Hi Bruce,

I have previously tried a completely clean recon-all and got the same problem, but I did not use "-make all". I'll try that.

One thing I'm not sure if you noticed, though: 

If you look at the extract of the .out file I sent (between the ---- below), you can see that the 5.1.0 version of mris_spherical_average crashes when trying to load a file called lh.white from the surf subdirectory in the V1_average (i.e. not from my data).

The 4.4.0 version of mris_spherical_average, when run on the same data as part of the -label-v1 pipeline, does not throw this error.

It's odd that it tries to load this file because, from what I can see, the V1_average subject provided in 5.1.0 (and 4.4.0) does not have any white surface reconstructions?

Many thanks,

Krish

--
Prof. Krish Singh
CUBRIC
School of Psychology / Ysgol Seicoleg
Cardiff University /  Prifysgol Caerdydd
Park Place / Plas y Parc
Cardiff  / Caerdydd
CF10 3AT, UK
Tel / Ffôn: 02920 874690 / 870365 
Fax / Ffacs: 02920 870339
Email / Ebost : singhkd@cardiff.ac.uk




On 6 Jul 2011, at 15:15, Bruce Fischl wrote:

Hi Krish

sounds like the processing of the subject was not finished. Can you run recon-all -s <subject> -make all

then rerun the hinds stuff?

cheers
Bruce



On Wed, 6 Jul 2011, Krish Singh wrote:

Hi there,
I'm using Freesurfer version 5.1.0 to automatically define labels for left
and right V1 using the method outlined in Hinds et al.
To do this I add the -label-v1 flag to my recon-all command line.
The problem is that this always fails with the following error visible in
the .out file:
-------------------------------------------------------------------
mris_spherical_average -osurf v1.invivo.reg -n -o 240211-50 label
lh.v1.invivo.label lh v1.invivo.reg V1_average
/cubric/scratch/CCGG/Freesurf/240211-50/label/lh.v1.prob.label
output surface = v1.invivo.reg
painting output onto subject 240211-50.
processing subject V1_average...
MRISreadVertexPosition(white): could not open file
/cubric/scratch/CCGG/Freesurf/V1_average/surf/lh.white
No such file or directory
MRISreadOriginalProperties: could not read surface file white
No such file or directory
could not read surface positions from white
No such file or directory
-------------------------------------------------------------------
The problem seems to be with the current version of mris_spherical_average -
 if I modify the command line above to explicitly execute the old (4.4.0)
version of mris_spherical_average then I do not get this error and the
script completes without problems.
I'd be grateful of any advice/help on this.
Best Wishes,
Krish
--
Prof. Krish Singh
CUBRIC
School of Psychology / Ysgol Seicoleg
Cardiff University /  Prifysgol Caerdydd
Park Place / Plas y Parc
Cardiff  / Caerdydd
CF10 3AT, UK
Tel / Ffôn: 02920 874690 / 870365 
Fax / Ffacs: 02920 870339
Email / Ebost : singhkd@cardiff.ac.uk



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