hmmmm, we'll take a look On Wed, 6 Jul 2011, Krish Singh wrote:
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 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.