Hi,
I need the output from fslhd on both of the images to see what has
happened.
I suspect that you have sform_code=0 and qform_code=1 before you do the
swap, but I really want to check. Can you please send me the fslhd from
both images?
All the best,
Mark
On 23 Apr 2008, at 16:21, Emily T Stoneham wrote:
> Mark,
>
> Before the image was swapped, I converted the DICOM in MRIconvert to
> FSL NIFTI format. Beyond that, the only processing done at this
> point is the swapping of the sagittal image. Here is the output
> from fslhd on one of the swapped images (below).
>
> Thanks!
> Emily
>
> Byte swapping
> filename swapped_7_ep2d_pace_moco_3DFilter_20080107_0001.nii.gz
>
> sizeof_hdr 348
> data_type INT16
> dim0 3
> dim1 64
> dim2 64
> dim3 48
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 4
> nbyper 2
> bitpix 16
> pixdim0 0.0000000000
> pixdim1 3.0000000000
> pixdim2 3.0000000000
> pixdim3 3.1799850464
> pixdim4 0.0000000000
> pixdim5 0.0000000000
> pixdim6 0.0000000000
> pixdim7 0.0000000000
> vox_offset 352
> cal_max 0.0000
> cal_min 0.0000
> scl_slope 1.000000
> scl_inter 0.000000
> phase_dim 2
> freq_dim 1
> slice_dim 3
> slice_name alternating_increasing
> slice_code 3
> slice_start 0
> slice_end 47
> slice_duration 0.040000
> 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 3.000000 -0.000000 -0.000000 -87.939758
> qto_xyz:2 0.000000 2.987657 0.288172 -109.990044
> qto_xyz:3 0.000000 0.271861 -3.166901 73.481400
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Left-to-Right
> qform_yorient Posterior-to-Anterior
> qform_zorient Superior-to-Inferior
> sform_name Scanner Anat
> sform_code 1
> sto_xyz:1 3.000000 0.000000 0.000000 -87.939758
> sto_xyz:2 0.000000 2.987657 0.288172 -109.990044
> sto_xyz:3 0.000000 0.271861 -3.166901 73.481400
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Left-to-Right
> sform_yorient Posterior-to-Anterior
> sform_zorient Superior-to-Inferior
> file_type NIFTI-1+
> file_code 1
> descrip FSL4.0
>
> ----- Original Message -----
> From: Mark Jenkinson <[log in to unmask]>
> Date: Wednesday, April 23, 2008 11:02 am
> Subject: Re: [FSL] Header data
>
>> Hi,
>>
>> If you have swapped LR and SI dimensions then FSLView will show
>> the axial slices with the left (L) on the left - this is normal.
>> Re-orienting
>> to match that of the standard brain is a good idea in this case as it
>> preserves your left-right labelling correctly (-x y -z is fine for
>> this) and
>> should keep all the other labels attached to the correct anatomy.
>>
>> So I would recommend using this fslswapdim command in general.
>>
>> However, the sform outputs are a bit puzzling. Are you sure that
>> all you did was apply fslswapdim to
>> 7_ep2d_pace_moco_3DFilter_20080107_0085.nii
>> which gave you
>> swapped_7_ep2d_pace_moco_3DFilter_20080107_0085.nii.gz?
>> It is doing what I'd expect in x and z, but not in y. It seems to
>> be
>> creating an
>> arbitrary coordinate offset there which I don't normally see. This
>> isn'tnecessary a problem, it just creates slightly strange
>> coordinates. Can
>> you send me the output of fslhd run on these images (and let me
>> know if
>> any other processing went on)?
>>
>> On a separate note, it sounds like you are worried about the mm
>> coordinates. These will not be in standard space if you look at the
>> first-level outputs. Only the higher-level FEAT outputs are in
>> standardspace. If you want to see your first-level outputs in
>> standard space, then
>> I recommend using Renderhighres to resample your first-level FEAT
>> output into standard space, where you will see the usual standard
>> space coordinates (with negative mm ones).
>>
>> All the best,
>> Mark
>>
>>
>> Emily T Stoneham wrote:
>>> Hello-
>>> When I pull up the FSLView image, it shows L on the Left of the
>> image.
>>> However, I must caveat this: Our scaner flips the Sagittal and
>> the Coronal functionals (the structurals are fine though). When I
>> fix this, that is when I see the change in L R labels in FSL View.
>> The Standard Image from the subject looks fine in FSLView (R on
>> left, L on right side of image). I fixd the sagittal and coronal
>> image by doing this:
>>> for fn in *.nii ; do fslswapdim $fn -x y -z swapped_$fn ; done
>>> (I have 290 images that need to be swapped, this fixes them all
>> at once)
>>>
>>> The original reason I am trying to straighten this out is that
>> when I am viewing the FEAT data, the voxel and mm data in FSLView
>> is WAY off what it should be. For instance, it will tell me that
>> something clearly in the parietal lobe is actually in the
>> cerebellum. It is as if FSL view doesn't recognize negative values
>> (I never see any except in the mm section, although these aren't
>> right either), and so I figured it was something I did in the
>> inital stages. While trying to figure it out- I noticed the
>> difference in the labelling in FSLView and began to tackle that
>> first off.
>>>
>>> Here is the output I got from one image before I swapped it:
>>> Command: fslorient -getsform
>> 7_ep2d_pace_moco_3DFilter_20080107_0085.nii> Output: -3 0 0 0 0 3
>> 0 0 0 0 3.17999 0 0 0 0 1
>>>
>>> Here is the output I got from one image after I swapped it:
>>> Command: fslorient -getsform
>> swapped_7_ep2d_pace_moco_3DFilter_20080107_0085.nii.gz> Output: 3
>> 0 0 -87.9398 0 2.98766 0.288172 -109.99 0 0.271861 -3.1669 73.4814
>> 0 0 0 1
>>>
>>> Regards,
>>> Emily
>>>
>>
>>
>>
>> Mark Jenkinson wrote:
>>> Hi,
>>>
>>> How are you determining that the displayed orientation is
>>> neurological?
>>> Are the labels right? That is the most crucial thing. The
>> terms> neurological
>>> and radiological for display get a bit confusing when the
>> brain is
>>> not in the
>>> same orientation as the standard brain.
>>>
>>> If the labels are correct (including left and right) then *do
>> not*> do a fslswapdim
>>> as that will muck the labels up. I would also avoid using
>>> fslorient to change
>>> things unless you know the labels are wrong.
>>>
>>> Can you explain more about what you see in FSLView, what you
>>> expect to see, and
>>> what the labels are like? Don't worry about the sform values
>> for> now, although it would
>>> be helpful to send us the output of fslhd.
>>>
>>> All the best,
>>> Mark
>>>
>>>
>>>
>>> On 22 Apr 2008, at 19:25, Emily Stoneham wrote:
>>>
>>>> Hello all,
>>>> I have performed an fslorient -getorient, and it tells me
>> it is
>>>> RADIOLOGICAL, however, when viewed
>>>> in FSLView, it shows it in Neurological orientation. If I run
>>>> fslswapdim, I can change that (albeit I get
>>>> a warning), but I suspect I should be using fslorient to do
>> that>> instead- (i.e., change the header)?
>>>> When I run fslorient -getsform, I get a string of numbers,
>> but I
>>>> don't know what they mean, or
>>>> how/if I should change one or more (and which) of them. Can
>> you>> help?
>>>>
>>>> Thanks,
>>>> Emily
>>>>
>>>
>>
> <estoneha.vcf>
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