Print

Print


Hi Walid,

Please see below:

On Tuesday, 1 August 2017, Walid Yassin <[log in to unmask]> wrote:
Hello Anderson,


Thank you very much for your answers. Please see my replies and clarifications below.


On 2017 Aug 1, at 22:51, Anderson M. Winkler <[log in to unmask]> wrote:

Hi Walid,

Please see below:


On 31 July 2017 at 04:20, Walid Yassin <[log in to unmask]m> wrote:
Hello,

I would like to report the coordinates of the regions found in my clusters.


This is what I did so far.

1- TBSS, followed by randomize (All is well till here).
2- I got my clusters using the autoaq command and the results are 4 clusters. Each cluster has several regions in it.
I have the voxel# of the clusters and the coordinates of the clusters.
I want to get the coordinate and voxel number of each of the sub clusters.
So to get the coordinates I wrote the cluster command with --olmax.
Now to name the clusters, I went to atlasquery and used -c for each of the coordinates.
Until now I have all the sub cluster coordinates and names, however I don’t know the cluster size of each sub cluster region.

Can someone help me know the cluster size of each of the sub cluster region?

Could you describe what is meant by subcluster? I'm not sure I follow... Each peak (local maximum) within a cluster doesn't define a new cluster within that cluster. Same for regions spanned by the cluster, but maybe I'm not following...
 
All I’m asking here is about the size of the regions inside each cluster. I wanted to know how many voxels are possibly found inside of each of those reigns.

Example:

Cluster 3  (2000voxcels)
-SLF (how many?)
-ILF (how many?)


Sorry if the use of “subcluster” is confusing..


The way as atlasquery works is by using the probabilities that a voxel belongs to a region of the atlas. To obtain what you want perhaps the simplest is to go to the atlases' directory, i.e., ${FSLDIR}/data/atlases/, then use fslmaths to define a mask for each of the regions of the atlas, then use fslstats to see the volume of the intersection.
 


Also, I have another question.
Since in one of my clusters, for e.g., I saw that the superior longitudinal fasciculus (SLF), exists twice. Each having separate coordinates.
Also the SLF not only exists twice in the same cluster, but also is a sub region in other clusters

Example

Cluster 1

1-SLF                   coordinates
2- Some region  coordinates
3- SLF                  coordinates


Cluster 2

1- Some region
2- SLF
3-Some regions  coordinates

Could you copy/paste the actual output from the command?

Yes! Here it is..

ClusterIndex Voxels MAX MAX X (mm) MAX Y (mm) MAX Z (mm) COG X (mm) COG Y (mm) COG Z (mm)
4 4689 0.97 45 -41 32 37.2 -20.4 32.8
3 924 0.96 15 33 0 20.2 36 15.2
2 345 0.956 51 -48 5 48.9 -46 -2.57
1 18 0.951 46 -10 26 46.2 -10.3 26.8
------------------------------------------
Structures to which each center of mass belongs to:
4,37.2,-20.4,32.8,JHU White-Matter Tractography Atlas,79% Superior longitudinal fasciculus R, 42% Superior longitudinal fasciculus (temporal part) R
3,20.2,36,15.2,JHU White-Matter Tractography Atlas,39% Forceps minor, 18% Anterior thalamic radiation R
2,48.9,-46,-2.57,JHU White-Matter Tractography Atlas,24% Superior longitudinal fasciculus R, 23% Superior longitudinal fasciculus (temporal part) R
1,46.2,-10.3,26.8,JHU White-Matter Tractography Atlas,26% Superior longitudinal fasciculus R, 6% Superior longitudinal fasciculus (temporal part) R
------------------------------------------
Structures to which each cluster belongs to:

Cluster #4
Anterior thalamic radiation R:0.0230326
Corticospinal tract R:1.8859
Cingulum (cingulate gyrus) R:0.00703775
Inferior fronto-occipital fasciculus R:0.319898
Inferior longitudinal fasciculus R:1.39966
Superior longitudinal fasciculus R:8.39241
Superior longitudinal fasciculus (temporal part) R:2.46534

Cluster #3
Anterior thalamic radiation R:10.7403
Cingulum (cingulate gyrus) R:0.0844156
Forceps minor:25.2511
Inferior fronto-occipital fasciculus R:6.5368
Superior longitudinal fasciculus R:0.0974026
Uncinate fasciculus L:0.012987
Uncinate fasciculus R:1
Superior longitudinal fasciculus (temporal part) R:0.0162338

Cluster #2
Inferior fronto-occipital fasciculus R:0.00869565
Inferior longitudinal fasciculus R:1.24348
Superior longitudinal fasciculus R:7.90435
Superior longitudinal fasciculus (temporal part) R:8.37681

Cluster #1
Superior longitudinal fasciculus R:31
Superior longitudinal fasciculus (temporal part) R:7.55556



The above is fine. The SLF is large and multiple clusters end up overlapping with it.
 
 


Is it proper to make a ROI (SLF) and try to check how many significant voxels are in that ROI instead of what I did above?
If that is okay, how can I do that?

E.g. SLF is the ROI

To get the # voxels in ROI

-Go to FSL view, load the JHU tact atlas SLF, save it as make and binarize it, then how do I get the # of voxels inside that ROI?


Yes, it's possible but then how could we know whether the result is significant? That is, whether however many voxels are found within the ROI is something worth reporting or not? Instead, if the objective is to investigate only the SLF, consider supplying it as a mask to randomise.

Maybe I didn’t clarify enough what I’m asking.
I meant when I already got the results of randomize between the 2 groups and I found some significant voxels and made a sig. voxel mask. If I overlay the SLF ROI from an atlas over the significant voxel mask, can I know how many voxels that are in the sig. voxel mask are also in the ROI? That way I could know how many sig. voxels are in the SLF (ROI)… I'm not sure if this is possible which is why I’m asking (The objective is not only SLF). 

Yes, you should be able to do as above. However, doing so is still a problem, because this number -- voxel count within the ROI -- is on its own right a test statistic, which should be interpreted with some measure of uncertainty, which on its turn is given by the p-value and that you'd obtain from randomise, using the ROI as mask.

Hope this helps!

All the best,

Anderson

 

 

For coordinates of this ROI, should I just report the local max of SLF itself? If not, how do I get that as well

We should report what is sufficient to characterise the effect. Coordinates alone probably aren't sufficient, but are useful in meta-analyses. The full region is probably more useful.


Thank you very much for all the above..

Best,

WY


All the best,

Anderson

 

Sorry for asking several Qs..


Thank you in advance,

WY