Hi,

you are right! The Talairach ccordinates change. Unfortunately, the centroid coordinate of my data are outside the cluster. Do you have any suggestions about that?

I also tried your version of the script. The following message appeared:

mri_surfcluster: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory

Since I use Ubuntu it is not so simple to switch from my current version libnetcdf.so.7 back to libnetcdf.so.6. Do you know a workaround?

Respectfully yours pfannmoe

On Fri, 04 Apr 2014 15:38:09 -0400 Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

I'm not sure, when I run it it results in different xyz. What version are you using?

I've put a copy of my version (for linux) here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surfcluster

doug

On 04/03/2014 03:56 AM, Joerg Pfannmoeller wrote:

...

Hi,

I am trying to compute centroid coordinates of maps for functional activation obtained from fsfast with mri_surfcluster. The command is:

mri_surfcluster --in /.../sig.nii.gz --thmin 3 --thmax infinity--sign pos --subject subjid --hemi rh --surf white --annot aparc --frame 0 --minarea 0 --sum ./tabular_surfcluster.txt -- centroid

Unfortunately, the centroid option has no effect. Results in tabular_surfcluster.txt with and without centroid option are identical. What am I doing wrong?

Respectfully yours

              pfannmoe

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On Mon, 07 Apr 2014 12:02:24 -0400 Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

Is this group data? Or otherwise on fsaverage? Or on the subject's surface?

It is on a single subject on its on anatomy (self).

How are you determining that the centroid is outside of the cluster?

The coordinates are outside the cluster, there is nothing to worry about that.

It should give you a vertex number for the centroid (I think).

As you told in your last mail it gives Tal-coordinates and not vertices.

I opted not to use the centroid by default for this reason. This can happen because the centroid is irregular.

I don not understand this: What do you mean by irregular?

Hi,

I am sorry to disappoint you. I wrote another srcipt to compute the centroid in order to clarify whats happening. The centroid computed by the script is in the center of the cluster. However, the differences could be due to details of the computation. I was not able to unriddle all the details in the freesurfer code. Probably I am going to keep this script since it fits what I would like to compute. Before I forget about it, I use freesurfer 5.3.

Greetings pfannmoe

On Wed, 9 Apr 2014 08:33:26 -0400 (EDT) Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Jeorg

if the cluster is non-convex, the centroid is not guaranteed to be in the interior. Think of a C or U shape.

cheers Bruce On Wed, 9 Apr 2014, Joerg Pfannmoeller wrote:

...

On Mon, 07 Apr 2014 12:02:24 -0400 Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

...

Is this group data? Or otherwise on fsaverage? Or on the subject's surface?

It is on a single subject on its on anatomy (self).

...

How are you determining that the centroid is outside of the cluster?

The coordinates are outside the cluster, there is nothing to worry about that.

...

It should give you a vertex number for the centroid (I think).

As you told in your last mail it gives Tal-coordinates and not vertices.

...

I opted not to use the centroid by default for this reason. This can happen because the centroid is irregular.

I don not understand this: What do you mean by irregular?

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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.