Hi,
Have you ran fieldsign-sess after your selxavg3-sess?
On Thu, Sep 4, 2014 at 8:35 AM, Francesca Strappini <
francescastrapp...@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
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--
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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