[Freesurfer] how i can compute volume of a VOI

2012-08-31 Thread Eustratios Karavasilis 
Dear all, 
 
i am new Freesurfer user (Freesurfer 5.0 installed). I want to calculate the 
volume of a VOI that is not calculated from recon all. 
I ll decribe you the steps that were followed. Using tkmedit and tkmedit tools 
i created ROIs in many slices. Every ROI i saved it as label,
then i merge all the labels using the mri_mergelabels. I am trying create a 
volume from this final label using mri_label2vol, using as label the new 
final label, 
as template volume the origin volume (orig.mgz) but i don't have the 
register.dat file. How i can create it?
The above way is the appropriate way to calculate a VOI?
 
Thank you in advance!___
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[Freesurfer] Help Error running recon-all-s during installation test

2012-04-23 Thread Eustratios Karavasilis 
Dear all,

I am new freesurfer user (version 5.0.0 installed to windows using virtual 
machine),
during the installation i was trying to test the installation, following the 
recommended steps.
The recon-all -s terminated with errors, andi can't find the bug.

I send you the command line and the report including the error message to help 
you.

--
FREESURFER_HOME   /home/virtualuser/freesurfer
SUBJECTS_DIR  /home/virtualuser/freesurfer/subjects
--

FreeSurfer:~ recon-all -s ernie -i $SUBJECTS_DIR/sample-001.mgz -i 
$SUBJECTS_DIR/sample-002.mgz -autorecon1
Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects
Actual FREESURFER_HOME /home/virtualuser/freesurfer
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 
i686 GNU/Linux
/home/virtualuser/freesurfer/subjects/ernie
 mri_convert /home/virtualuser/freesurfer/subjects/sample-001.mgz 
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz
mri_convert /home/virtualuser/freesurfer/subjects/sample-001.mgz 
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
reading from /home/virtualuser/freesurfer/subjects/sample-001.mgz...
TR=7.25, TE=3.22, TI=600.00, flip angle=7.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz...
/home/virtualuser/freesurfer/subjects/ernie
 mri_convert /home/virtualuser/freesurfer/subjects/sample-002.mgz 
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz
mri_convert /home/virtualuser/freesurfer/subjects/sample-002.mgz 
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz
$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
reading from /home/virtualuser/freesurfer/subjects/sample-002.mgz...
TR=7.25, TE=3.22, TI=600.00, flip angle=7.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz...
#
#@# MotionCor Mon Apr 23 04:55:18 EDT 2012
Found 2 runs
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz
Checking for (invalid) multi-frame inputs...
Checking for (invalid) multi-frame inputs...
#---
/home/virtualuser/freesurfer/subjects/ernie
 mri_robust_template --mov 
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz 
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz --average 1 
--template /home/virtualuser/freesurfer/subjects/ernie/mri/rawavg.mgz --satit 
--inittp 1 --fixtp --noit --iscale --iscaleout 
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001-iscale.txt 
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002-iscale.txt --subsample 
200 --lta /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.lta 
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.lta
$Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $
--mov: Using /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz as 
movable/source volume.
--mov: Using /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz as 
movable/source volume.
    Total: 2 input volumes
--average: Using method 1 for template computation.
--template: Using /home/virtualuser/freesurfer/subjects/ernie/mri/rawavg.mgz as 
template output volume.
--satit: Will estimate SAT iteratively!
--inittp: Using TP 1 as target for initialization
--fixtp: Will map everything to init TP!
--noit: Will output only first template (no iterations)!
--iscale: Enableing intensity scaling!
--iscaleout: Will perform intensity scaling and output results
--subsample: Will subsample if size is larger than 200 on all axes!
--lta: Will output LTA transforms
reading source '/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz'...
reading source '/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz'...
MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 
0.01 ) :
[init] = TP 2 to TP 1 ==
 Register TP 2 ( 
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz )
  to  TP 1 ( 
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz )
Registration::setSourceAndTarget ...
   Mov: (1, 1, 1.32812)mm  and dim (256, 256, 128)
   Dst: (1, 1, 1.32812)mm  and dim (256, 256, 128)
   Asserting both images: 1mm isotropic and (256, 256, 170) voxels
   Original : (1, 1, 1.32812) mm size and (256, 256, 128) voxels.
   Resampled: (1, 1, 1) mm size and (256, 256, 170) voxels.
   Reslicing using trilinear interpolation
   Original : (1, 1, 1.32812) mm size and (256, 256, 128)