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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