is this still a problem?
On 03/04/2016 01:24 PM, Sahil Bajaj wrote:
Dear all,
I am working on calculation of cortical thickness from a set of subjects. I am following the instructions from https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness and I am able to run up-to step-2 successfully i.e. I can display the ROIs on fsaverage subject volume. But when I run step-3 using:
*mri_vol2surf --mov /media/Storage/FTD_Data/S01_LP/mri/lh_cuneus.nii --reg TT.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out ROI5.mgh --reshape*
It runs as follow:
(here lh_cuneus.nii is one of the ROIs,FTD_Data is my subject directory for FreeSurfer and S01_LP is the output folder for one of the subjects after running recon -all)
srcvol = /media/Storage/FTD_Data/S01_LP/mri/lh_cuneus.nii srcreg = TT.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = 0.5 reshape = 1 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /media/Storage/FTD_Data/fsaverage/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 1 using old 2 0.1 0 1 using old 3 0.2 0 1 using old 4 0.3 0 1 using old 5 0.4 0 1 using old 6 0.5 0 1 using old 7 0.6 0 1 using old 8 0.7 0 1 using old 9 0.8 0 1 using old 10 0.9 0 1 using old Done mapping volume to surface Number of source voxels hit = 75054 Reshaping 7 (nvertices = 163842) Writing to ROI5.mgh Dim: 23406 1 7
Although I don't see any error here but when I display using:
*tksurfer fsaverage lh inflated -overlay ROI5.mgh -fthresh 0.5*
it runs as follow:
setting fthresh to 0.5000 subject is fsaverage hemi is lh surface is inflated surfer: current subjects dir: /media/Storage/FTD_Data surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /media/Storage/FTD_Data/fsaverage/surf checking for nofix files in 'inflated' Reading image info (/media/Storage/FTD_Data/fsaverage) Reading /media/Storage/FTD_Data/fsaverage/mri/orig.mgz surfer: Reading header info from /media/Storage/FTD_Data/fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 tkmedit: Trying to open ROI5.dat surfer: Interpreting overlay volume ROI5.mgh as encoded scalar volume. surfer: curvature read: min=-0.673989 max=0.540227 surfer: single buffered window surfer: tkoInitWindow(fsaverage) surfer: using interface /home/sahil/Softwares/freesurfer/tktools/tksurfer.tcl Reading /home/sahil/Softwares/freesurfer/tktools/tkm_common.tcl Reading /home/sahil/Softwares/freesurfer/tktools/tkm_wrappers.tcl Reading /home/sahil/Softwares/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/sahil/Softwares/freesurfer/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations...
Again, I don't see any error here. But ROI ROI5.mgh is not displayed on the fsaverage surface. I tried to overlay ROI5.mgh on lh inflated using freeview as well but ROI5.mgh is nowhere.
I would really appreciate any help.
Thanks,
Sahil
Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. Office: 713-363-9003 E-mail:sahil.neuro@gmail.com mailto:E-mail%3Asahil.phy@gmail.com
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