Thanks!
----- Original Message -----
From: Mark Jenkinson <[log in to unmask]>
Date: Thursday, April 24, 2008 3:43 am
Subject: Re: [FSL] Header data
> Hi,
>
> That's great.
> It is exactly what I was expecting, which means that everything is
> working fine.
>
> This image has a qform that is set (qform_name = Scanner Anat)
> but no sform set (sform_name = Unknown). Hence the sform
> values that you get from fslorient in this image are uninteresting
> defaults - it is the qform that contains all the useful info.
>
> After running fslswapdim the qform gets modified (correctly) and
> then its contents are copied into the sform. That is why the sform
> after the swapdim contains offsets that are not clear in the sform
> prior to swapping, as these offsets were in the qform.
>
> The bottom line is that fslswapdim is working correctly, what you
> report is exactly what I'd expect for every stage, your left and
> right orientations are being preserved correctly and that you
> should continue to run fslswapdim on your data in order to make
> the rest of the pipeline more straightforward.
>
> All the best,
> Mark
>
>
> On 23 Apr 2008, at 22:51, Emily T Stoneham wrote:
>
> > Hi,
> >
> > Here it is:
> >
> > Thanks!
> > Emily
> >
> > filename 7_ep2d_pace_moco_3DFilter_20080107_0001.nii
> >
> > 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 Unknown
> > 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 101.060242
> > qto_xyz:2 0.000000 2.987657 -0.288172 -96.445969
> > qto_xyz:3 0.000000 0.271861 3.166901 -75.362930
> > 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 Unknown
> > sform_code 0
> > sto_xyz:1 0.000000 0.000000 0.000000 0.000000
> > sto_xyz:2 0.000000 0.000000 0.000000 0.000000
> > sto_xyz:3 0.000000 0.000000 0.000000 0.000000
> > sto_xyz:4 0.000000 0.000000 0.000000 0.000000
> > sform_xorient Unknown
> > sform_yorient Unknown
> > sform_zorient Unknown
> > file_type NIFTI-1+
> > file_code 1
> > descrip ep2d_pace_moco_3DFilter
> > aux_file
> >
> >
> > ----- Original Message -----
> > From: Mark Jenkinson <[log in to unmask]>
> > Date: Wednesday, April 23, 2008 5:30 pm
> > Subject: Re: [FSL] Header data
> >
> >> 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
> >> theswap, 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>
> >>
> > <estoneha.vcf>
>
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