Hi Krish,

I'm still having some issues, right now I receive the error:

threshold_labelfile_at0p8: command not found

Any suggestions?

Andrew

On Tue, Nov 15, 2011 at 9:37 AM, Andrew Bock <abock@u.washington.edu> wrote:

Thanks Krish!

Andrew

On Tue, Nov 15, 2011 at 9:29 AM, Krish Singh <singhkd@cardiff.ac.uk> wrote:

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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