Hi Steve,

Thank you so much for your helpful comments.

>Your registrations generally look ok - the non-yellow parts of the
>"sum of all input masks" summary image are simply due to the variable
>field-of-view across all subjects - the yellow parts show the common
>field-of-view across all subjects, so as long as the area you care
>about is inside there then things are ok.
>
>I would note though that in each input image different slices seem to
>have different intensities, which is either an artefact or may be
>cause by different slices being converted with different intensity
>scalings. Either way it is worth asking your local physics person
>about that to see if you can get it removed.

The artifacts, I'm guessing are due to movement in the scanner? In any case,
thank you for noting this. I have definitely forwarded this comment to the
researcher who acquired these images.

>By default the max intensity used for the overlay colourmap is the max
>for that single session's data. This will not affect higher-level
>analyses. This is covered in the manual though - please read the FEAT
>manual!

I'm so sorry about that previous novice question. I am very new to fMRI
analysis and I did read the manual several times before asking. I just
didn't understand the differences between the different Z thresholds. But
this answered my particular question so thank you again.

>Example_func is a single volume from the original 4D FMRI data,
>extracted before any other preprocessing (like smoothing) is carried
>out.
>In the report "standard" is the image that you chose (or left as
>default) to use for the standard space image. If you didn't change the
>default there is no difference.

So in the registration report for a first-level analysis where it says
"Summary registration, FMRI to standard space", FMRI is the 4D FMRI data
after preprocessing?

>Not exactly sure what you're doing here - have you tried using
>Featquery instead, with your pre-selected masks/ROIs input as
>required? Have a careful look at the FEAT and Featquery manuals.

I was confused earlier about how one would make a mask for an ROI but I
think I've got a handle on it now after reading the posts about spherical
ROI's. Once I've made all my masks, I want the average intensity within the
ROI for each of my four EVs (neural initial, neutral repeat, angry initial,
angry repeat). Would the only way to extract this information is to set up
contrasts for each of these EVs ( i.e. [1 0 0 0] ) and select their
corresponding stats images in featquery?
Also, are these numbers are directly comparable? Would I have to calculate
the % signal change? From a previous post, it sounds like I can compare the
raw numbers without having to calculate the %signal change because the
timing and design matrix are the same for each subject. Am I understanding
this right?

THe raw numbers themselves are not actually meaningful and may not be 
> directly comparable across groups (or indeed, across individuals). If 
> the design matrices are all identical across session, subject, and 
> group then yes, the raw numbers should be directly comparable. 

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind03&L=FSL&P=R60620&X=7C2406707A4D32EAC0&Y=nga%40usc.edu&m=1771

Sorry for all the pesky questions but thanks a million for all of your help.

Lin























On Sun, 1 Feb 2009 13:29:19 +0000, Steve Smith <[log in to unmask]> wrote:

>Hi,
>
>On 30 Jan 2009, at 17:04, Lin Nga wrote:
>
>> Hi everyone,
>>
>> I must apologize ahead of time for the novice questions I am about
>> to ask.
>>
>> 1) Unique missing-mask voxels:
>> (I've uploaded a word doc with screen shots of the results I got
>> from my
>> gfeat analysis: http://drop.io/linspace/media )
>> -From this picture, how would I go about figuring out who it is that's
>> missing those voxels?
>> -If this is a registration problem, how would I fix it?
>> -Any general comments or suggestions from looking at my results?
>
>Your registrations generally look ok - the non-yellow parts of the
>"sum of all input masks" summary image are simply due to the variable
>field-of-view across all subjects - the yellow parts show the common
>field-of-view across all subjects, so as long as the area you care
>about is inside there then things are ok.
>
>I would note though that in each input image different slices seem to
>have different intensities, which is either an artefact or may be
>cause by different slices being converted with different intensity
>scalings. Either way it is worth asking your local physics person
>about that to see if you can get it removed.
>
>> 2) (First Level Analysis) Threshold activation images:
>> I've noticed that the threshold end points varied between subjects.
>> Why is
>> this the case? For example one subject's threshold is 2.3-9 while
>> another
>> went from 2.3-11.8. I left the Z threshold at the default value for
>> all of them.
>
>By default the max intensity used for the overlay colourmap is the max
>for that single session's data. This will not affect higher-level
>analyses. This is covered in the manual though - please read the FEAT
>manual!
>
>> 3) Registration report:
>> -What is the difference between FMRI and example_func in the
>> registration
>> report?
>
>Example_func is a single volume from the original 4D FMRI data,
>extracted before any other preprocessing (like smoothing) is carried
>out.
>
>> -What is the difference between standard space and standard in the
>> registration report?
>
>In the report "standard" is the image that you chose (or left as
>default) to use for the standard space image. If you didn't change the
>default there is no difference.
>
>> 4) ROI analysis
>> I have a set of localizer scans in which I hope to define the FFA
>> and use
>> that to analyze my experimental fmri's. I have several points of
>> confusion:
>>
>> - I've tried fslroi and fslmaths and the result was blank, yet still
>> showed
>> activation in the timeseries plots in fslview. After looking through
>> the
>> forums I realized that in coordinates for these fslutils require
>> voxel space
>> coordinates. I am looking for the highest activating voxel within
>> 30<x<50,
>> -60<y<-30, -30<z<-5 (Talairach coordinates) and I am defining the
>> ROI as the
>> area 8mm from that point (in all directions). Once I convert to MNI
>> (FSL's
>> coordinate system, if I'm not mistaken), how would I go from MNI to
>> voxels?
>> If I had to draw the ROI in fslview how would I determine the highest
>> activating voxel there? (I'm still a bit confused about what the
>> different
>> sets of coordinates in the cluster browser are).
>
>Not exactly sure what you're doing here - have you tried using
>Featquery instead, with your pre-selected masks/ROIs input as
>required? Have a careful look at the FEAT and Featquery manuals.
>
>Cheers.
>
>
>
>> - While playing around with fslroi and fslmaths, I became increasingly
>> confused about whether I should be extracting from my 4D fMRI image
>> or the
>> thresh_zstat image.
>>
>> - When would one use featquery? How would one choose which mask to
>> use?
>> Would this be the mask I drew in fslview?
>>
>> -Has anyone had experience with fslroi toolbox? This seems relevant
>> to what
>> I am trying to do but I'm not quite sure how to use it. Is it run
>> from the
>> unix command line or does this need to be linked to matlab somehow?
>>
>> Again, I'm very sorry for the bombardment of novice questions; I'm
>> relatively new to FSL and fMRI analysis. Any help would help me out
>> a lot.
>> Thank you all so much for all your help.
>>
>> Lin Nga
>>
>
>
>---------------------------------------------------------------------------
>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
>---------------------------------------------------------------------------