What is fICL161363_000006_1_MRI_9746_series_2_MPRAGE_ADNI_P2.nii ? In general,
you should not give mri_coreg a reference when using --s unless it is the same
geometry as the orig.mgz
On 3/29/19 11:55 AM, ?? wrote:
External Email - Use Caution
Hi developers,
I am using the petsurfer now to do the PVC for my dynamic analysis, however
there is something error happened.
Here is my commends:
mri_coreg --mov fICL161363_000006_1_BU99008_9744_merged_00015.nii --ref
fICL161363_000006_1_MRI_9746_series_2_MPRAGE_ADNI_P2.nii --reg template.reg.lta
--s subject6
mri_gtmpvc --i fICL161363_000006_1_BU99008_9744_merged.nii --reg
template.reg.lta --psf-col 9.2 --psf-row 10.5 --psf-slice 14.6 --seg
subject6/mri/gtmseg.mgz --default-seg-merge --mgx .01 --o gtmpvc.output
--km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale
the coreg was ok, however the gtmpvc is not ok, here is the lines show my
terminal, could you tell me what's the problem and how to fix it, Thanks so
much for help me.
Loading input fICL161363_000006_1_BU99008_9744_merged.nii
WARNING: niiRead(): unknown time units 0 in
/Volumes/NIU20/analysis/volumetric_FS/trail/fICL161363_000006_1_BU99008_9744_merged.nii
INFO: using NIfTI-1 qform
done loading input 28 frames
$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $
setenv SUBJECTS_DIR /Volumes/NIU20/analysis/volumetric_FS/trail
cd /Volumes/NIU20/analysis/volumetric_FS/trail
mri_gtmpvc --i fICL161363_000006_1_BU99008_9744_merged.nii --reg
template.reg.lta --psf-col 9.2 --psf-row 10.5 --psf-slice 14.6 --seg
subject6/mri/gtmseg.mgz --default-seg-merge --mgx .01 --o gtmpvc.output
--km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale
sysname Darwin
hostname cengzhoudeMacBook-Air.local
machine x86_64
user cengzhou
vgthresh 0.001000
nReplace 18
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
4 avail.processors, using 1
Creating output directory gtmpvc.output
Loading seg for gtm subject6/mri/gtmseg.mgz
Loading seg ctab subject6/mri/gtmseg.ctab
Reading subject6/mri/gtmseg.lta
ERROR: LTAconcat(): LTAs 0 and 1 do not match
LTA 0 -------------------
type = 0 # LINEAR_VOX_TO_VOX
nxforms = 1
mean = 0.0000 0.0000 0.0000
sigma = 10000.0000
1 4 4
5.000000000000000e-01 0.000000000000000e+00 0.000000000000000e+00
4.875000000000000e+01
0.000000000000000e+00 5.000000000000000e-01 0.000000000000000e+00
3.475000000000000e+01
0.000000000000000e+00 0.000000000000000e+00 5.000000000000000e-01
1.775000000000000e+01
0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
1.000000000000000e+00
src volume info
valid = 1 # volume info valid
filename =
/Volumes/NIU20/analysis/volumetric_FS/trail/subject6/mri/apas+head.mgz
volume = 316 440 438
voxelsize = 5.000000000000000e-01 5.000000000000000e-01 5.000000000000000e-01
xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
yras = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00
zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
cras = 2.500000000000000e-01 -7.500000000000000e-01 -1.675000000000000e+01
dst volume info
valid = 1 # volume info valid
filename =
/Volumes/NIU20/analysis/volumetric_FS/trail/subject6/mri/apas+head.mgz
volume = 256 256 256
voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00
xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
yras = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00
zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
cras = 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
subject subject6
fscale 0.150000
LTA 1 -------------------
type = 0 # LINEAR_VOX_TO_VOX
nxforms = 1
mean = 0.0000 0.0000 0.0000
sigma = 10000.0000
1 4 4
1.490079522132874e+00 -1.009208321571350e+00 -9.591113924980164e-01
8.742171478271484e+01
9.481825828552246e-01 1.776931047439575e+00 -3.772042095661163e-01
-4.950695037841797e+01
1.042477130889893e+00 -1.736743301153183e-01 1.714007139205933e+00
2.799880599975586e+01
0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
1.000000000000000e+00
src volume info
valid = 1 # volume info valid
filename = fICL161363_000006_1_BU99008_9744_merged_00015.nii
volume = 128 128 82
voxelsize = 2.050889968872070e+00 2.050889968872070e+00 2.000000000000000e+00
xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
yras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
zras = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
cras = 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
dst volume info
valid = 1 # volume info valid
filename = fICL161363_000006_1_MRI_9746_series_2_MPRAGE_ADNI_P2.nii
volume = 160 240 256
voxelsize = 1.000000953674316e+00 1.000000000000000e+00 1.000000000000000e+00
xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
yras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
zras = -0.000000000000000e+00 -0.000000000000000e+00 1.000000000000000e+00
cras = 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
subject subject6
fscale 0.150000
--------------------------
ERROR: LTAconcat()
mri_gtmpvc exited with errors
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
