Hi Gwenaelle,
Thank you very much for the helpful advice. I've tried your
suggestions and am
making forward progress. However, I have a several follow-up questions I was
hoping you could kindly answer:
1. When I apply the binary mask (thresholded at 0.95) to mean_FA to obtain the
text file all_voxels_significant.txt:
a. Does the upper half of this large text file contain the MNI coordinates
of all the voxels in the binary mask? If so, is the format: x1[double
space]y1[double space]z1[double space]x2[double space]y2[double
space]z2[double
space]x3[double space]y3[double space]z3[double space]...?
b. Since the input file in fslmeants is mean_FA, do the FA values in the
lower half of the text file represent mean values for the entire sample
(controls and patients mixed together)? If so, how can I do this so I get
means of each group separately? Finally, is the first FA value the mean for
the first set of coordinates (x y z), the second FA for the second set of
coordinates, third FA for third set of coordinate, and so on?
2. Creating ROI's from the structures in the JHU White-Matter Tractography
Atlas, a probabilistic atlas:
a. What is the acceptable threshold range when creating the mask using
fslmaths?
b. I understand this setting is arbitrary. Thus, is there any
disadvantage
or contraindication to use an even lower threshold (say 1%)?
3. When intersecting each ROI created from the structures in the JHU
White-Matter Tractography Atlas with my mask of significant results:
a. What is the chance that identified voxel(s) present in one mask, be
present in many others?
b. What is the best way to use the mask resulting from the intersection
(i.e. mymask_unc in your example below), to obtain mean ROI FA on each of the
subject individually?
Again, thank you very much for your kind help as I learn FSL. As
always, please
let me know if I can clarify any of the above. If anyone else wants to
throw in
their two cents, please feel free!
Regards,
Roger
Quoting Gwenaëlle DOUAUD <[log in to unmask]>:
> Hi Roger,
>
>
>> 1. Is there any way to use the cluster program (or
>> any other program in
>> FSL) to capture both MNI coordinates and corresponding mean
>> FA values (for
>> patient and control groups) of ALL voxels that are
>> significantly different
>> between the compared groups?
>
> You can use fslmeants on your mean FA map, using a mask that you can
> create by thresholding/binarising your significant results, e.g.:
>
> fslmaths -i tfce_corrp_tstat1 -thr 0.95 -bin mymask
> fslmeants -i mean_FA -m mymask -o all_voxels_significant.txt --showall
>
>> 2.Can a report be generated listing the
>> total count of significantly
>> different voxels for each involved white matter structure,
>> as identified by
>> the voxels’ MNI coordinates and corresponding labels in
>> the JHU White-Matter
>> Tractography Atlas?
>
> I would then intersect each ROI of the atlas (see previous posts on
> this) with your mask of significant results, e.g.:
> fslmaths mymask -mas uncinate mymask_unc
>
> To get the number of voxels, just do a fslstats -V on each of your new masks.
>
>> 3. Can mean FA also be calculated (for patient and
>> control groups) for
>> these significantly different voxels grouped by white
>> matter structure?
>
> Just repeat the fslmeants command above with the appropriate new masks.
>
> Hope this helps,
> Gwenaelle
>
>
>
>
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