>
>
> ___
> 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
gr...@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/

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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps

2015-08-14 Thread Elijah Mak 
Hi Douglas,

Thanks for the help! However, when I tried the --nofixmni flag, all the
ROIs appeared to have identical MNI coordinates. I have pasted the output
from 3 ROIS in the LH.

# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZNVtxs
   13.332   83949  82219.39-29.4  -22.0   17.4  163842
   13.533  117158  82219.39-29.4  -22.0   17.4  163842
   13.170   83424  82219.39-29.4  -22.0   17.4  163842


The same thing happens to the ROIs on the RH (XYZ: 29.8 29.8 18.0).

Best Wishes,
Elijah

-- 

Elijah Mak, Gates Scholar

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
___
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps

2015-08-17 Thread Douglas Greve 
sorry, what is this in reference too? Please remember to include the 
text from previous exchanges so we have context for questions. We answer 
a lot of email on freesurfer@...  and it is hard to keep track of  things.


On 8/14/15 7:00 AM, Elijah Mak wrote:

Hi Douglas,

Thanks for the help! However, when I tried the --nofixmni flag, all 
the ROIs appeared to have identical MNI coordinates. I have pasted the 
output from 3 ROIS in the LH.


# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ   NVtxs

   13.332   83949 82219.39-29.4  -22.0   17.4  163842
   13.533  117158 82219.39-29.4  -22.0   17.4  163842
   13.170   83424 82219.39-29.4  -22.0   17.4  163842


The same thing happens to the ROIs on the RH (XYZ: 29.8 29.8 18.0).

Best Wishes,
Elijah

--

Elijah Mak, Gates Scholar

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ




___
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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.

Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps

2015-08-17 Thread Elijah Mak 
Hi Douglas,


Sorry about that! I hope this works. I have pasted the earlier
correspondence here with your response below:


Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas:
Checking steps 
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+Extracting+MNI+Coordinates+from+the+Destrieux+Atlas%5C%3A+Checking+steps%22&o=newest>

Douglas N Greve
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22>
Wed, 12 Aug 2015 07:27:49 -0700
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20150812>

Those are more-or-less talairach coords, not MNI. If you add --nofixmni,
the results will be reported in mni305 coords.

Those are more-or-less talairach coords, not MNI. If you add --nofixmni,
the results will be reported in mni305 coords.

On 08/10/2015 08:39 AM, Elijah Mak wrote:
> Hi Freesurfer Experts,
>
> For the purpose of defining nodes in a graph theory analysis, I would
> like to generate a list of X Y Z coordinates in MNI space for all the
> labels in the Destrieux atlas. I came across a previous post with the
> following steps:
>
> Step 1:
>
> mri_annotation2label --subject fsaverage --hemi lh --annotation
> aparc.a2009s --outdir /Users/ElijahMak
>
> Step 2:
>
> mri_surfcluster --in
> /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel
> lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin
> --centroid --thmin 0 --hemi lh --subject fsaverage
>
>
> Everything went smoothly, but I would like to check my steps with you before
> I proceed to generate the coordinates individually for each ROI per
> hemisphere.
>
>
> The output from #2 issum.lh.G_and_S_frontomargin. When I load it, I see
>
> dhcp-172-17-218-173:~ ElijahMak$ cat sum.lh.G_and_S_frontomargin
>
>
> # Cluster Growing Summary (mri_surfcluster)
>
>
> # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
>
>
> # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
>
>
> # CreationTime 2015/08/10-12:29:31-GMT
>
>
> # cmdline mri_surfcluster --in
> /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel
> lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin
> --centroid --thmin 0 --hemi lh --subject fsaverage
>
>
> # cwd /Users/ElijahMak
>
>
> # sysname  Darwin
>
>
> # hostname dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk
> <http://dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk>
>
>
> # machine  x86_64
>
>
> # FixVertexAreaFlag 1
>
>
> # FixSurfClusterArea 1
>
>
> #
>
>
> # Input  /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness
>
>
> # Frame Number  0
>
>
> # srcsubj fsaverage
>
>
> # hemi lh
>
>
> # surface white
>
>
> # SUBJECTS_DIR /Applications/freesurfer/subjects
>
>
> # SearchSpace_mm2 65416.6
>
>
> # SearchSpace_vtx 932
>
>
> # Bonferroni 0
>
>
> # Minimum Threshold 0
>
>
> # Maximum Threshold infinity
>
>
> # Threshold Signabs
>
>
> # AdjustThreshWhenOneTail 1
>
>
> # Area Threshold0 mm^2
>
>
> # clabelfile lh.G_and_S_frontomargin.label
>
>
> # clabelinv  0
>
>
> # Overall max 3.33248 at vertex 83949
>
>
> # Overall min 0 at vertex 0
>
>
> # NClusters  1
>
>
> # Total Cortical Surface Area 65416.6 (mm^2)
>
>
> # FixMNI = 1
>
>
> #
>
>
> # ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZNVtxs
>
>13.332   83949  82219.39-29.4  -22.0   17.4  163842
>
>
>
>
> Are those TalX TalY TalZ the values I'm looking for?
>
>
> Many thanks for your time.
>
>
> Best Wishes,
> Elijah
>
>
> --
>
> Elijah Mak,
>
> PhD Candidate *|* Psychiatry
>
> University of Cambridge
>
> Trinity College, Cambridge, CB2 1TQ
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR centergr...@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/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-ma

Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps

2015-08-17 Thread Douglas Greve 
sorry, can you include them in a single email. I already deleted your 
previous one :)


On 8/17/15 11:30 AM, Elijah Mak wrote:

Hi Douglas,

Sorry about that! I hope this works. I have pasted the earlier correspondence 
here with your response below:


  Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux
  Atlas: Checking steps
  
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+Extracting+MNI+Coordinates+from+the+Destrieux+Atlas%5C%3A+Checking+steps%22&o=newest>

Douglas N Greve 
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22> 
Wed, 12 Aug 2015 07:27:49 -0700 
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20150812>


Those are more-or-less talairach coords, not MNI. If you add --nofixmni,
the results will be reported in mni305 coords.
Those are more-or-less talairach coords, not MNI. If you add --nofixmni,
the results will be reported in mni305 coords.

On 08/10/2015 08:39 AM, Elijah Mak wrote:
> Hi Freesurfer Experts,
>
> For the purpose of defining nodes in a graph theory analysis, I would
> like to generate a list of X Y Z coordinates in MNI space for all the
> labels in the Destrieux atlas. I came across a previous post with the
> following steps:
>
> Step 1:
>
> mri_annotation2label --subject fsaverage --hemi lh --annotation
> aparc.a2009s --outdir /Users/ElijahMak
>
> Step 2:
>
> mri_surfcluster --in
> /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel
> lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin
> --centroid --thmin 0 --hemi lh --subject fsaverage
>
>
> Everything went smoothly, but I would like to check my steps with you before
> I proceed to generate the coordinates individually for each ROI per
> hemisphere.
>
>
> The output from #2 issum.lh.G_and_S_frontomargin. When I load it, I see
>
> dhcp-172-17-218-173:~ ElijahMak$ cat sum.lh.G_and_S_frontomargin
>
>
> # Cluster Growing Summary (mri_surfcluster)
>
>
> # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
>
>
> # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
>
>
> # CreationTime 2015/08/10-12:29:31-GMT
>
>
> # cmdline mri_surfcluster --in
> /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel
> lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin
> --centroid --thmin 0 --hemi lh --subject fsaverage
>
>
> # cwd /Users/ElijahMak
>
>
> # sysname  Darwin
>
>
> # hostnamedhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk  <http://dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk>  
> <http://dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk>

>
>
> # machine  x86_64
>
>
> # FixVertexAreaFlag 1
>
>
> # FixSurfClusterArea 1
>
>
> #
>
>
> # Input  /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness
>
>
> # Frame Number  0
>
>
> # srcsubj fsaverage
>
>
> # hemi lh
>
>
> # surface white
>
>
> # SUBJECTS_DIR /Applications/freesurfer/subjects
>
>
> # SearchSpace_mm2 65416.6
>
>
> # SearchSpace_vtx 932
>
>
> # Bonferroni 0
>
>
> # Minimum Threshold 0
>
>
> # Maximum Threshold infinity
>
>
> # Threshold Signabs
>
>
> # AdjustThreshWhenOneTail 1
>
>
> # Area Threshold0 mm^2
>
>
> # clabelfile lh.G_and_S_frontomargin.label
>
>
> # clabelinv  0
>
>
> # Overall max 3.33248 at vertex 83949
>
>
> # Overall min 0 at vertex 0
>
>
> # NClusters  1
>
>
> # Total Cortical Surface Area 65416.6 (mm^2)
>
>
> # FixMNI = 1
>
>
> #
>
>
> # ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZNVtxs
>
>13.332   83949  82219.39-29.4  -22.0   17.4  163842
>
>
>
>
> Are those TalX TalY TalZ the values I'm looking for?
>
>
> Many thanks for your time.
>
>
> Best Wishes,
> Elijah
>
>
> --
>
> Elijah Mak,
>
> PhD Candidate *|* Psychiatry
>
> University of Cambridge
>
> Trinity College, Cambridge, CB2 1TQ
>
>
>
>
> ___
> Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu  <mailto:gr...@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting  
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop:http