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Hi Ben, 

The difference between the subject that worked and the one that didn’t is that the failed subject image has multiple volumes (61). The error message you provided also indicates this is the source. Prior to running tbss, what steps have you performed? You have some images with a single volume, and others with many volumes. 

The source of your error is the multivolume issue, which is causing registration to fail. 


Cheers,

-Taylor

On 6 Mar 2019, at 12:11, Benjamin Davidson <[log in to unmask]> wrote:

Hi Taylor,
Thanks for the help, here's the info you requested:
cat tbss_2_reg.e12293.1
Image Exception : #75 :: 3D only method called by higher-dimensional volume.
Error occured during estimation at first level of subsampling
Exception thrown with message: 3D only method called by higher-dimensional volume.
Image Exception : #63 :: No image files match: subj10Day1_FA_to_target_warp
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: subj10Day1_FA_to_target_warp
Aborted (core dumped)
Image Exception : #63 :: No image files match: subj10Day1_FA_to_target_tmp
Image Exception : #22 :: Failed to read volume subj10Day1_FA_to_target_tmp
Error : No image files match: subj10Day1_FA_to_target_tmp
Failed to read volume subj10Day1_FA_to_target_tmp
Error : No image files match: subj10Day1_FA_to_target_tmp

Subject that worked:
fslhd subj1Day1_FA.nii.gz
filename    subj1Day1_FA.nii.gz
size of header    348
data_type    FLOAT32
dim0        3
dim1        128
dim2        128
dim3        72
dim4        1
dim5        1
dim6        1
dim7        1
vox_units    mm
time_units    s
datatype    16
nbyper        4
bitpix        32
pixdim0        -1.000000
pixdim1        1.875000
pixdim2        1.875000
pixdim3        2.000000
pixdim4        9.000000
pixdim5        0.000000
pixdim6        0.000000
pixdim7        0.000000
vox_offset    352
cal_max        0.000000
cal_min        0.000000
scl_slope    1.000000
scl_inter    0.000000
phase_dim    0
freq_dim    0
slice_dim    0
slice_name    Unknown
slice_code    0
slice_start    0
slice_end    0
slice_duration    0.000000
toffset        0.000000
intent        Unknown
intent_code    0
intent_name   
intent_p1    0.000000
intent_p2    0.000000
intent_p3    0.000000
qform_name    Scanner Anat
qform_code    1
qto_xyz:1    -1.875000 0.000000 -0.000000 118.906998
qto_xyz:2    0.000000 1.875000 -0.000000 -80.184006
qto_xyz:3    0.000000 0.000000 2.000000 -74.371902
qto_xyz:4    0.000000 0.000000 0.000000 1.000000
qform_xorient    Right-to-Left
qform_yorient    Posterior-to-Anterior
qform_zorient    Inferior-to-Superior
sform_name    Scanner Anat
sform_code    1
sto_xyz:1    -1.875000 0.000000 0.000000 118.906998
sto_xyz:2    0.000000 1.875000 0.000000 -80.184006
sto_xyz:3    0.000000 0.000000 2.000000 -74.371902
sto_xyz:4    0.000000 0.000000 0.000000 1.000000
sform_xorient    Right-to-Left
sform_yorient    Posterior-to-Anterior
sform_zorient    Inferior-to-Superior
file_type    NIFTI-1+
file_code    1
descrip        6.0.0
aux_file   

Subject that didn't work (session):
fslhd subj1Month3_FA.nii.gz
filename    subj1Month3_FA.nii.gz
size of header    348
data_type    FLOAT32
dim0        4
dim1        128
dim2        128
dim3        61
dim4        61
dim5        1
dim6        1
dim7        1
vox_units    mm
time_units    s
datatype    16
nbyper        4
bitpix        32
pixdim0        -1.000000
pixdim1        1.875000
pixdim2        1.875000
pixdim3        2.000000
pixdim4        9.000000
pixdim5        0.000000
pixdim6        0.000000
pixdim7        0.000000
vox_offset    352
cal_max        0.000000
cal_min        0.000000
scl_slope    1.000000
scl_inter    0.000000
phase_dim    0
freq_dim    0
slice_dim    0
slice_name    Unknown
slice_code    0
slice_start    0
slice_end    0
slice_duration    0.000000
toffset        0.000000
intent        Unknown
intent_code    0
intent_name   
intent_p1    0.000000
intent_p2    0.000000
intent_p3    0.000000
qform_name    Scanner Anat
qform_code    1
qto_xyz:1    -1.875000 0.000000 -0.000000 120.000000
qto_xyz:2    0.000000 1.875000 -0.000000 -98.750000
qto_xyz:3    0.000000 0.000000 2.000000 -65.687798
qto_xyz:4    0.000000 0.000000 0.000000 1.000000
qform_xorient    Right-to-Left
qform_yorient    Posterior-to-Anterior
qform_zorient    Inferior-to-Superior
sform_name    Scanner Anat
sform_code    1
sto_xyz:1    -1.875000 0.000000 0.000000 120.000000
sto_xyz:2    0.000000 1.875000 0.000000 -98.750000
sto_xyz:3    0.000000 0.000000 1.999996 -65.687798
sto_xyz:4    0.000000 0.000000 0.000000 1.000000
sform_xorient    Right-to-Left
sform_yorient    Posterior-to-Anterior
sform_zorient    Inferior-to-Superior
file_type    NIFTI-1+
file_code    1
descrip        6.0.0
aux_file   

Thanks!


On Tue, Mar 5, 2019 at 6:31 AM Taylor Hanayik <[log in to unmask]> wrote:
Hi Ben,

Could you supply the contents of one of your tbss log files (the ones with a “.e” in the filename)?

One that has a size greater than zero (such as `cat tbss_2_reg.e18618.10`). If you have re-run this since we last spoke then the file name may be different, but any file with a size greater than zero should work. 

Also, for the subjects that have registration errors, the FA image size is much smaller than the ones that succeeded. 

Could you run fslhd on an FA image that worked, and one that did not, and email back the results?




