... and of course, I was referring to this post:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;fa2e3db6.1208
Hi Mark,
I start fsl from terminal. I usually load up my images like so: fsflview myStruct.nii.gz mask.nii.gz
I'm running this on CentOS, v 6.3
I typically run fslreorient2std to make it look right in fslview, but the mask left-right switching problem occurs regardless. Note that if I save a mask, it switches, and if I save it again, the mask is saved flipped (although L and R remain in the same place in FSLview.
Below is the output of fslhd before fslreorient2std
Thanks!
filename DKA803cT2Down.nii.gz
sizeof_hdr 348
data_type INT16
dim0 3
dim1 337
dim2 449
dim3 36
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 0.4463999867
pixdim2 0.4463999867
pixdim3 1.8999999762
pixdim4 3.2000000477
pixdim5 1.0000000000
pixdim6 1.0000000000
pixdim7 1.0000000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 0.000000
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
time_offset 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 -0.446400 -0.000000 0.000000 72.119125
qto_xyz:2 0.000000 -0.252844 -1.565840 92.150291
qto_xyz:3 0.000000 -0.367890 1.076172 86.733788
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Superior-to-Inferior
qform_zorient Anterior-to-Posterior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 -0.446400 0.000000 0.000000 72.119125
sto_xyz:2 0.000000 -0.252844 -1.565840 92.150291
sto_xyz:3 0.000000 -0.367890 1.076172 86.733788
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Superior-to-Inferior
sform_zorient Anterior-to-Posterior
file_type NIFTI-1+
file_code 1
descrip FreeSurfer May 22 2011
aux_file
Also
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805
On Thu, Aug 23, 2012 at 4:32 AM, Mark Jenkinson <[log in to unmask]> wrote:
Dear Joshua,
What system are you using (e.g. Windows, Mac, Debian, Ubuntu, etc.) and how are you starting FSLView (i.e. from the FSL Gui, from a desktop icon, or from a terminal)? Also, can you send me the result of "fslhd" run on the image created by mri_convert?
The answers to the above will determine what needs to be done.
All the best,
Mark
On 22 Aug 2012, at 18:21, Joshua Lee <[log in to unmask]> wrote:
Hi All,
Im not sure if this is known behavior, but I'm getting a strange behavior in fslview.
Scanario: Tracing brain regions with fslview.
Used mri_convert to go from dicoms to .nii.gz, and the fslreorient2std so that fslview displays the brains in a familiar orientation (confirmed actual orientation is correct via orientation labels in fslview)
Created new mask and traced brain ROI.
Saved mask.
Suddenly, upon next refresh, my mask has flipped left to right.
close fslview and reload image and mask image. Now mask's ROI appears on the side I traced. If I save again, it flips again.
So I assume that the orientation in the header of the masks is correct. It is a little annoying because it makes saving before finishing the ROI a pain (restart FSL, reassign colors to the masks, etc)
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805
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