Now it is clearer.
Is it thus only possible to used proj_thresh if I have "probtrackxed" with MORE THAN ONE classification targets in ONE command
or can I also take several seed_to_blahs together from several probtrackx runs from the same seedmask
Hi Markus,
proj_thresh is suitable as a within-subject tool. I don't think it
does make sense to use it as a between-subject tool as you have
suggested. It is however meant to give (within-subject) results that
are more comparable between subjects!
proj_thresh does the following:
say you have a seed voxel for which you ran probtrackx with 3
"classification targets" A, B and C.
Then probtrackx will give you three files called seed_to_<A,B,C>.
Say now that for this particular seed voxel, the values in seed_to_blah are:
seed_to_A: 10
seed_to_B: 100
seed_to_C: 150
(these numbers do not necessarily sum to the total number of samples
ran from the seed voxel, since some of the sample tracts might not
connect to either A,B or C).
Then if you run proj_thresh with a threshold of 10 or less, you will have:
seed_to_A_proj_seg_thr: 10/(10+100+150) = 0.0385
seed_to_B_proj_seg_thr: 100/(10+100+150) = 0.385
seed_to_C_proj_seg_thr: 150/(10+100+150) = 0.5769
If you choose a threshold of 11 (or more and <=100):
seed_to_A_proj_seg_thr: 0/(0+100+150) = 0
seed_to_B_proj_seg_thr: 100/(0+100+150) = 0.4
seed_to_C_proj_seg_thr: 150/(0+100+150) = 0.6
I hope this makes it a bit clearer?
Saad.
On 2 Jul 2008, at 16:16, Markus Gschwind wrote:
Hello FSL experts!
I have a question concerning the *proj_thresh* function.
There is not so much on the site and neither in the forum.
Is correct to use it as a within-subject tool in order to evaluate the seeds going from a given seedmask to differnt target masks
list of volumes :
subject1_seed1_2_target1
subject1_seed1_2_target2
subject1_seed1_2_target3
subject1_seed1_2_target4
etc
or is it a between-subject tool to evaluate the seeds coming from the same seedmask and going to the same targe mask?
subject1_seed1_2_target1
subject2_seed1_2_target1
subject3_seed1_2_target1
subject4_seed1_2_target1
etc.
On the website it says:
For each voxel in the seeds mask that has a value above threshold
*[which I have do define, e.g. if I have 20 subjects I take 20. Correct?]* for at least one target mask, proj_thresh calculates the number of samples reaching each target mask as a proportion of the total number of samples reaching any target mask. The output of proj_thresh is a single volume for each target mask.
What disturbed me was that I got for each subject[xy] _seed1_2_target1 a volume s[xy]_myseed_seed_proj_seg_thr_14.nii.gz and each one looks different...
I seem not to understand this function.
Could anyone explain a little bit please?
Thanks a lot!!
Markus
--
Dr. med. Markus Gschwind, M.D.
Laboratory for Neurology and Imaging of Cognition
Dept of Neurosciences
University Medical Center (CMU)
1 Michel-Servet - 1211 GENEVA - CH
Tel 0041 (0) 22 379 5324
Fax 0041 (0) 22 379 5402
------------------------------------------------------------------------ ---
Saad Jbabdi,
Postdoctoral Research Assistant,
Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222545 (fax 222717)
------------------------------------------------------------------------ ---
Dr. med. Markus Gschwind, M.D.