Thank you Saad!
So I tried - but
1.) it seems that I am struggeling with the "list_of_volumes":
I have them all in one folder like:
subject1_seed1_2_target1
subject1_seed1_2_target2
subject1_seed1_2_target3
subject1_seed1_2_target4
I tried the command
proj_thresh thisfolder/* threshold
no success,
neither with a list which I entered into a txt-file (cannot read this file)
proj_thresh .../listofvolumes.txt threshold
How do I have to feed in this list of volumes?
2.) How do I determine the threshold?
Thanks!
Markus
Quoting Saad Jbabdi <[log in to unmask]>:
> Hi Markus,
> It shouldn't matter which way you do it, but you don't want to do
> separate calls to probtrackx for that, since it is much faster to do
> it all in once!
>
> Saad.
>
>
> On 3 Jul 2008, at 08:52, Markus Gschwind wrote:
>
>> 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
>>
>
> ------------------------------------------------------------------------ ---
> 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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