First check the value of the BBR cost function. If it is over .8, then
something is wrong. To check whether it is an LR flip, you can flip the
volume LR and re-run the registration to see if it gets better.
doug
On 02/25/2013 11:19 AM, Sudhin A. Shah wrote:
> Hi Doug,
>
> When I initially pulled out the correlation values (using the matlab code
> below) after the automated registration process: regfeat2anat & aseg2feat,
> some ROIS reported NaNs.
>
> When I manually checked the registration and adjusted it using tkregister2, I
> found myself stretching/scaling to make it fit. Consequently I do not have
> NaNs BUT I am now realising that I should'nt have to scale.
>
> 1) How can I check if left-right reversals have happened - its not obvious by
> eye
> 2) I am going to re-run the automated registration and I can send you a pic
> and the cost function..
>
> Thanks,
> S
>
> ________________________________________
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, February 25, 2013 10:44 AM
> To: Bruce Fischl
> Cc: Sudhin A. Shah
> Subject: Re: [Freesurfer] Registration & segmentation with FSL -
> obtaining correlation matrix..
>
> Hi Sudhin, I'm not sure what the problem is. NaNs in the data?
> Stretching the registration? You should not need to stretch the reg.Are
> you 100% positive that the func and anat come from the same subject and
> there have been on left-right reversals? What is the final value of the
> cost function?
> doug
>
> On 02/25/2013 10:06 AM, Bruce Fischl wrote:
>> Hi Sudhin
>>
>> Doug would have some. You definitely shouldn't have to stretch/scale
>> to get it to fit. If you do, something critical is wrong. Also, please
>> cc the list so that the right person (Doug in this case!) can answer.
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 25 Feb 2013, Sudhin A. Shah wrote:
>>
>>> Hi Bruce,
>>>
>>> They were a result of the registration (between structural and
>>> functional) being 'off'. When I manually correct this using
>>> tkregister2, they were fine. However, I found that I had to stretch
>>> (scale) to get them to fit so (i started a new thread regarding this)
>>> are there image examples on what this should look like so I can use
>>> as a guide?
>>>
>>> Thanks,
>>> S
>>>
>>>
>>> On Feb 25, 2013, at 9:27 AM, Bruce Fischl wrote:
>>>
>>>> Hi Sudhin
>>>>
>>>> are you sure that the NaNs don't exist before registration and
>>>> extraction? Cany you check? I don't see why anything we would have
>>>> done would introduce them.
>>>>
>>>> cheers
>>>> Bruce
>>>> On Fri, 22 Feb 2013, Sudhin A. Shah wrote:
>>>>
>>>>> Hello
>>>>> I have run free surfer and co-registered with the rsfMRI via FSL
>>>>> (reg-feat2anat & aseg2feat)
>>>>> When I extract the values (as per the matlab code below), I see
>>>>> NaNs in certain regions. Of the 19 datasets that I have analyzed I
>>>>> have
>>>>> see NaNs for the following labels
>>>>> 1006 1033 2006 2013 2033
>>>>> Is this a known problem? Is there a solution?
>>>>> Thanks,
>>>>> S
>>>>> On Jan 31, 2013, at 3:41 PM, Douglas N Greve wrote:
>>>>>
>>>>> Sorry, I don't think we have such a program. You could do it
>>>>> in matlab
>>>>> fairly easily, eg,
>>>>>
>>>>> f = MRIread('filtered_func_data');
>>>>> fmat = fast_vol2mat(f);
>>>>> a = MRIread('aparc+aseg');
>>>>> seglist = unique(a.vol(:));
>>>>> seglist = seglist(2:end); % remove segid=0 (unkown)
>>>>> clear roimean
>>>>> for nthseg = 1:length(seglist)
>>>>> ind = find(a.vol == seglist(nthseg));
>>>>> roimean(:,nthseg) = mean(fmat(:,ind),2);
>>>>> end
>>>>>
>>>>> m = roimean'*roimean;
>>>>>
>>>>> On 01/31/2013 01:29 PM, Sudhin A. Shah wrote:
>>>>>
>>>>> Hello,
>>>>>
>>>>> This worked perfectly 2 years ago :), but now I am
>>>>> having some trouble.
>>>>>
>>>>> I run reg-feat2anat & aseg2feat with no problem.
>>>>>
>>>>> I now need a correlation matrix of every ROI (created by
>>>>> freesurfer)
>>>>>
>>>>> against every other ROI. For this I used @ROI_Corr_Mat
>>>>>
>>>>> (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html).
>>>>>
>>>>>
>>>>> Again - this worked fine in the past.
>>>>>
>>>>> Now I get an error (working with AFNI to see if it can
>>>>> be fixed).
>>>>>
>>>>> Question: Is there any alternative to getting this
>>>>> correlation matrix?
>>>>>
>>>>> i.e every ROI against every other ROI?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> S
>>>>>
>>>>> _______________________________________________
>>>>>
>>>>> Freesurfer mailing list
>>>>>
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>> --
>>>>> Douglas N. Greve, Ph.D.
>>>>> MGH-NMR Center
>>>>> gr...@nmr.mgh.harvard.edu
>>>>> Phone Number: 617-724-2358
>>>>> Fax: 617-726-7422
>>>>>
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>>>>>
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>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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