RE: [Freesurfer] w file to label

Hi Doug,

I'm starting analysis of a new study after a long FSFAST hiatus, and am noting your remark about moving away from using w files. In the FSwiki page for paint-sess, it seems like its output is still w files. Does the current way to present functional data include a command instead of paint-sess? Which? Could you direct me to instructions about the new procedure?

Thanks,

Dahlia.

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Doug Greve Sent: Wednesday, June 06, 2007 6:27 PM To: Robert Levy Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] w file to label

I've modifed mri_cor2label to (almost) do what you want to do. You can

get the new version from here:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_cor2label

It will operate on mgh files, not .w files. Convert your .w file into an

mgh with mri_surf2surf, then follow the instructions in the help.

Note: we are moving away from using w files. If you' re using the dev

version of freesurfer, you should not have to create w files.

doug

Robert Levy wrote:

Hello,

I am trying to convert a w file into a label file, and the best way I

came up with seems like it is too complicated to be the actual best way.

What I am doing below is reading a list of subjects, and then for each

subject, 1.) running mri_surfcluster, 2.) merging its output into a

new label, and 3.) removing the component labels that went into it.

# entered in bash shell

# generate the .w file paint-sess -sf Subject_Lists/bw-group-error-5

-analysis EMerror -contrast rACC_lh_pos_0_ASce68 -map mask -hemi lh

# merge labels

cat Subject_Lists/bw-group-error-5 | while read subject;

do

mri_surfcluster --in

$subject/bold/EMerror/rACC_lh_pos_0_ASce68/mask-0-lh.w --thmin 0.5

--sign pos --subject $subject --hemi lh --surf orig --annot aparc

--minarea 1 --sum

$subject/bold/EMerror/rACC_lh_pos_0_ASce68/mask-0-h-label.sum --olab

$subject/label/rACC_lh_pos_0_ASce68 ;

cd $subject/label;

mri_mergelabels $(ls rACC_lh_pos_0_ASce68*.label | sed 's/rACC/-i

rACC/g') -o rACC_lh_pos_0_ASce68.label;

rm rACC_lh_pos_0_ASce68-0*.label;

cd $SUBJECTS_DIR;

done

#check in tksurfer

surf-sess -s mano001 -analysis EMerror -contrast rACC_lh_pos_0_ASce68

-map mask -hemi lh -fthresh 1

It seems to work, but if there is a more direct way, it may be better

just because there is potential room for error the way I am doing it.

Thanks,

Rob