Hi - this is the same issue - if the values are negative then the
"maximum" is not defined, hence the cope4 result. Hence this voxel is
negative. We'll fix/clarify this in the next release.
Cheers.
On 19 Apr 2007, at 17:36, Paymon Hosseini wrote:
> Dear all,
> changing the threshold value in featquery also does not solve the
> problem of incorrectly reported voxels. i was wondering if is there
> any way around this?
> thank you very much for any help,
> paymon
>
>
> Paymon Hosseini wrote:
>> Dear Steve ,
>>
>> I am having a similar problem. I am trying to find the % signal
>> change of several COPE files for one subject for a single voxel
>> using featquery. The featquery report uses the correct voxel for
>> some COPE files, and not for others.
>>
>> here is an example featquery output report:
>> 1 stats/cope1 1 0.00 0.30 0.30 0.30 0.30 0.30 30 53 15 -2.45 57.30
>> 20.36 (correct voxel)
>> 1 stats/cope2 1 0.00 0.36 0.36 0.36 0.36 0.36 30 53 15 -2.45 57.30
>> 20.36 (correct voxel)
>> 1 stats/cope3 1 0.00 0.18 0.18 0.18 0.18 0.18 30 53 15 -2.45 57.30
>> 20.36 (correct voxel)
>> 1 stats/cope4 1 -0.00 -0.00 -0.00 -0.00 -0.00 0.00 0 0 0 107.32
>> -107.92 -38.02 (incorrect voxel)
>>
>> for example in the above, stats/cope1 to stats/cope3 are evaluate
>> at the voxel i specified, but stats/cope4 is evaluate at some
>> other voxel.
>>
>> Both the mask and the voxel are in standard space, and there are
>> no registration problems. All the cope images have an intensity
>> value at voxel i am interested in, when viewed in fslview. You
>> said "if there are no voxels above the threshold then the co-
>> ordinates reported are meaningless". what threshold are you
>> referring to?
>> Could you please explain in more detail why one cannot get a %
>> signal change (e.g stats/cope4 above), even though the stats/
>> cope4.nii.gz has a valid intensity value at the given voxel of
>> interest?
>>
>> thanks
>> paymon hosseini
>>
>>
>>
>>
>> Steve Smith wrote:
>>> Hi - yes, sorry, if there are no voxels above the threshold then
>>> the co-ordinates reported are meaningless - we'll get that fixed
>>> in the next release.
>>> Cheers.
>>>
>>>
>>> On 4 Apr 2007, at 00:24, Sang Lee wrote:
>>>
>>>> Hi Steve,
>>>>
>>>> The mask image was set to the standard space reference image
>>>> used in the registrations, and the mm coordinates were in the
>>>> space of this image. Also, there were no registration failure
>>>> nor that the voxel that I specified was outside the field-of-
>>>> view-of the datasets.
>>>>
>>>> Possible that this error is generated when there is no real
>>>> activation in the voxel that I soecified? Looking at each
>>>> individuals that had these errors, all of them did not have any
>>>> activations in the specified voxel. i.e. no activation in the
>>>> voxel is generating these errors. If so, for these individuals,
>>>> would it be ok to assume that the mean % signal change is zero
>>>> (for the % signal change plot)?
>>>>
>>>> Thank you again for your help.
>>>>
>>>> From Sang
>>>> Sang Lee
>>>> Phenotype Genotype Project
>>>> Athinoula Martinos Center for
>>>> Biomedical Imaging
>>>> 149 13th St. Rm. 2302
>>>> Charlestown, MA 02129
>>>> Fax: 617-726-1351
>>>>
>>>>
>>>> On Apr 1, 2007, at 5:29 AM, Steve Smith wrote:
>>>>
>>>>> Hi - did you make sure that the mask image was set to the
>>>>> standard space reference image used in your registrations, and
>>>>> that the mm co-ordinates were in the space of this image? Also,
>>>>> is it possible that the registration had failed for the
>>>>> problematic FEAT runs, or that the voxel you specified was
>>>>> outside the field-of-view of those datasets?
>>>>>
>>>>> Cheers, Steve.
>>>>>
>>>>>
>>>>> On 31 Mar 2007, at 21:37, Sang Lee wrote:
>>>>>
>>>>>> Dear FSL user,
>>>>>>
>>>>>> I am using PE files to calculate the percentage signal change
>>>>>> via featquery for a single voxel for
>>>>>> each of my subjects (total n = 28).
>>>>>>
>>>>>> Given that I am using PE file, an anatomical mask, and a mm
>>>>>> coordinate for a single voxel, using
>>>>>> featquery tool with convert PE/COPE to % signal change option
>>>>>> turned on, I should get % signal
>>>>>> change for each of my subjects for that single voxel.
>>>>>>
>>>>>> However, several of the subjects report file comes out with a
>>>>>> coordinate that I did not specify.
>>>>>>
>>>>>> For example, I specified (-16 -4 -16) for my mm coordinates.
>>>>>> However, several of my subjects'
>>>>>> report file comes out with % signal change values with the
>>>>>> following coordinate (90 -126 -72).
>>>>>> This happens with one third of my subjects. Is there something
>>>>>> that I am doing wrong? How do I
>>>>>> deal with those results with the coordinates that I did not
>>>>>> specify?
>>>>>>
>>>>>> I am trying to plot mean % signal change plot for all 28
>>>>>> subjects, but I am not sure what to do with
>>>>>> those subejct's mean % signal change that comes out with a
>>>>>> coordinate that I did not specify.
>>>>>>
>>>>>> Any input would be a great help!
>>>>>>
>>>>>> Thank you in advance.
>>>>>>
>>>>>> From Sang
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------
>>>>> ---------
>>>>> Stephen M. Smith, Professor of Biomedical Engineering
>>>>> Associate Director, Oxford University FMRIB Centre
>>>>>
>>>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>>>> +44 (0) 1865 222726 (fax 222717)
>>>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>>>> ------------------------------------------------------------------
>>>>> ---------
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>>>
>>>
>>> --------------------------------------------------------------------
>>> -------
>>> Stephen M. Smith, Professor of Biomedical Engineering
>>> Associate Director, Oxford University FMRIB Centre
>>>
>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>> +44 (0) 1865 222726 (fax 222717)
>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>> --------------------------------------------------------------------
>>> -------
------------------------------------------------------------------------
---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
------------------------------------------------------------------------
---
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