Cheers,

Taylor Hanayik


Taylor Hanayik PhD
FMRIB, John Radcliffe Hospital
University of Oxford





On Feb 28, 2019, at 4:37 PM, Benjamin Davidson <[log in to unmask]> wrote:

Running the TBSS 1 and 2 steps again with just the first 3 subjects yields this:
nir@nir-ThinkStation:/media/nir/SharedDrive/Ben/DTItest/TBSS-backup$ tbss_1_preproc *
processing subj1Day1
processing subj1Month3
processing subj1Month6
processing subj1PREOP
processing subj2Day1
processing subj2Month3
processing subj2Month6
processing subj2PREOP
processing subj3Day1
processing subj3Month3
processing subj3Month6
processing subj3PREOP
Now running "slicesdir" to generate report of all input images
Finished. To view, point your web browser at
file:/media/nir/SharedDrive/Ben/DTItest/TBSS-backup/FA/slicesdir/index.html

nir@nir-ThinkStation:/media/nir/SharedDrive/Ben/DTItest/TBSS-backup$ tbss_2_reg -T
subj1Day1_FA_to_target
subj1Month3_FA_to_target
subj1Month6_FA_to_target
subj1PREOP_FA_to_target
subj2Day1_FA_to_target
subj2Month3_FA_to_target
subj2Month6_FA_to_target
subj2PREOP_FA_to_target
subj3Day1_FA_to_target
subj3Month3_FA_to_target
subj3Month6_FA_to_target
subj3PREOP_FA_to_target
18618

nir@nir-ThinkStation:/media/nir/SharedDrive/Ben/DTItest/TBSS-backup$ ls -Ral
.:
total 32
drwxrwxrwx 1 nir nir  8192 Feb 28 11:09 .
drwxrwxrwx 1 nir nir  4096 Feb 28 09:11 ..
drwxrwxrwx 1 nir nir 12288 Feb 28 11:28 FA
drwxrwxrwx 1 nir nir  4096 Feb 28 11:09 origdata
-rwxrwxrwx 1 nir nir  2494 Feb 28 11:12 .tbsslog

./FA:
total 14160
drwxrwxrwx 1 nir nir   12288 Feb 28 11:28 .
drwxrwxrwx 1 nir nir    8192 Feb 28 11:09 ..
-rwxrwxrwx 1 nir nir    1002 Feb 28 11:12 .commands
drwxrwxrwx 1 nir nir    4096 Feb 28 11:10 slicesdir
-rwxrwxrwx 1 nir nir   50271 Feb 28 10:50 subj1Day1_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir 1286363 Feb 28 10:49 subj1Day1_FA.nii.gz
-rwxrwxrwx 1 nir nir    2156 Feb 28 11:13 subj1Day1_FA_to_target.log
-rwxrwxrwx 1 nir nir     187 Feb 28 11:13 subj1Day1_FA_to_target.mat
-rwxrwxrwx 1 nir nir      19 Feb 28 11:14 subj1Day1_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  774585 Feb 28 11:14 subj1Day1_FA_to_target_warp.nii.gz
-rwxrwxrwx 1 nir nir  141002 Feb 28 10:52 subj1Month3_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  331266 Feb 28 10:50 subj1Month3_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 28 11:15 subj1Month3_FA_to_target.log
-rwxrwxrwx 1 nir nir     183 Feb 28 11:15 subj1Month3_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 28 11:15 subj1Month3_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  153849 Feb 28 10:54 subj1Month6_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  370819 Feb 28 10:53 subj1Month6_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 28 11:16 subj1Month6_FA_to_target.log
-rwxrwxrwx 1 nir nir     185 Feb 28 11:16 subj1Month6_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 28 11:16 subj1Month6_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir   32622 Feb 28 10:54 subj1PREOP_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  887725 Feb 28 10:54 subj1PREOP_FA.nii.gz
-rwxrwxrwx 1 nir nir    2159 Feb 28 11:16 subj1PREOP_FA_to_target.log
-rwxrwxrwx 1 nir nir     190 Feb 28 11:16 subj1PREOP_FA_to_target.mat
-rwxrwxrwx 1 nir nir      20 Feb 28 11:17 subj1PREOP_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  780378 Feb 28 11:17 subj1PREOP_FA_to_target_warp.nii.gz
-rwxrwxrwx 1 nir nir  164499 Feb 28 10:57 subj2Day1_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  395279 Feb 28 10:55 subj2Day1_FA.nii.gz
-rwxrwxrwx 1 nir nir    2156 Feb 28 11:19 subj2Day1_FA_to_target.log
-rwxrwxrwx 1 nir nir     188 Feb 28 11:19 subj2Day1_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 28 11:19 subj2Day1_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  169698 Feb 28 10:59 subj2Month3_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  399289 Feb 28 10:58 subj2Month3_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 28 11:20 subj2Month3_FA_to_target.log
-rwxrwxrwx 1 nir nir     189 Feb 28 11:20 subj2Month3_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 28 11:20 subj2Month3_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  157672 Feb 28 11:02 subj2Month6_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  374665 Feb 28 11:00 subj2Month6_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 28 11:21 subj2Month6_FA_to_target.log
-rwxrwxrwx 1 nir nir     191 Feb 28 11:21 subj2Month6_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 28 11:21 subj2Month6_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir   38171 Feb 28 11:02 subj2PREOP_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir 1057605 Feb 28 11:02 subj2PREOP_FA.nii.gz
-rwxrwxrwx 1 nir nir    2159 Feb 28 11:22 subj2PREOP_FA_to_target.log
-rwxrwxrwx 1 nir nir     191 Feb 28 11:22 subj2PREOP_FA_to_target.mat
-rwxrwxrwx 1 nir nir      21 Feb 28 11:23 subj2PREOP_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  775158 Feb 28 11:23 subj2PREOP_FA_to_target_warp.nii.gz
-rwxrwxrwx 1 nir nir  153030 Feb 28 11:04 subj3Day1_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  371069 Feb 28 11:03 subj3Day1_FA.nii.gz
-rwxrwxrwx 1 nir nir    2156 Feb 28 11:24 subj3Day1_FA_to_target.log
-rwxrwxrwx 1 nir nir     189 Feb 28 11:24 subj3Day1_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 28 11:24 subj3Day1_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  162497 Feb 28 11:07 subj3Month3_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  390669 Feb 28 11:05 subj3Month3_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 28 11:25 subj3Month3_FA_to_target.log
-rwxrwxrwx 1 nir nir     186 Feb 28 11:25 subj3Month3_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 28 11:25 subj3Month3_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  168689 Feb 28 11:09 subj3Month6_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  399471 Feb 28 11:08 subj3Month6_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 28 11:26 subj3Month6_FA_to_target.log
-rwxrwxrwx 1 nir nir     184 Feb 28 11:26 subj3Month6_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 28 11:26 subj3Month6_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir   30435 Feb 28 11:09 subj3PREOP_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  905172 Feb 28 11:09 subj3PREOP_FA.nii.gz
-rwxrwxrwx 1 nir nir    2159 Feb 28 11:27 subj3PREOP_FA_to_target.log
-rwxrwxrwx 1 nir nir     192 Feb 28 11:27 subj3PREOP_FA_to_target.mat
-rwxrwxrwx 1 nir nir      20 Feb 28 11:28 subj3PREOP_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  777661 Feb 28 11:28 subj3PREOP_FA_to_target_warp.nii.gz
-rwxrwxrwx 1 nir nir 2646918 Feb 28 11:12 target.nii.gz
drwxrwxrwx 1 nir nir    4096 Feb 28 11:26 tbss_logs

