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 : [email protected]
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 <[email protected]> wrote:
> Thanks Krish!
>
> Andrew
>
>
> On Tue, Nov 15, 2011 at 9:29 AM, Krish Singh <[email protected]> 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 : [email protected]
>
>
>
>
> 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
>> [email protected]
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