Hi Saad!
> 1) the first one should work. what happens when you do that?
In fact there were two problems.
1. Problem of loop in my script ;-/
2. It seems like the file "total.nii.gz" is only created if I go
directly into the directory to run the proj_thresh
cd ${groupprobtrackxdir}/rawseeds/${myside}${myseed}/
proj_thresh *seed.nii.gz 10
but NOT if I do it like this, using the whole filename:
proj_thresh ${groupprobtrackxdir}/rawseeds/${myside}${myseed}/*seed.nii.gz 10
How come?
Tanks!
Markus
Quoting Saad Jbabdi <[log in to unmask]>:
>
> 1) the first one should work. what happens when you do that?
>
> 2) there is no simple answer to this, but it shouldn't matter too much
> for most applications, e.g. comparing connectivity fingerprints across
> subjects or across seeds. you may set the threshold to 1, which would
> simply mean no thresholding at all!
>
> Saad.
>
> On 3 Jul 2008, at 12:38, Markus Gschwind wrote:
>
>> 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
>>
>
> ------------------------------------------------------------------------ ---
> 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