./FA/slicesdir:
total 1412
drwxrwxrwx 1 nir nir   4096 Feb 28 11:10 .
drwxrwxrwx 1 nir nir  12288 Feb 28 11:28 ..
-rwxrwxrwx 1 nir nir  11498 Feb 28 11:10 grota.png
-rwxrwxrwx 1 nir nir  12747 Feb 28 11:10 grotb.png
-rwxrwxrwx 1 nir nir  12808 Feb 28 11:10 grotc.png
-rwxrwxrwx 1 nir nir  10728 Feb 28 11:10 grotd.png
-rwxrwxrwx 1 nir nir  10214 Feb 28 11:10 grote.png
-rwxrwxrwx 1 nir nir   8768 Feb 28 11:10 grotf.png
-rwxrwxrwx 1 nir nir  13121 Feb 28 11:10 grotg.png
-rwxrwxrwx 1 nir nir  12545 Feb 28 11:10 groth.png
-rwxrwxrwx 1 nir nir  11948 Feb 28 11:10 groti.png
-rwxrwxrwx 1 nir nir   1182 Feb 28 11:10 index.html
-rwxrwxrwx 1 nir nir 120652 Feb 28 11:09 subj1Day1_FA.png
-rwxrwxrwx 1 nir nir 120652 Feb 28 11:10 subj1Month3_FA.png
-rwxrwxrwx 1 nir nir 120652 Feb 28 11:10 subj1Month6_FA.png
-rwxrwxrwx 1 nir nir  99752 Feb 28 11:10 subj1PREOP_FA.png
-rwxrwxrwx 1 nir nir  99752 Feb 28 11:10 subj2Day1_FA.png
-rwxrwxrwx 1 nir nir  99752 Feb 28 11:10 subj2Month3_FA.png
-rwxrwxrwx 1 nir nir  99752 Feb 28 11:10 subj2Month6_FA.png
-rwxrwxrwx 1 nir nir 105817 Feb 28 11:10 subj2PREOP_FA.png
-rwxrwxrwx 1 nir nir 105817 Feb 28 11:10 subj3Day1_FA.png
-rwxrwxrwx 1 nir nir 105817 Feb 28 11:10 subj3Month3_FA.png
-rwxrwxrwx 1 nir nir 105817 Feb 28 11:10 subj3Month6_FA.png
-rwxrwxrwx 1 nir nir  93310 Feb 28 11:10 subj3PREOP_FA.png

./FA/tbss_logs:
total 48
drwxrwxrwx 1 nir nir  4096 Feb 28 11:26 .
drwxrwxrwx 1 nir nir 12288 Feb 28 11:28 ..
-rwxrwxrwx 1 nir nir     0 Feb 28 11:12 tbss_2_reg.e18618.1
-rwxrwxrwx 1 nir nir   776 Feb 28 11:25 tbss_2_reg.e18618.10
-rwxrwxrwx 1 nir nir   776 Feb 28 11:26 tbss_2_reg.e18618.11
-rwxrwxrwx 1 nir nir     0 Feb 28 11:26 tbss_2_reg.e18618.12
-rwxrwxrwx 1 nir nir   776 Feb 28 11:15 tbss_2_reg.e18618.2
-rwxrwxrwx 1 nir nir   776 Feb 28 11:16 tbss_2_reg.e18618.3
-rwxrwxrwx 1 nir nir     0 Feb 28 11:16 tbss_2_reg.e18618.4
-rwxrwxrwx 1 nir nir   762 Feb 28 11:19 tbss_2_reg.e18618.5
-rwxrwxrwx 1 nir nir   776 Feb 28 11:20 tbss_2_reg.e18618.6
-rwxrwxrwx 1 nir nir   776 Feb 28 11:21 tbss_2_reg.e18618.7
-rwxrwxrwx 1 nir nir     0 Feb 28 11:21 tbss_2_reg.e18618.8
-rwxrwxrwx 1 nir nir   762 Feb 28 11:24 tbss_2_reg.e18618.9
-rwxrwxrwx 1 nir nir     0 Feb 28 11:12 tbss_2_reg.o18618.1
-rwxrwxrwx 1 nir nir     0 Feb 28 11:24 tbss_2_reg.o18618.10
-rwxrwxrwx 1 nir nir     0 Feb 28 11:25 tbss_2_reg.o18618.11
-rwxrwxrwx 1 nir nir     0 Feb 28 11:26 tbss_2_reg.o18618.12
-rwxrwxrwx 1 nir nir     0 Feb 28 11:14 tbss_2_reg.o18618.2
-rwxrwxrwx 1 nir nir     0 Feb 28 11:15 tbss_2_reg.o18618.3
-rwxrwxrwx 1 nir nir     0 Feb 28 11:16 tbss_2_reg.o18618.4
-rwxrwxrwx 1 nir nir     0 Feb 28 11:17 tbss_2_reg.o18618.5
-rwxrwxrwx 1 nir nir     0 Feb 28 11:19 tbss_2_reg.o18618.6
-rwxrwxrwx 1 nir nir     0 Feb 28 11:20 tbss_2_reg.o18618.7
-rwxrwxrwx 1 nir nir     0 Feb 28 11:21 tbss_2_reg.o18618.8
-rwxrwxrwx 1 nir nir     0 Feb 28 11:23 tbss_2_reg.o18618.9

./origdata:
total 604960
drwxrwxrwx 1 nir nir     4096 Feb 28 11:09 .
drwxrwxrwx 1 nir nir     8192 Feb 28 11:09 ..
-rwxrwxrwx 1 nir nir  1789774 Feb 13 14:37 subj1Day1.nii.gz
-rwxrwxrwx 1 nir nir 66748698 Feb 13 15:27 subj1Month3.nii.gz
-rwxrwxrwx 1 nir nir 74085143 Feb 13 15:57 subj1Month6.nii.gz
-rwxrwxrwx 1 nir nir  1151150 Feb 13 17:23 subj1PREOP.nii.gz
-rwxrwxrwx 1 nir nir 76984226 Feb 13 14:49 subj2Day1.nii.gz
-rwxrwxrwx 1 nir nir 76445651 Feb 13 15:29 subj2Month3.nii.gz
-rwxrwxrwx 1 nir nir 73634633 Feb 13 15:56 subj2Month6.nii.gz
-rwxrwxrwx 1 nir nir  1369361 Feb 13 17:23 subj2PREOP.nii.gz
-rwxrwxrwx 1 nir nir 73563109 Feb 13 14:49 subj3Day1.nii.gz
-rwxrwxrwx 1 nir nir 77269912 Feb 13 15:29 subj3Month3.nii.gz
-rwxrwxrwx 1 nir nir 95243052 Feb 13 15:57 subj3Month6.nii.gz
-rwxrwxrwx 1 nir nir  1158008 Feb 13 17:24 subj3PREOP.nii.gz


On Thu, Feb 28, 2019 at 11:20 AM Benjamin Davidson <[log in to unmask]> wrote:
Hi Taylor,  thanks again for the help.
Here's the ls - Ral output from the TBSS folder below. I'm now on the tbss_2 step of re-running the process with just 3 subjects so. You're right, it looks like some of the subjects/sessions are not getting warp.nii.gz files while others are....Not sure why that would be.
.:
total 64
drwxrwxrwx 1 nir nir  8192 Feb 26 15:11 .
drwxrwxrwx 1 nir nir  4096 Feb 28 09:11 ..
drwxrwxrwx 1 nir nir 40960 Feb 26 15:11 FA
drwxrwxrwx 1 nir nir  8192 Feb 26 10:49 origdata
drwxrwxrwx 1 nir nir     0 Feb 26 15:11 stats
-rwxrwxrwx 1 nir nir  1152 Feb 26 13:35 .tbsslog

