Yes, this was the command line
fieldsign-sess -a rtopy.LG.lh -s SUBJ02 -patch lh.full.flat.patch.3d -fwhm 0
Thanks! Francesca
2014-09-04 15:52 GMT+03:00 SHAHIN NASR shahin@nmr.mgh.harvard.edu:
Hi, Have you ran fieldsign-sess after your selxavg3-sess?
On Thu, Sep 4, 2014 at 8:35 AM, Francesca Strappini francescastrappini@gmail.com wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shahin Nasr
PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School
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.