Thanks a lot for your reply

I'm using ANALYZE format

fslhd output is:

sizeof_hdr 348

data_type

db_name

extents 0

session_error 0

regular a

hkey_un0

dim0 4

dim1 181

dim2 217

dim3 181

dim4 1

dim5 0

dim6 0

dim7 0

vox_units

cal_units

unused1 0

datatype 2

bitpix 8

pixdim0 2.000000

pixdim1 1.000000

pixdim2 1.000000

pixdim3 1.000000

pixdim4 0.000000

pixdim5 0.000000

pixdim6 0.000000

pixdim7 0.000000

vox_offset 0.0000

funused1 1.0000

funused2 0.0000

funused3 0.0000

cal_max 0.0000

cal_min 0.0000

compressed 0

verified 0

glmax 255

glmin 0

descrip

aux_file

orient 0

originator Z

origin1 90

origin2 126

origin3 72

generated

scannum

patient_id

exp_date

exp_time

hist_un0

vols_added 0

start_field 0

field_skip 0

omax 0

omin 0

smin 0

file_type ANALYZE-7.5

file_code 0

On Thu, Feb 1, 2018 at 9:33 AM, Mark Jenkinson <[log in to unmask]> wrote:

Hi,

This sounds very odd.
Are you using a nifti file?
If so, what is the output of fslhd when run on this file?

All the best,
Mark

> On 1 Feb 2018, at 07:22, Moran Artzi <[log in to unmask]> wrote:
>
> Dear all,
> When uploading Automated Anatomical Labeling template in FSL viewer, there seems there is a L/R flip of the directions
> For example, based on the AAL list of labels (http://neuro.imm.dtu.dk/wiki/Automated_Anatomical_Labeling)
> Label #41 = Amygdala_L
> However looking at FSL viewer, this area appears in the right side (annotated R on viewer and the various FSL templates)
> How can this be explained and what is the correct markup?
> Thanks
> Moran

Artzi Moran, PhD
The Functional Brain Center, Tel Aviv Sourasky Medical Center
Sackler Faculty of Medicine, Tel Aviv University
Tel Aviv, Israel