./FA:
total 40633
drwxrwxrwx 1 nir nir   40960 Feb 26 15:11 .
drwxrwxrwx 1 nir nir    8192 Feb 26 15:11 ..
-rwxrwxrwx 1 nir nir       7 Feb 26 15:11 best.msf
-rwxrwxrwx 1 nir nir    2919 Feb 26 13:35 .commands
drwxrwxrwx 1 nir nir    8192 Feb 26 10:51 slicesdir
-rwxrwxrwx 1 nir nir  158087 Feb 26 09:47 subj10Day1_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  382330 Feb 26 09:46 subj10Day1_FA.nii.gz
-rwxrwxrwx 1 nir nir    2159 Feb 26 13:36 subj10Day1_FA_to_target.log
-rwxrwxrwx 1 nir nir     188 Feb 26 13:36 subj10Day1_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 13:36 subj10Day1_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir   31767 Feb 26 09:47 subj10PREOP_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  936363 Feb 26 09:47 subj10PREOP_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 26 13:36 subj10PREOP_FA_to_target.log
-rwxrwxrwx 1 nir nir     190 Feb 26 13:36 subj10PREOP_FA_to_target.mat
-rwxrwxrwx 1 nir nir      20 Feb 26 13:37 subj10PREOP_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  777828 Feb 26 13:37 subj10PREOP_FA_to_target_warp.nii.gz
-rwxrwxrwx 1 nir nir   50271 Feb 26 09:47 subj1Day1_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir 1286363 Feb 26 09:47 subj1Day1_FA.nii.gz
-rwxrwxrwx 1 nir nir    2156 Feb 26 13:38 subj1Day1_FA_to_target.log
-rwxrwxrwx 1 nir nir     187 Feb 26 13:38 subj1Day1_FA_to_target.mat
-rwxrwxrwx 1 nir nir      19 Feb 26 13:39 subj1Day1_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  774585 Feb 26 13:39 subj1Day1_FA_to_target_warp.nii.gz
-rwxrwxrwx 1 nir nir  141002 Feb 26 09:49 subj1Month3_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  331266 Feb 26 09:48 subj1Month3_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 26 13:40 subj1Month3_FA_to_target.log
-rwxrwxrwx 1 nir nir     183 Feb 26 13:40 subj1Month3_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 13:40 subj1Month3_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  153849 Feb 26 09:52 subj1Month6_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  370819 Feb 26 09:50 subj1Month6_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 26 13:41 subj1Month6_FA_to_target.log
-rwxrwxrwx 1 nir nir     185 Feb 26 13:41 subj1Month6_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 13:41 subj1Month6_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir   32622 Feb 26 09:52 subj1PREOP_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  887725 Feb 26 09:52 subj1PREOP_FA.nii.gz
-rwxrwxrwx 1 nir nir    2159 Feb 26 13:41 subj1PREOP_FA_to_target.log
-rwxrwxrwx 1 nir nir     190 Feb 26 13:41 subj1PREOP_FA_to_target.mat
-rwxrwxrwx 1 nir nir      20 Feb 26 13:43 subj1PREOP_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  780378 Feb 26 13:43 subj1PREOP_FA_to_target_warp.nii.gz
-rwxrwxrwx 1 nir nir  164499 Feb 26 09:54 subj2Day1_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  395279 Feb 26 09:53 subj2Day1_FA.nii.gz
-rwxrwxrwx 1 nir nir    2156 Feb 26 13:44 subj2Day1_FA_to_target.log
-rwxrwxrwx 1 nir nir     188 Feb 26 13:44 subj2Day1_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 13:44 subj2Day1_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  169698 Feb 26 09:57 subj2Month3_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  399289 Feb 26 09:55 subj2Month3_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 26 13:45 subj2Month3_FA_to_target.log
-rwxrwxrwx 1 nir nir     189 Feb 26 13:45 subj2Month3_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 13:45 subj2Month3_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  157672 Feb 26 10:00 subj2Month6_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  374665 Feb 26 09:58 subj2Month6_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 26 13:46 subj2Month6_FA_to_target.log
-rwxrwxrwx 1 nir nir     191 Feb 26 13:46 subj2Month6_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 13:46 subj2Month6_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir   38171 Feb 26 10:00 subj2PREOP_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir 1057605 Feb 26 10:00 subj2PREOP_FA.nii.gz
-rwxrwxrwx 1 nir nir    2159 Feb 26 13:47 subj2PREOP_FA_to_target.log
-rwxrwxrwx 1 nir nir     191 Feb 26 13:47 subj2PREOP_FA_to_target.mat
-rwxrwxrwx 1 nir nir      21 Feb 26 13:48 subj2PREOP_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  775158 Feb 26 13:48 subj2PREOP_FA_to_target_warp.nii.gz
-rwxrwxrwx 1 nir nir  153030 Feb 26 10:02 subj3Day1_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  371069 Feb 26 10:01 subj3Day1_FA.nii.gz
-rwxrwxrwx 1 nir nir    2156 Feb 26 13:49 subj3Day1_FA_to_target.log
-rwxrwxrwx 1 nir nir     189 Feb 26 13:49 subj3Day1_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 13:49 subj3Day1_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  162497 Feb 26 10:05 subj3Month3_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  390669 Feb 26 10:03 subj3Month3_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 26 13:50 subj3Month3_FA_to_target.log
-rwxrwxrwx 1 nir nir     186 Feb 26 13:50 subj3Month3_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 13:50 subj3Month3_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  168689 Feb 26 10:07 subj3Month6_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  399471 Feb 26 10:06 subj3Month6_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 26 13:51 subj3Month6_FA_to_target.log
-rwxrwxrwx 1 nir nir     184 Feb 26 13:51 subj3Month6_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 13:51 subj3Month6_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir   30435 Feb 26 10:07 subj3PREOP_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  905172 Feb 26 10:07 subj3PREOP_FA.nii.gz
-rwxrwxrwx 1 nir nir    2159 Feb 26 13:52 subj3PREOP_FA_to_target.log
-rwxrwxrwx 1 nir nir     192 Feb 26 13:52 subj3PREOP_FA_to_target.mat
-rwxrwxrwx 1 nir nir      20 Feb 26 13:53 subj3PREOP_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  777661 Feb 26 13:53 subj3PREOP_FA_to_target_warp.nii.gz
-rwxrwxrwx 1 nir nir  160827 Feb 26 10:10 subj4Day1_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  389456 Feb 26 10:08 subj4Day1_FA.nii.gz
-rwxrwxrwx 1 nir nir    2156 Feb 26 13:54 subj4Day1_FA_to_target.log
-rwxrwxrwx 1 nir nir     188 Feb 26 13:54 subj4Day1_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 13:54 subj4Day1_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  573501 Feb 26 10:19 subj4Month3_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir 1460625 Feb 26 10:13 subj4Month3_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 26 13:58 subj4Month3_FA_to_target.log
-rwxrwxrwx 1 nir nir     187 Feb 26 13:58 subj4Month3_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 13:59 subj4Month3_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir   31082 Feb 26 10:19 subj4PREOP_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir 1016367 Feb 26 10:19 subj4PREOP_FA.nii.gz
-rwxrwxrwx 1 nir nir    2159 Feb 26 13:59 subj4PREOP_FA_to_target.log
-rwxrwxrwx 1 nir nir     187 Feb 26 13:59 subj4PREOP_FA_to_target.mat
-rwxrwxrwx 1 nir nir      19 Feb 26 14:01 subj4PREOP_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  777666 Feb 26 14:01 subj4PREOP_FA_to_target_warp.nii.gz
-rwxrwxrwx 1 nir nir  161404 Feb 26 10:22 subj5Day1_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  392629 Feb 26 10:20 subj5Day1_FA.nii.gz
-rwxrwxrwx 1 nir nir    2156 Feb 26 14:02 subj5Day1_FA_to_target.log
-rwxrwxrwx 1 nir nir     187 Feb 26 14:02 subj5Day1_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 14:02 subj5Day1_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir   82466 Feb 26 10:22 subj5PREOP_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir 3836624 Feb 26 10:22 subj5PREOP_FA.nii.gz
-rwxrwxrwx 1 nir nir    2159 Feb 26 14:03 subj5PREOP_FA_to_target.log
-rwxrwxrwx 1 nir nir     189 Feb 26 14:03 subj5PREOP_FA_to_target.mat
-rwxrwxrwx 1 nir nir      19 Feb 26 14:04 subj5PREOP_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  776643 Feb 26 14:04 subj5PREOP_FA_to_target_warp.nii.gz
-rwxrwxrwx 1 nir nir  168765 Feb 26 10:24 subj6Day1_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  409281 Feb 26 10:23 subj6Day1_FA.nii.gz
-rwxrwxrwx 1 nir nir    2156 Feb 26 14:05 subj6Day1_FA_to_target.log
-rwxrwxrwx 1 nir nir     189 Feb 26 14:05 subj6Day1_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 14:05 subj6Day1_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  168852 Feb 26 10:27 subj6Month3_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  409285 Feb 26 10:25 subj6Month3_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 26 14:06 subj6Month3_FA_to_target.log
-rwxrwxrwx 1 nir nir     189 Feb 26 14:06 subj6Month3_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 14:07 subj6Month3_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  165299 Feb 26 10:29 subj6Month6_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  405039 Feb 26 10:28 subj6Month6_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 26 14:08 subj6Month6_FA_to_target.log
-rwxrwxrwx 1 nir nir     188 Feb 26 14:08 subj6Month6_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 14:08 subj6Month6_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir   32392 Feb 26 10:30 subj6PREOP_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir 1037096 Feb 26 10:29 subj6PREOP_FA.nii.gz
-rwxrwxrwx 1 nir nir    2159 Feb 26 14:08 subj6PREOP_FA_to_target.log
-rwxrwxrwx 1 nir nir     191 Feb 26 14:08 subj6PREOP_FA_to_target.mat
-rwxrwxrwx 1 nir nir      19 Feb 26 14:10 subj6PREOP_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  774851 Feb 26 14:10 subj6PREOP_FA_to_target_warp.nii.gz
-rwxrwxrwx 1 nir nir  165299 Feb 26 10:32 subj7Day1_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  405039 Feb 26 10:31 subj7Day1_FA.nii.gz
-rwxrwxrwx 1 nir nir    2156 Feb 26 14:11 subj7Day1_FA_to_target.log
-rwxrwxrwx 1 nir nir     188 Feb 26 14:11 subj7Day1_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 14:11 subj7Day1_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  167722 Feb 26 10:35 subj7Month3_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  391566 Feb 26 10:33 subj7Month3_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 26 14:12 subj7Month3_FA_to_target.log
-rwxrwxrwx 1 nir nir     187 Feb 26 14:12 subj7Month3_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 14:12 subj7Month3_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir   32852 Feb 26 10:35 subj7Month6_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  875869 Feb 26 10:35 subj7Month6_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 26 14:13 subj7Month6_FA_to_target.log
-rwxrwxrwx 1 nir nir     192 Feb 26 14:13 subj7Month6_FA_to_target.mat
-rwxrwxrwx 1 nir nir      21 Feb 26 14:14 subj7Month6_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  774311 Feb 26 14:14 subj7Month6_FA_to_target_warp.nii.gz
-rwxrwxrwx 1 nir nir   30089 Feb 26 10:35 subj7PREOP_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  838958 Feb 26 10:35 subj7PREOP_FA.nii.gz
-rwxrwxrwx 1 nir nir    2159 Feb 26 14:14 subj7PREOP_FA_to_target.log
-rwxrwxrwx 1 nir nir     190 Feb 26 14:14 subj7PREOP_FA_to_target.mat
-rwxrwxrwx 1 nir nir      20 Feb 26 14:16 subj7PREOP_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  776440 Feb 26 14:16 subj7PREOP_FA_to_target_warp.nii.gz
-rwxrwxrwx 1 nir nir  157314 Feb 26 10:37 subj8Day1_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  381883 Feb 26 10:36 subj8Day1_FA.nii.gz
-rwxrwxrwx 1 nir nir    2156 Feb 26 14:17 subj8Day1_FA_to_target.log
-rwxrwxrwx 1 nir nir     188 Feb 26 14:17 subj8Day1_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 14:17 subj8Day1_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  160146 Feb 26 10:40 subj8Month3_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  386925 Feb 26 10:38 subj8Month3_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 26 14:18 subj8Month3_FA_to_target.log
-rwxrwxrwx 1 nir nir     190 Feb 26 14:18 subj8Month3_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 14:18 subj8Month3_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  160763 Feb 26 10:42 subj8Month6_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  389269 Feb 26 10:41 subj8Month6_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 26 14:19 subj8Month6_FA_to_target.log
-rwxrwxrwx 1 nir nir     186 Feb 26 14:19 subj8Month6_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 14:19 subj8Month6_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir   32060 Feb 26 10:42 subj8PREOP_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  930600 Feb 26 10:42 subj8PREOP_FA.nii.gz
-rwxrwxrwx 1 nir nir    2159 Feb 26 14:20 subj8PREOP_FA_to_target.log
-rwxrwxrwx 1 nir nir     189 Feb 26 14:20 subj8PREOP_FA_to_target.mat
-rwxrwxrwx 1 nir nir      19 Feb 26 14:21 subj8PREOP_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  776908 Feb 26 14:21 subj8PREOP_FA_to_target_warp.nii.gz
-rwxrwxrwx 1 nir nir  163953 Feb 26 10:45 subj9Day1_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  392097 Feb 26 10:43 subj9Day1_FA.nii.gz
-rwxrwxrwx 1 nir nir    2156 Feb 26 14:22 subj9Day1_FA_to_target.log
-rwxrwxrwx 1 nir nir     189 Feb 26 14:22 subj9Day1_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 14:22 subj9Day1_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  160146 Feb 26 10:47 subj9Month3_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  386925 Feb 26 10:46 subj9Month3_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 26 14:24 subj9Month3_FA_to_target.log
-rwxrwxrwx 1 nir nir     190 Feb 26 14:24 subj9Month3_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 14:24 subj9Month3_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  156813 Feb 26 10:49 subj9Month6_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir  377569 Feb 26 10:48 subj9Month6_FA.nii.gz
-rwxrwxrwx 1 nir nir    2162 Feb 26 14:25 subj9Month6_FA_to_target.log
-rwxrwxrwx 1 nir nir     188 Feb 26 14:25 subj9Month6_FA_to_target.mat
-rwxrwxrwx 1 nir nir       0 Feb 26 14:25 subj9Month6_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir   34676 Feb 26 10:49 subj9PREOP_FA_mask.nii.gz
-rwxrwxrwx 1 nir nir 1027489 Feb 26 10:49 subj9PREOP_FA.nii.gz
-rwxrwxrwx 1 nir nir    2159 Feb 26 14:25 subj9PREOP_FA_to_target.log
-rwxrwxrwx 1 nir nir     191 Feb 26 14:25 subj9PREOP_FA_to_target.mat
-rwxrwxrwx 1 nir nir      20 Feb 26 14:27 subj9PREOP_FA_to_target_warp.msf
-rwxrwxrwx 1 nir nir  779534 Feb 26 14:27 subj9PREOP_FA_to_target_warp.nii.gz
-rwxrwxrwx 1 nir nir 2646918 Feb 26 13:35 target.nii.gz
-rwxrwxrwx 1 nir nir     266 Feb 26 15:11 .tbsslog
drwxrwxrwx 1 nir nir   20480 Feb 26 14:25 tbss_logs

