See the usage statement for 'mris_anatomical_stats' below -- just end your command with the surface name (i.e., pial).

Also, you don't need the -t flag (lh.pial is not a thickness file, and thickness is independent of whether stats are computed on the 'white' vs. 'pial' surface).

usage: mris_anatomical_stats [options] <subject name> <hemi> [<surface name>]

cheers, -MH

On Wed, 2011-04-06 at 17:05 +0100, Lena Palaniyappan wrote:

    Hi all

    is it possible to obtain the surface area computations for
    each of the parcellations in Destrieux annot from pial instead
    of white surfaces? As the vertex addresses are likely to be
    different between white and pial surfaces, I suppose the
    following command is not appropriate – any ideas?

mris_anatomical_stats -a aparc.a2009s.annot -t subjid/surf/lh.pial -f subjid/stats/lh.pialparc.stats subjid lh

Lena

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Hi Christian

try the following:

1. Remove the 1st two lines from the file so there is no header info. 2. Load this file using the file->curvature->load curvature command. 3. At the tcl prompt type "curv_to_val". 4. Reload the curvature you want to display (e.g. curv or sulc)

we'll figure out what's going wrong with the more direct route.

cheers Bruce

On Fri, 8 Apr 2011, Rummel, Christian wrote:

Dear FreeSurfer team,

unfortunately I continue having this problem. Maybe it's a very small thing but I couldn't find a solution on the web.

The ascii file I want to overlay has the following form:

#!ascii 145819 and then 145819 lines of format <vertexnumber> <value>

In addition I tried a different format <vertexnumber> <x> <y> <z> <value> and omitting the first (#...) and second line. The vertex number seems to be correct.

When trying to load one of these ascii files into tksurfer (File -> Load Overlay) I get the following error messages:

mri_read(): couldn't determine type of file /usr/local/freesurfer/subjects/AA_m_31/lh.thickness-sphere2.asc surfer: couldn't load /usr/local/freesurfer/subjects/AA_m_31/lh.thickness-sphere2.asc. If you were trying to load a functional volume, make sure you selected the right registration method, and if necessary, that the registration file exists. If you were trying to load a volume-encoded value file, make sure it has the same number of values as this surface does vertices (145819). sclv_read_from_volume: error in FunD_New

Omitting the .asc in the file name doesn't help either. Does anyone see what is causing the error?

Thanks in advance, Christian

---

Christian Rummel (PhD)

Support Center for Advanced Neuroimaging (SCAN) Institute for Diagnostic and Interventional Neuroradiology Inselspital, 3010 Bern, Switzerland

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Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] im Auftrag von Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 6. April 2011 16:55 An: Rummel, Christian Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] How to overlay anatomical surfaces with externally calculated quantities?

Hi Christian,

I think you should be able to load the .asc file directly into tksurfer. Let us know if that doesn't work and we'll fix it.

cheers Bruce On Wed, 6 Apr 2011, Rummel, Christian wrote:

...

Dear FreeSurfer team,

I want to analyze regional cortical thickness using higher-order statistics implemented in an external C routine. This is currently done exporting thickness information in spherical coordinates for all subjects to ascii files for subsequent analysis (mris_convert -c lh.thickness lh.sphere lh.thickness-sphere.asc) After analysis I end up with one file for each subject having the same format as lh.thickness-sphere.asc but with thickness replaced by some higher-order statistics.

Is there an easy way of bringing back this information into FreeSurfer format for display with tksurfer? If not, what else would one do to display information on anatomical surfaces, given FreeSurfer's vertex identification number and a scalar quantity?

Thanks, Christian

---

Christian Rummel (PhD)

Support Center for Advanced Neuroimaging (SCAN) Institute for Diagnostic and Interventional Neuroradiology Inselspital, 3010 Bern, Switzerland

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