Thanks a lot Saad!
Now it is clearer.
Just in order to understand it better:
Is it thus only possible to used proj_thresh if I have "probtrackxed"
with MORE THAN ONE classification targets in ONE command
probtrackx seed1 to target1 /target2 / target3 -os2t
or can I also take several seed_to_blahs together from several
probtrackx runs from the same seedmask
probtrackx seed1 to target1 -os2t
probtrackx seed1 to target2 -os2t
probtrackx seed1 to target3 -os2t
and then run proj_thresh on them?
Thanks again!
Markus
Quoting Saad Jbabdi <[log in to unmask]>:
> 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
>> email: [log in to unmask]
>> http://labnic.unige.ch
>>
>
> ------------------------------------------------------------------------ ---
> Saad Jbabdi,
> Postdoctoral Research Assistant,
> Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222545 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~saad
> ------------------------------------------------------------------------ ---
--
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
email: [log in to unmask]
http://labnic.unige.ch
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