Oops.

Sorry Andrew, that is a script that I think just takes some lines from the recon-all script. I can't remember whether I wrote it, or someone else (sorry), but here it is:

-------------------------------------------------- #!/bin/bash # thresholds probabilities in one file to another at the optimal # threshold of p=0.8. this threshold is based on comparisons of actual # and predicted V1 boundary with and independent dataset (zilles # brains) infile=$1 outfile=$2

echo -n "thresholding the label..." cat $infile | sed "/^#/d;/^[0-9]*$/d;/.* 0\.[0-7].*$/d" \ > /tmp/tmpthreshout numlab=`wc -l /tmp/tmpthreshout | sed "s/ .*$//"`

echo "# v1 atlaspredict label file auto-generated" > $outfile echo $numlab >> $outfile cat /tmp/tmpthreshout >> $outfile echo "done" --------------------------------------------------

Just put these in a file called threshold_labelfile_at0p8, somewhere in your executable path (and make sure the x permission flag is set).

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 15 Nov 2011, at 19:47, Andrew Bock wrote:

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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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.