Hi,
Yes, this message is produced precisely so that you
can achieve your desired orientation *without*
performing any problematic flips. As your image
is currently stored in neurological ordering, then
you need LR PA IS to avoid flipping your data's
handedness.
So just follow the suggested command and all
will be fine.
All the best,
Mark
On 16 Feb 2010, at 14:14, Lena Palaniyappan wrote:
> Many thanks.
> When I run
> fslswapdim invol RL PA IS outvol
> It produces a warning
> Cannot perform requested swap (NEUROLOGICAL/RADIOLOGICAL storage
> inverted)
> Try the following command instead:
> fslswapdim CONT_MPRAGE04 LR PA IS CONTR_MPRAGE04
>
>
> Is this valid: I don’t want to flip the images: I only want to
> reorient all my T1s in accordance with standard templates.
>
> Many thanks
> Lena
>
>
> On 15/02/2010 09:42, "Stephen Smith" <[log in to unmask]> wrote:
>
>> Hi - I assume that fsl_vbm_1_bet completed ok?
>>
>> From your attached image it looks like BET hasn't worked - probably
>> because the standard-space registration used to aid the brain
>> extraction has failed - and that it probably due to a combination
>> of the large amounts of neck in the input data, and the fact that
>> the orientation is different from the MNI152 image. Did you use
>> the -b or -N option for fsl_vbm_1_bet ? If you already used -N
>> then you could try re-orienting the input data with fslswapdim and
>> if that doesn't help, cut the neck with fslroi
>>
>> Cheers.
>>
>>
>> On 14 Feb 2010, at 15:43, Lena Palaniyappan wrote:
>>
>>> HI ALL
>>>
>>> After some investigation I found the following output when I
>>> attempted to
>>> run fslvbm_2_template. One row of te slicesdir image from original
>>> T1
>>> weighted images is attached, all rows look similiar
>>>
>>> Whats wrong? I used fslchfiletype to convert img/hdr to nifti_gz
>>> using fslchfiletype NIFTI_GZ <filename>
>>>
>>> Please help!!
>>> Thanks in advance
>>> Lena
>>>
>>>
>>> Console log:
>>> ____________________________
>>>
>>> lkphome:~ lkphome$ /Users/lkphome/Desktop/fslvbm2a ; exit;
>>> ** ERROR (nifti_image_read): failed to find header file for
>>> 'CON_SS_01_struc_brain'
>>> ** ERROR: nifti_image_open(CON_SS_01_struc_brain): bad header info
>>> Error: failed to open file CON_SS_01_struc_brain
>>> ERROR: Could not open image CON_SS_01_struc_brain
>>> Image Exception : #22 :: Failed to read volume CON_SS_01_struc_brain
>>> terminate called after throwing an instance of
>>> 'RBD_COMMON::BaseException'
>>> /Users/lkphome/Desktop/fslvbm2a: line 1: 5449 Abort trap
>>> /Users/lkphome/imaging/fsl/bin/fast -R 0.3 -H 0.1
>>> CON_SS_01_struc_brain
>>> ** ERROR (nifti_image_read): failed to find header file for
>>> 'CON_SS_03_struc_brain'
>>> ** ERROR: nifti_image_open(CON_SS_03_struc_brain): bad header info
>>> Error: failed to open file CON_SS_03_struc_brain
>>> ERROR: Could not open image CON_SS_03_struc_brain
>>> Image Exception : #22 :: Failed to read volume CON_SS_03_struc_brain
>>> terminate called after throwing an instance of
>>> 'RBD_COMMON::BaseException'
>>> /Users/lkphome/Desktop/fslvbm2a: line 2: 5499 Abort trap
>>> /Users/lkphome/imaging/fsl/bin/fast -R 0.3 -H 0.1
>>> CON_SS_03_struc_brain
>>> ** ERROR (nifti_image_read): failed to find header file for
>>> 'CON_SS_07_struc_brain'
>>> <slicedir.jpg>
>>
>>
>>
>> ---------------------------------------------------------------------------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>> ---------------------------------------------------------------------------
>>
>>
>>
>>
>>
>
> _______________________________________________________
> Lena Palaniyappan
> Clinical Lecturer & Honorary StR | Division of Psychiatry
> ( University of Nottingham)
> South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
>
>
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