./FA/slicesdir:
total 4308
drwxrwxrwx 1 nir nir   8192 Feb 26 10:51 .
drwxrwxrwx 1 nir nir  40960 Feb 26 15:11 ..
-rwxrwxrwx 1 nir nir  12552 Feb 26 10:51 grota.png
-rwxrwxrwx 1 nir nir  12267 Feb 26 10:51 grotb.png
-rwxrwxrwx 1 nir nir  12656 Feb 26 10:51 grotc.png
-rwxrwxrwx 1 nir nir  11918 Feb 26 10:51 grotd.png
-rwxrwxrwx 1 nir nir  11732 Feb 26 10:51 grote.png
-rwxrwxrwx 1 nir nir   9237 Feb 26 10:51 grotf.png
-rwxrwxrwx 1 nir nir  14715 Feb 26 10:51 grotg.png
-rwxrwxrwx 1 nir nir  14428 Feb 26 10:51 groth.png
-rwxrwxrwx 1 nir nir  13114 Feb 26 10:51 groti.png
-rwxrwxrwx 1 nir nir   3310 Feb 26 10:51 index.html
-rwxrwxrwx 1 nir nir  96504 Feb 26 10:50 subj10PREOP_FA.png
-rwxrwxrwx 1 nir nir 120652 Feb 26 10:50 subj1Day1_FA.png
-rwxrwxrwx 1 nir nir 120652 Feb 26 10:50 subj1Month3_FA.png
-rwxrwxrwx 1 nir nir 120652 Feb 26 10:50 subj1Month6_FA.png
-rwxrwxrwx 1 nir nir  99752 Feb 26 10:50 subj1PREOP_FA.png
-rwxrwxrwx 1 nir nir  99752 Feb 26 10:50 subj2Day1_FA.png
-rwxrwxrwx 1 nir nir  99752 Feb 26 10:50 subj2Month3_FA.png
-rwxrwxrwx 1 nir nir  99752 Feb 26 10:50 subj2Month6_FA.png
-rwxrwxrwx 1 nir nir 105817 Feb 26 10:50 subj2PREOP_FA.png
-rwxrwxrwx 1 nir nir 105817 Feb 26 10:50 subj3Day1_FA.png
-rwxrwxrwx 1 nir nir 105817 Feb 26 10:50 subj3Month3_FA.png
-rwxrwxrwx 1 nir nir 105817 Feb 26 10:50 subj3Month6_FA.png
-rwxrwxrwx 1 nir nir  93310 Feb 26 10:50 subj3PREOP_FA.png
-rwxrwxrwx 1 nir nir  93310 Feb 26 10:50 subj4Day1_FA.png
-rwxrwxrwx 1 nir nir  93310 Feb 26 10:50 subj4Month3_FA.png
-rwxrwxrwx 1 nir nir 100289 Feb 26 10:50 subj4PREOP_FA.png
-rwxrwxrwx 1 nir nir 100289 Feb 26 10:50 subj5Day1_FA.png
-rwxrwxrwx 1 nir nir 290851 Feb 26 10:50 subj5PREOP_FA.png
-rwxrwxrwx 1 nir nir 290851 Feb 26 10:50 subj6Day1_FA.png
-rwxrwxrwx 1 nir nir 290851 Feb 26 10:51 subj6Month3_FA.png
-rwxrwxrwx 1 nir nir 290851 Feb 26 10:51 subj6Month6_FA.png
-rwxrwxrwx 1 nir nir  99895 Feb 26 10:51 subj6PREOP_FA.png
-rwxrwxrwx 1 nir nir  99895 Feb 26 10:51 subj7Day1_FA.png
-rwxrwxrwx 1 nir nir  99895 Feb 26 10:51 subj7Month3_FA.png
-rwxrwxrwx 1 nir nir  92598 Feb 26 10:51 subj7Month6_FA.png
-rwxrwxrwx 1 nir nir  88396 Feb 26 10:51 subj7PREOP_FA.png
-rwxrwxrwx 1 nir nir  88396 Feb 26 10:51 subj8Day1_FA.png
-rwxrwxrwx 1 nir nir  88396 Feb 26 10:51 subj8Month3_FA.png
-rwxrwxrwx 1 nir nir  88396 Feb 26 10:51 subj8Month6_FA.png
-rwxrwxrwx 1 nir nir  95929 Feb 26 10:51 subj8PREOP_FA.png
-rwxrwxrwx 1 nir nir  95929 Feb 26 10:51 subj9Day1_FA.png
-rwxrwxrwx 1 nir nir  95929 Feb 26 10:51 subj9Month3_FA.png
-rwxrwxrwx 1 nir nir  95929 Feb 26 10:51 subj9Month6_FA.png
-rwxrwxrwx 1 nir nir 100598 Feb 26 10:51 subj9PREOP_FA.png

