[Mristudio-users] A clarification on the statistics table

Wed Aug 15 15:15:25 EDT 2012

Hi Venkat,

I think you can use the mean value to compare across people.

As you may already know, you can get two types of reports; an overall mean
of all pixels in the 3D tract volume and the slice-by-slice report. It the
tract of your interest, in your case CST, travels linearly and is more or
less perpendicular to one of the planes (for CST, it is perpendicular to
axial slices), the slice-by-slice report would be informative. If you use
the whole-tract report, not the slice-by-slice, you may also want to try
some metrics other than the overall mean, such as median (as KRT suggested)
or histogram. You can save the tract as a raw 3D file, load it to RoiEditor
as an object, also load an FA map, apply the object as an ROI to the FA
map, and then you can save FA values of all individual pixels in the object
(ROI), from which you can create a histogram by Excel. This could be an
interesting approach for fibers like corpus callosum, uncinate, or SLF,
which make a large turn and slice-by-slice report may not be a good idea.

When you use slice-by-slice report, you have to normalize the slice
locations across subjects. For example, the CST at pons could be slice #12
in Subject A and #15 in Subject B. The total length of the CST of Subject
#A could be 35 slices while that of Subject #b could be 38 slices. This
requires "spatial normalization".

What we did in old days is, load all slice-by-slice reports from multiple
subjects to an Excel sheet, slide the whole column up and down to make sure
that the CST at the pons of all subjects align in the Excel sheet. This is
the same as rigid translation to adjust the slice locations. Even if the
CST locations are now aligned at the pons level, This doesn't guarantee
that the CST is aligned in the motor cortex because the CST lengths are
different among subjects. Then you can stretch or shrink the Excel column
of each subject so that everybody has the same column length. This is the
same as linear alignment using two-point scaling.

While all the location normalization is performed using Excel in this
example, you can also do image normalization in the imaging domain. For
this, you need to use DiffeoMap (or other kinds of brain normalization
software such as SPM and FSL). You can do fiber tracking in the native
data. Then linearly normalize all subject data to the MNI space, from which
you can get slice-by-slice report in a normalized manner. All slice
locations and fiber lengths are the same in Excel, without further
modifications.

You can also do normalization of images first to the MNI space and then do
fiber tracking in the MNI space. If you want to do this, you have to
normalize your tensor data.

If we push this logic further, then we can ask, "do we need tractography?".

> Suppose one location of CST, say, at the cerebral peduncle (CP) level, is
affected and has low FA values in a patient population.

> If we do CST tracking and get an overall averaged FA, we can say, "it's
not a sensitive way because we mix all pixels from other normal locations".
This is a valid logic.

>Then we say, "ok, let's look at slice-by-slice report. This should show
low FA at the CP level." The only problem is, the CP level slices are not
consistent across subjects. So, for each subject, we have to identify slice
#. To make sure that the low FA happens only at CP, we want to compare FAs
at pons level, internal capsule level, corona radiata level, etc. Then we
have to identify slice # of these multiple locations for all subjects.
That's a lot of work.

> So, what we usually do is to use one of the image "normalization" tools
that can adjust the location, rotation, and size of the brain across
subjects. Then all slice levels are the same. We can do slice-by-slice
comparison across subjects.

> Well, however, if all brains are well normalized, we can do
voxel-by-voxel comparison across subjects without fiber tracking. If
patient populations have consistently low FA at the CP, the voxel-by-voxel
comparison should show it anyway. This is the logic for voxel-based
analysis (VBA), which is a widely used technique.

> There could be two reasons why you want to use tractography over VBA.
First, VBA always have normalization error. In this case, if the CP
structures are not well aligned after normalization, we may fail to detect
the FA loss. Using tractography in each subject, we know that we are
accurately comparing CST vs CST (or CP vs CP). In this sense, we can call
tractography a "registration tool", with which we can define voxels that
belong to the CST in all subjects accurately. Another point is that
tractography groups pixels. If the grouped pixels share the same property,
such as reduced FA, it can provide much higher SNR compared to
voxel-by-voxel comparison. In this sense, you can call tractography a
"spatial filter". SNR is always a problem in VBA and we usually group
pixels using isotropic filters. Tractography is a structure-specific
spatial filter.

> One counter argument is, tractography is not a stable operation. It
requires subjective ROI delineation. Also, it is sensitive to noise; if you
scan the same patient twice, the tractography results are not the same. So
there is a downside of tractography. This is a precision (reliability)
issue.

> Another approach we often use is Atlas-based analysis (ABA), which is
also based on the whole brain normalization, followed by whole-brain
segmentation by applying a pre-defined segmentation file. This pre-defined
segmentation file is another kind of structure-specific spatial filter,
defining which pixels should be grouped.

> These methods are all related and have pros & cons.

Hope this gives you a big picture about DTI data analysis.

Susumu

On Wed, Aug 15, 2012 at 11:05 AM, Rajagopalan, Venkateswaran <
rajagov2 at ccf.org> wrote:

>  Thanks, Is it ok to take the mean of this mean value (if the data
> meets assumptions of t-test and you want to do t-test) across subjects when
> you perform stats
>
> Thanks
> Venkat
>
>
>
> I would use mean values.
>
> Atul.
> On Aug 14, 2012, at 4:53 PM, "Rajagopalan, Venkateswaran" <rajagov2 at
> ccf.org <http://lists.mristudio.org/mailman/listinfo/mristudio-users>
> <mailto:rajagov2 at ccf.org<http://lists.mristudio.org/mailman/listinfo/mristudio-users>
> >>
> wrote:
>
> Dear All,
>
> I am calculating changes in FA and other DTI metrics along CST. After
> tract reconstruction I use statistics option to see FA/other DTI metrics
> values. The statistics gives me Max, Min, Mean, SD values in each and every
> slice in my image volume. I am wondering whether I can use Max, value (or
> only mean has to be used) to study changes between my control and patients.
>
> Thanks
> Venkat
>
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