Dear FS experts,
I got an error while running selxavg3-sess for a single subject. The log
(attached) says the following:
*************************************************************
** Input 018/tmp.mc-afni2.7515/invol.nii.gz and base
018/tmp.mc-afni2.7515/tempvol.nii.gz don't have same dimensions!
Input: nx=64 ny=64 nz=35
Base: nx=64 ny=64 nz=37
** FATAL ERROR: perhaps you could make your datasets match?
ERROR: 3dvolreg
*************************************************************
I am wondering which 'template.nii' file the script reads to create
tempvol.nii.gz. We have different functional runs (with different TRs) under
the subject's bold directory and for the run '/018' the TR should be 1900 ms.
It looks like the script is reading from a 'template.nii' located elsewhere for
which the TR is 2000 ms.
*************************************************************
reading from template.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998769, -0.00721698, 0.0490727)
j_ras = (-1.73634e-08, -0.989358, -0.145502)
k_ras = (0.0496006, -0.145323, 0.98814)
changing data type from short to float (noscale = 0)...
writing to 018/tmp.mc-afni2.7515/tempvol.nii.gz...
*************************************************************
Many thanks for your help!
Hamdi
--
Hamdi Eryilmaz, PhD
Massachusetts General Hospital
A.A. Martinos Center for Biomedical Imaging
Psychiatric Neuroimaging Division
149 13th St, Charlestown, MA 02129
Phone: +1 617 643 7462
Email: hamdi.eryil...@mgh.harvard.edu<mailto:heryil...@partners.org>
selxavg3-sess log file
/usr/local/freesurfer/stable5_0_0/fsfast/bin/selxavg3-sess
-sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/FruitTask_030815 -analysis FT_TEST -overwrite
$Id: selxavg3-sess,v 1.52.2.5 2010/08/25 19:07:37 greve Exp $
uid=3429288(hhe0) gid=3429288(hhe0) groups=3429288(hhe0),1506(roffmagp)
/autofs/cluster/roffman/users/Stable5_PerRun
Linux audrey 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Sun Mar 8 18:17:22 EDT 2015
preproc-sess -s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -a FT_TEST -nolog
--------------------------------------------------------------
preproc-sess logfile is /dev/null
--------------------------------------------------------------
$Id: preproc-sess,v 1.31.2.6 2011/01/10 17:05:53 greve Exp $
hhe0
setenv FREESURFER_HOME /usr/local/freesurfer/stable5_0_0
setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun
Linux audrey 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
/autofs/cluster/roffman/users/Stable5_PerRun
/usr/local/freesurfer/stable5_0_0/fsfast/bin/preproc-sess
-s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -a FT_TEST -nolog
Sun Mar 8 18:17:22 EDT 2015
instem f
mc 1 f fmc
stc 0 fmc
sm 1 fmc fmc.sm5
mask 1 brain
GDDA074 Template -----------------------------
mktemplate-sess -s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -rlf runlistFT -nolog -update
Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA074 ----------------
Sun Mar 8 18:17:22 EDT 2015
Detected input format at nii
GDDA074 Update not needed
Run: 018 ----------------
Sun Mar 8 18:17:22 EDT 2015
GDDA074 018 Update not needed
Sun Mar 8 18:17:22 EDT 2015
mktemplate-sess completed
GDDA074 Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -rlf runlistFT -nolog -update
------------------------------------------------
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA074
Sun Mar 8 18:17:22 EDT 2015
GDDA074 Update not needed for session-level mask
GDDA074 Update not needed for run 018 mask
GDDA074 Update not needed for run 018 meanval
Sun Mar 8 18:17:22 EDT 2015
mkbrainmask-sess done
GDDA074 Registration -----------------------------
register-sess -s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf runlistFT -per-session -nolog -update
--------------------------------------------------------------
register-sess logfile is /dev/null
--------------------------------------------------------------
Sun Mar 8 18:17:23 EDT 2015
setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun
cd /autofs/cluster/roffman/users/Stable5_PerRun
/usr/local/freesurfer/stable5_0_0/fsfast/bin/register-sess -s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf runlistFT -per-session -nolog -update
freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319
Linux audrey 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA074 ----------------
Sun Mar 8 18:17:23 EDT 2015
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA074
Sun Mar 8 18:17:23 EDT 2015
register-sess completed
GDDA074 MC -----------------------------
mc-sess -fstem f -fmcstem fmc -s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -rlf runlistFT -per-session -nolog -update
Logfile is /dev/null
-------------------------------------------
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA074
RunList: 018
------- ************************** -----------
------- Motion Correcting Run 018 -----------
------- ************************** -----------
sess = GDDA074
Sun Mar 8 18:17:23 EDT 2015
mc-afni2 --i 018/f.nii --t template.nii --o 018/fmc.nii --mcdat 018/fmc.mcdat
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA074/bold
mri_info --nframes --o /tmp/mriinfo.11554 template.nii
log file is 018/fmc.nii.mclog
mcdat file is 018/fmc.mcdat
tmp dir is 018/tmp.mc-afni2.11554
#@# --------------------------------
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA074/bold
mri_convert template.nii 018/tmp.mc-afni2.11554/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float
mri_convert template.nii 018/tmp.mc-afni2.11554/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float
nskip = 0
ndrop = 0
$Id: mri_convert.c,v 1.166.2.6 2010/11/24 15:19:30 nicks Exp $
reading from template.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998769, -0.00721698, 0.0490727)
j_ras = (-1.73634e-08, -0.989358, -0.145502)
k_ras = (0.0496006, -0.145323, 0.98814)
changing data type from short to float (noscale = 0)...
writing to 018/tmp.mc-afni2.11554/tempvol.nii.gz...
#@# --------------------------------
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA074/bold
mri_convert 018/f.nii 018/tmp.mc-afni2.11554/invol.nii.gz -odt float
mri_convert 018/f.nii 018/tmp.mc-afni2.11554/invol.nii.gz -odt float
$Id: mri_convert.c,v 1.166.2.6 2010/11/24 15:19:30 nicks Exp $
reading from 018/f.nii...
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.99868, -0.00791632, 0.0507533)
j_ras = (-3.94096e-08, -0.988053, -0.154114)
k_ras = (0.0513669, -0.153911, 0.986749)
changing data type from short to float (noscale = 0)...
writing to 018/tmp.mc-afni2.11554/invol.nii.gz...
#@# --------------------------------
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA074/bold
3dvolreg -verbose -dfile 018/fmc.mcdat -1Dmatrix_save 018/fmc.mat -base 018/tmp.mc-afni2.11554/tempvol.nii.gz -prefix 018/tmp.mc-afni2.11554/outvol.nii.gz 018/tmp.mc-afni2.11554/invol.nii.gz
++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Dec 23 2014) [64-bit]
++ Authored by: RW Cox
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as 018/tmp.mc-afni2.11554/tempvol.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:018/tmp.mc-afni2.11554/tempvol.nii.gz is 8.832977 degrees from plumb.
++ Reading in base dataset 018/tmp.mc-afni2.11554/tempvol.nii.gz
++ Oblique dataset:018/tmp.mc-afni2.11554/invol.nii.gz is 9.337868 degrees from plumb.
++ centers of base and input datasets are 1.57 mm apart
** Input 018/tmp.mc-afni2.11554/invol.nii.gz and base 018/tmp.mc-afni2.11554/tempvol.nii.gz don't have same dimensions!
Input: nx=64 ny=64 nz=35
Base: nx=64 ny=64 nz=37
** FATAL ERROR: perhaps you could make your datasets match?
ERROR: 3dvolreg
Invalid null command.
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