Hi Andrew,

Glad it's not just me! I'm still not sure whether this is a generic problem with version 5.1.0 (which I use) or a local problem.

I can only find a rather inelegant hack. What I do is complete the recon-all (5.1.0) and then run a bunch of steps using mris_spherical_average from version 4.4.0:

Here's what I do <stuff in angle brackets is for you to fill in>

cd $SUBJECTS_DIR
<PATH TO VERSION 4.4.0>/bin/mris_spherical_average -osurf v1.invivo.reg -n -o <SUBJECTNAME> label rh.v1.invivo.label rh v1.invivo.reg V1_average ./<SUBJECTNAME>/label/rh.v1.prob.label
<PATH TO VERSION 4.4.0>/bin/mris_spherical_average -osurf v1.invivo.reg -n -o <SUBJECTNAME> label lh.v1.invivo.label lh v1.invivo.reg V1_average ./<SUBJECTNAME>/label/lh.v1.prob.label
threshold_labelfile_at0p8 ./<SUBJECTNAME>/label/lh.v1.prob.label ./<SUBJECTNAME>/label/lh.v1.predict.labe
threshold_labelfile_at0p8 ./<SUBJECTNAME>/label/rh.v1.prob.label ./<SUBJECTNAME>/label/rh.v1.predict.label
mris_anatomical_stats -l ./<SUBJECTNAME>/label/lh.v1.predict.label <SUBJECTNAME> lh >> ./<SUBJECTNAME>/stats/hinds_v1_lh
mris_anatomical_stats -l ./<SUBJECTNAME>/label/rh.v1.predict.label <SUBJECTNAME> rh >> ./<SUBJECTNAME>/stats/hinds_v1_rh

This seems to work, but I'm not sure if there is any fall-out from mixing versions. (Note you need to link or copy a version of V1_average into your SUBJECTS_DIR first)

Good luck!

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 11 Nov 2011, at 22:04, Andrew Bock wrote:

Hello,

I am having a similar problem to one described on the freesurfer mail archive, where I receive the following error when trying to identify V1 using the Hinds method (i.e. recon-all -s <subject> -label_v1):

processing subject V1_average...
MRISreadVertexPosition(white): could not open file /usr/local/freesurfer/
subjects/V1_average/surf/rh.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


As Prof. Krish Singh indicated in July, it appears the problem occurs when trying to open rh.white (or lh.white) from the surf subdirectory in V1_average, which doesn't exist.

I have run recon-all -s <subject> -make all, but it returns "make: Nothing to be done for `all'."

Any help you can provide would be greatly appreciated!

Thanks in advance,

Andrew

--
Andrew Bock, Ph.D.
Department of Psychology
University of Washington
Seattle, WA 98195
Tel: 206.543.3817
Fax: 206.685.3157
abock@u.washington.edu
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