./FA/tbss_logs:
total 152
drwxrwxrwx 1 nir nir 20480 Feb 26 14:25 .
drwxrwxrwx 1 nir nir 40960 Feb 26 15:11 ..
-rwxrwxrwx 1 nir nir   769 Feb 26 13:36 tbss_2_reg.e12293.1
-rwxrwxrwx 1 nir nir     0 Feb 26 13:46 tbss_2_reg.e12293.10
-rwxrwxrwx 1 nir nir   762 Feb 26 13:49 tbss_2_reg.e12293.11
-rwxrwxrwx 1 nir nir   776 Feb 26 13:50 tbss_2_reg.e12293.12
-rwxrwxrwx 1 nir nir   776 Feb 26 13:51 tbss_2_reg.e12293.13
-rwxrwxrwx 1 nir nir     0 Feb 26 13:51 tbss_2_reg.e12293.14
-rwxrwxrwx 1 nir nir   762 Feb 26 13:54 tbss_2_reg.e12293.15
-rwxrwxrwx 1 nir nir   776 Feb 26 13:59 tbss_2_reg.e12293.16
-rwxrwxrwx 1 nir nir     0 Feb 26 13:59 tbss_2_reg.e12293.17
-rwxrwxrwx 1 nir nir   762 Feb 26 14:02 tbss_2_reg.e12293.18
-rwxrwxrwx 1 nir nir     0 Feb 26 14:02 tbss_2_reg.e12293.19
-rwxrwxrwx 1 nir nir     0 Feb 26 13:36 tbss_2_reg.e12293.2
-rwxrwxrwx 1 nir nir   762 Feb 26 14:05 tbss_2_reg.e12293.20
-rwxrwxrwx 1 nir nir   776 Feb 26 14:07 tbss_2_reg.e12293.21
-rwxrwxrwx 1 nir nir   776 Feb 26 14:08 tbss_2_reg.e12293.22
-rwxrwxrwx 1 nir nir     0 Feb 26 14:08 tbss_2_reg.e12293.23
-rwxrwxrwx 1 nir nir   762 Feb 26 14:11 tbss_2_reg.e12293.24
-rwxrwxrwx 1 nir nir   776 Feb 26 14:12 tbss_2_reg.e12293.25
-rwxrwxrwx 1 nir nir     0 Feb 26 14:12 tbss_2_reg.e12293.26
-rwxrwxrwx 1 nir nir     0 Feb 26 14:14 tbss_2_reg.e12293.27
-rwxrwxrwx 1 nir nir   762 Feb 26 14:17 tbss_2_reg.e12293.28
-rwxrwxrwx 1 nir nir   776 Feb 26 14:18 tbss_2_reg.e12293.29
-rwxrwxrwx 1 nir nir     0 Feb 26 13:37 tbss_2_reg.e12293.3
-rwxrwxrwx 1 nir nir   776 Feb 26 14:19 tbss_2_reg.e12293.30
-rwxrwxrwx 1 nir nir     0 Feb 26 14:19 tbss_2_reg.e12293.31
-rwxrwxrwx 1 nir nir   762 Feb 26 14:22 tbss_2_reg.e12293.32
-rwxrwxrwx 1 nir nir   776 Feb 26 14:24 tbss_2_reg.e12293.33
-rwxrwxrwx 1 nir nir   776 Feb 26 14:25 tbss_2_reg.e12293.34
-rwxrwxrwx 1 nir nir     0 Feb 26 14:25 tbss_2_reg.e12293.35
-rwxrwxrwx 1 nir nir   776 Feb 26 13:40 tbss_2_reg.e12293.4
-rwxrwxrwx 1 nir nir   776 Feb 26 13:41 tbss_2_reg.e12293.5
-rwxrwxrwx 1 nir nir     0 Feb 26 13:41 tbss_2_reg.e12293.6
-rwxrwxrwx 1 nir nir   762 Feb 26 13:44 tbss_2_reg.e12293.7
-rwxrwxrwx 1 nir nir   776 Feb 26 13:45 tbss_2_reg.e12293.8
-rwxrwxrwx 1 nir nir   776 Feb 26 13:46 tbss_2_reg.e12293.9
-rwxrwxrwx 1 nir nir     0 Feb 26 13:35 tbss_2_reg.o12293.1
-rwxrwxrwx 1 nir nir     0 Feb 26 13:46 tbss_2_reg.o12293.10
-rwxrwxrwx 1 nir nir     0 Feb 26 13:48 tbss_2_reg.o12293.11
-rwxrwxrwx 1 nir nir     0 Feb 26 13:49 tbss_2_reg.o12293.12
-rwxrwxrwx 1 nir nir     0 Feb 26 13:50 tbss_2_reg.o12293.13
-rwxrwxrwx 1 nir nir     0 Feb 26 13:51 tbss_2_reg.o12293.14
-rwxrwxrwx 1 nir nir     0 Feb 26 13:53 tbss_2_reg.o12293.15
-rwxrwxrwx 1 nir nir     0 Feb 26 13:54 tbss_2_reg.o12293.16
-rwxrwxrwx 1 nir nir     0 Feb 26 13:59 tbss_2_reg.o12293.17
-rwxrwxrwx 1 nir nir     0 Feb 26 14:01 tbss_2_reg.o12293.18
-rwxrwxrwx 1 nir nir     0 Feb 26 14:02 tbss_2_reg.o12293.19
-rwxrwxrwx 1 nir nir     0 Feb 26 13:36 tbss_2_reg.o12293.2
-rwxrwxrwx 1 nir nir     0 Feb 26 14:04 tbss_2_reg.o12293.20
-rwxrwxrwx 1 nir nir     0 Feb 26 14:05 tbss_2_reg.o12293.21
-rwxrwxrwx 1 nir nir     0 Feb 26 14:07 tbss_2_reg.o12293.22
-rwxrwxrwx 1 nir nir     0 Feb 26 14:08 tbss_2_reg.o12293.23
-rwxrwxrwx 1 nir nir     0 Feb 26 14:10 tbss_2_reg.o12293.24
-rwxrwxrwx 1 nir nir     0 Feb 26 14:11 tbss_2_reg.o12293.25
-rwxrwxrwx 1 nir nir     0 Feb 26 14:12 tbss_2_reg.o12293.26
-rwxrwxrwx 1 nir nir     0 Feb 26 14:14 tbss_2_reg.o12293.27
-rwxrwxrwx 1 nir nir     0 Feb 26 14:16 tbss_2_reg.o12293.28
-rwxrwxrwx 1 nir nir     0 Feb 26 14:17 tbss_2_reg.o12293.29
-rwxrwxrwx 1 nir nir     0 Feb 26 13:37 tbss_2_reg.o12293.3
-rwxrwxrwx 1 nir nir     0 Feb 26 14:18 tbss_2_reg.o12293.30
-rwxrwxrwx 1 nir nir     0 Feb 26 14:19 tbss_2_reg.o12293.31
-rwxrwxrwx 1 nir nir     0 Feb 26 14:21 tbss_2_reg.o12293.32
-rwxrwxrwx 1 nir nir     0 Feb 26 14:22 tbss_2_reg.o12293.33
-rwxrwxrwx 1 nir nir     0 Feb 26 14:24 tbss_2_reg.o12293.34
-rwxrwxrwx 1 nir nir     0 Feb 26 14:25 tbss_2_reg.o12293.35
-rwxrwxrwx 1 nir nir     0 Feb 26 13:39 tbss_2_reg.o12293.4
-rwxrwxrwx 1 nir nir     0 Feb 26 13:40 tbss_2_reg.o12293.5
-rwxrwxrwx 1 nir nir     0 Feb 26 13:41 tbss_2_reg.o12293.6
-rwxrwxrwx 1 nir nir     0 Feb 26 13:43 tbss_2_reg.o12293.7
-rwxrwxrwx 1 nir nir     0 Feb 26 13:44 tbss_2_reg.o12293.8
-rwxrwxrwx 1 nir nir     0 Feb 26 13:45 tbss_2_reg.o12293.9

