Hi FreeSurfer Developers,
I am trying to process a few MPRAGE sequences (different sessions), so I can edit the scans. And I am having trouble reconning the .mgz files.
I have looked into why my job terminated early and I have attached the message below. The error states that 'input(s) cannot have multiple frames'. And I then looked into the mri_info, which I have also attached below, and based off of some similar questions I found in the archive, my dimensions seem to be incorrect for freesurfer to process. My dimensions are 240 x 256 x 176 x 2, and I believe they should be 240 x 256 x 176 in order for it to work. How do I go about fixing my dimensions? Does it have to do with how I unpacked the DICOMS? I have not run into this issue before so I would love to learn what caused this error.
Thanks in advance,
Stephanie
Early termination error:
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /autofs/cluster/brutha/FS6
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0
Linux compute-0-85.nmr.mgh.harvard.eduhttp://compute-0-85.nmr.mgh.harvard.edu/3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
'/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/recon-all' -> '/autofs/cluster/brutha/FS6/SCD_021_BL/scripts/recon-all.local-copy'
/autofs/cluster/brutha/FS6/SCD_021_BL
mri_convert /autofs/cluster/brutha/FS6/SCD_021_BL-1.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz
mri_convert.bin /autofs/cluster/brutha/FS6/SCD_021_BL-1.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /autofs/cluster/brutha/FS6/SCD_021_BL-1.mgz...
TR=2300.00, TE=2.95, TI=900.00, flip angle=9.00
i_ras = (0.108201, -0.990984, 0.079018)
j_ras = (0.0145467, -0.0778978, -0.996855)
k_ras = (-0.994023, -0.10901, -0.00598659)
writing to /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz...
/autofs/cluster/brutha/FS6/SCD_021_BL
mri_convert /autofs/cluster/brutha/FS6/SCD_021_BL-2.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz
mri_convert.bin /autofs/cluster/brutha/FS6/SCD_021_BL-2.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /autofs/cluster/brutha/FS6/SCD_021_BL-2.mgz...
TR=2300.00, TE=2.95, TI=900.00, flip angle=9.00
i_ras = (0.108201, -0.990984, 0.079018)
j_ras = (0.0145467, -0.0778978, -0.996855)
k_ras = (-0.994023, -0.10901, -0.00598659)
writing to /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz...
#--------------------------------------------
#@# MotionCor Thu Dec 10 21:00:24 EST 2020
Found 2 runs
/autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz
/autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz has 2 frames
Linux compute-0-85.nmr.mgh.harvard.eduhttp://compute-0-85.nmr.mgh.harvard.edu/3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s SCD_021_BL exited with ERRORS at Thu Dec 10 21:00:25 EST 2020
mri_info on the session I am trying to run:
Volume information for SCD_021_BL-1.mgz
type: MGH
dimensions: 240 x 256 x 176 x 2
voxel sizes: 1.054688, 1.054688, 1.200000
type: SHORT (4)
fov: 270.000
dof: 0
xstart: -126.6, xend: 126.6
ystart: -135.0, yend: 135.0
zstart: -105.6, zend: 105.6
TR: 2300.00 msec, TE: 2.95 msec, TI: 900.00 msec, flip angle: 9.00 degrees
nframes: 2
PhEncDir: ROW
FieldStrength: 3.000000
ras xform present
xform info: x_r = 0.1082, y_r = 0.0145, z_r = -0.9940, c_r = 9.2070
: x_a = -0.9910, y_a = -0.0779, z_a = -0.1090, c_a = 36.6058
: x_s = 0.0790, y_s = -0.9969, z_s = -0.0060, c_s = -29.9521
talairach xfm :
Orientation : PIL
Primary Slice Direction: sagittal
voxel to ras transform:
0.1141 0.0153 -1.1928 98.5179
-1.0452 -0.0822 -0.1308 184.0548tel:184.0548
0.0833 -1.0514 -0.0072 95.2548
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1.33484
ras to voxel transform:
0.1026 -0.9396 0.0749 155.6942tel:155.6942
0.0138 -0.0739 -0.9452 102.2669tel:102.2669
-0.8284 -0.0908 -0.0050 98.8026
-0.0000 -0.0000 -0.0000 1.0000
Volume information for SCD_021_BL-2.mgz
type: MGH
dimensions: 240 x 256 x 176 x 2
voxel sizes: 1.054688, 1.054688, 1.200000
type: SHORT (4)
fov: 270.000
dof: 0
xstart: -126.6, xend: 126.6
ystart: -135.0, yend: 135.0
zstart: -105.6, zend: 105.6
TR: 2300.00 msec, TE: 2.95 msec, TI: 900.00 msec, flip angle: 9.00 degrees
nframes: 2
PhEncDir: ROW
FieldStrength: 3.000000
ras xform present
xform info: x_r = 0.1082, y_r = 0.0145, z_r = -0.9940, c_r = 9.2070
: x_a = -0.9910, y_a = -0.0779, z_a = -0.1090, c_a = 36.6058
: x_s = 0.0790, y_s = -0.9969, z_s = -0.0060, c_s = -29.9521
talairach xfm :
Orientation : PIL
Primary Slice Direction: sagittal
voxel to ras transform:
0.1141 0.0153 -1.1928 98.5179
-1.0452 -0.0822 -0.1308 184.0548tel:184.0548
0.0833 -1.0514 -0.0072 95.2548
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1.33484
ras to voxel transform:
0.1026 -0.9396 0.0749 155.6942tel:155.6942
0.0138 -0.0739 -0.9452 102.2669tel:102.2669
-0.8284 -0.0908 -0.0050 98.8026
-0.0000 -0.0000 -0.0000 1.0000
What are the 2 frames? You could extract the first or the second or average them or compute an RMS, but it depends on what is there
On 12/17/2020 2:03 PM, Hsieh, Stephanie wrote:
freesurfer@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
Hsieh, Stephanie