fieldsign map display - Freesurfer

4 Sep 2014


      Dear all,
I'm trying to display the fieldsign map. I used standard
rotating-wedge and expanding-ring paradigm, and I followed the steps
described in FsFastIndividualRetinotopy Analysis.
I'm running freesurfer on Ubuntu 14.04.
Polar angle and eccentricity map look good but I can't properly
display the fieldsign map as an alternation of two colours. I attached
a screen-shot as example.
Any suggestion?
Thanks for the help!
Francesca
The command line is;
 tksurfer-sess -a rtopy.DM.lh -s SUBJ01 -fieldsign
and that's the output:
shalim-ubuntu:/usr/local/freesurfer/fsfast/MeytalRetinotopy>
tksurfer-sess -a rtopy.DM.lh -s SUBJ01 -fieldsign
Surface DM lh
Map Surface DM lh
$Id: tksurfer-sess,v 1.16.2.2 2012/11/19 22:35:56 greve Exp $
Linux shalim-ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15
01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Tue Sep  2 17:28:57 IDT 2014
/usr/local/freesurfer/bin/tksurfer
list fieldsign
con/map fieldsign
/usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fieldsign.nii.gz
maplist /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fieldsign.nii.gz
mri_concat /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fieldsign.nii.gz
--o /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii
ninputs = 1
Checking inputs
nframestot = 1
Allocing output
Done allocing
nframes = 1
Writing to /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii
 cd /usr/local/freesurfer/fsfast/MeytalRetinotopy
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
tksurfer DM lh inflated -overlay
/usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii
-label-outline -colscalebarflag 1 -annot aparc -fthresh 0.5 -fmid
2.25000000000000000000 -fslope .28571428571428571428 -mask
/usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fsig.nii.gz
-mask-thresh 0.5 -fthresh .01
Contrasts
0 fieldsign
setting colscalebarflag to 1
setting fthresh to 0.5000
setting fmid to 2.2500
setting fslope to 0.2857
mrismaskfile /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fsig.nii.gz...
setting mrismaskthresh to 0.5000
setting fthresh to 0.0100
subject is DM
hemi    is lh
surface is inflated
surfer: current subjects dir: /usr/local/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer:     /usr/local/freesurfer/fsfast/MeytalRetinotopy
checking for nofix files in 'inflated'
Reading image info (/usr/local/freesurfer/subjects/DM)
Reading /usr/local/freesurfer/subjects/DM/mri/orig.mgz
surfer: Reading header info from /usr/local/freesurfer/subjects/DM/mri/orig.mgz
surfer: vertices=118099, faces=236194
tkmedit: Trying to open
/usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.dat
surfer: Interpreting overlay volume
/usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii
as encoded scalar volume.
surfer: curvature read: min=-1.094241 max=1.337460
reading colortable from annotation file...
colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Found embedded color table in annotation.
8089 vertices did not have an annotation!
surfer: single buffered window
surfer: tkoInitWindow(DM)
Reading mris mask
/usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fsig.nii.gz
surfer: using interface /usr/local/freesurfer/tktools/tksurfer.tcl
Reading /usr/local/freesurfer/tktools/tkm_common.tcl
Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl
Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /usr/local/freesurfer/tktools/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...
% ^CKilled
Area degli allegati
Visualizza anteprima allegato fieldsign_map.tiff
Fai clic qui per rispondere o inoltrare il messaggio
7,02 GB (46%) di 15 GB utilizzati
Gestisci
Ultima attività dell'account: 2 minuti fa
Dettagli