./origdata:
total 2007312
drwxrwxrwx 1 nir nir      8192 Feb 26 10:49 .
drwxrwxrwx 1 nir nir      8192 Feb 26 15:11 ..
-rwxrwxrwx 1 nir nir  77008759 Feb 13 15:28 subj10Day1.nii.gz
-rwxrwxrwx 1 nir nir   1193147 Feb 13 14:31 subj10PREOP.nii.gz
-rwxrwxrwx 1 nir nir   1789774 Feb 13 14:37 subj1Day1.nii.gz
-rwxrwxrwx 1 nir nir  66748698 Feb 13 15:27 subj1Month3.nii.gz
-rwxrwxrwx 1 nir nir  74085143 Feb 13 15:57 subj1Month6.nii.gz
-rwxrwxrwx 1 nir nir   1151150 Feb 13 17:23 subj1PREOP.nii.gz
-rwxrwxrwx 1 nir nir  76984226 Feb 13 14:49 subj2Day1.nii.gz
-rwxrwxrwx 1 nir nir  76445651 Feb 13 15:29 subj2Month3.nii.gz
-rwxrwxrwx 1 nir nir  73634633 Feb 13 15:56 subj2Month6.nii.gz
-rwxrwxrwx 1 nir nir   1369361 Feb 13 17:23 subj2PREOP.nii.gz
-rwxrwxrwx 1 nir nir  73563109 Feb 13 14:49 subj3Day1.nii.gz
-rwxrwxrwx 1 nir nir  77269912 Feb 13 15:29 subj3Month3.nii.gz
-rwxrwxrwx 1 nir nir  95243052 Feb 13 15:57 subj3Month6.nii.gz
-rwxrwxrwx 1 nir nir   1158008 Feb 13 17:24 subj3PREOP.nii.gz
-rwxrwxrwx 1 nir nir  80816877 Feb 13 15:02 subj4Day1.nii.gz
-rwxrwxrwx 1 nir nir 299588481 Feb 13 15:51 subj4Month3.nii.gz
-rwxrwxrwx 1 nir nir   1267534 Feb 13 17:25 subj4PREOP.nii.gz
-rwxrwxrwx 1 nir nir  80989956 Feb 13 15:03 subj5Day1.nii.gz
-rwxrwxrwx 1 nir nir   4521521 Feb 13 17:26 subj5PREOP.nii.gz
-rwxrwxrwx 1 nir nir  84822925 Feb 13 15:03 subj6Day1.nii.gz
-rwxrwxrwx 1 nir nir  84121038 Feb 13 15:42 subj6Month3.nii.gz
-rwxrwxrwx 1 nir nir  84835782 Feb 13 15:58 subj6Month6.nii.gz
-rwxrwxrwx 1 nir nir   1296186 Feb 13 14:27 subj6PREOP.nii.gz
-rwxrwxrwx 1 nir nir  84835782 Feb 13 15:15 subj7Day1.nii.gz
-rwxrwxrwx 1 nir nir  73957865 Feb 13 16:09 subj7Month3.nii.gz
-rwxrwxrwx 1 nir nir   1134848 Feb 19 16:26 subj7Month6.nii.gz
-rwxrwxrwx 1 nir nir   1071710 Feb 13 14:28 subj7PREOP.nii.gz
-rwxrwxrwx 1 nir nir  78839798 Feb 13 15:15 subj8Day1.nii.gz
-rwxrwxrwx 1 nir nir  78646324 Feb 13 15:43 subj8Month3.nii.gz
-rwxrwxrwx 1 nir nir  79970713 Feb 13 16:09 subj8Month6.nii.gz
-rwxrwxrwx 1 nir nir   1179760 Feb 13 14:29 subj8PREOP.nii.gz
-rwxrwxrwx 1 nir nir  80200133 Feb 13 15:15 subj9Day1.nii.gz
-rwxrwxrwx 1 nir nir  78646324 Feb 13 15:43 subj9Month3.nii.gz
-rwxrwxrwx 1 nir nir  75701912 Feb 13 16:09 subj9Month6.nii.gz
-rwxrwxrwx 1 nir nir   1315186 Feb 13 14:30 subj9PREOP.nii.gz

