Hi Dahlia,
I don't have a replacement for surf-sess yet that does not use the .w files, but you can run tksurfer directly, something like:
tksurfer subject lh inflated -overlay-reg sess/bold/register.dat -overlay sess/bold/analysis/contrast/sig.bhdr
btw, I am currently testing some new software that will replace a lot of the existing fsfast commands. It will be nifti-compliant (no more bfloats! yea!) and will make the group analysis a lot easier. It will be ready within two weeks.
doug
Dahlia Sharon wrote:
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
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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