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.edu3.10.0-1160.6.1.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.edu3.10.0-1160.6.1.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 184.0548

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 155.6942

0.0138 -0.0739 -0.9452 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