./stats:
total 8
drwxrwxrwx 1 nir nir    0 Feb 26 15:11 .
drwxrwxrwx 1 nir nir 8192 Feb 26 15:11 ..


On Thu, Feb 28, 2019 at 11:07 AM Taylor Hanayik <[log in to unmask]> wrote:
Hi Ben,

from your TBSS directory can you run “ls -Ral” in a terminal and then send back the results? Give the output a quick look just to make sure you’re not sending back confidential info. That output will be helpful since it will list more info about the files (e.g. the size of each one)

From your previous output it does seem like some of your registrations are failing. For example, subj4Month3_FA_to_target_warp.msf exists, but no warp.nii.gz file has been created for that subject.

The terminal output could be helpful. Send that when it’s been run again. 

Also, you had sent an earlier message to my email address rather than the FSL list. Try to reply to the FSL list email address so that all the context stays with the original conversation thread. 



Cheers,

Taylor Hanayik


Taylor Hanayik PhD
FMRIB, John Radcliffe Hospital
University of Oxford





On Feb 28, 2019, at 3:46 PM, Benjamin Davidson <[log in to unmask]> wrote:

Hi Taylor!
I start with a directory called TBSS with all my dti_FA.nii.gz files in it. After TBSS1 I get a directory called FA and origdata. I've been running all TBSS commands from the TBSS folder. I'm re-running the steps now on a subset of patients so I can send you the exact terminal output!

On Thu, Feb 28, 2019 at 10:38 AM Taylor Hanayik <[log in to unmask]> wrote:
Hi Ben, 

a few more Q’s:

1). what does your directory structure look like? 
2). Given your directory layout, which directory are you running tbss_2, and tbss_3 from?
3). Can you copy and paste the terminal output when you try to process the data. Send this back in a reply email so we can get more info


Cheers,

Taylor Hanayik


Taylor Hanayik PhD
FMRIB, John Radcliffe Hospital
University of Oxford





On Feb 28, 2019, at 2:23 PM, Ben Davidson <[log in to unmask]> wrote:

Thanks very much Taylor! I just emailed you. tbss2 is definitely finishing, and I've re-tried this process several times with the same result. I've emailed you the contents of the folders. Any tips would be greatly appreciated!

Ben

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