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
>> ---------------------------------------------------------------------------
>>
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