The cost (from .mincost) looks fine. Can you send a pic of the
registration inaccuracy?
doug
On 02/25/2013 11:53 AM, Sudhin A. Shah wrote:
> Hi Doug,
>
> Is the BBR cost function in anat2exf.register.dat.bbr.init?
> mwtp5
> 3.750000
> 4.000000
> 0.150000
> 9.689088e-01 6.952747e-02 -2.374479e-01 6.737892e+00
> 2.456762e-01 -1.566831e-01 9.566056e-01 -2.835866e+01
> 2.930631e-02 -9.851995e-01 -1.688930e-01 1.765446e+01
> 0 0 0 1
> round
>
> Or in anat2exf.register.dat.mincost
> 0.545185 785.020257 804.709380 1.199352
>
> This looks ok under manual inspection - although the head was not in an ideal
> position (patient data). However, I cannot extract data from ROI label 2013.
>
> Thanks,
>
> ________________________________________
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, February 25, 2013 11:39 AM
> To: Sudhin A. Shah; Freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Registration & segmentation with FSL -
> obtaining correlation matrix..
>
> 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
>>>>>>
>>>>>> 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/
>>>>>>
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>> The information in this e-mail is intended only for the person
>>>>>> to whom it is
>>>>>> addressed. If you believe this e-mail was sent to you in error
>>>>>> and the e-mail
>>>>>> contains patient information, please contact the Partners
>>>>>> Compliance HelpLine at
>>>>>> http://www.partners.org/complianceline . If the e-mail was
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>>>>>> but does not contain patient information, please contact the
>>>>>> sender and properly
>>>>>> dispose of the e-mail.
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> The information in this e-mail is intended only for the person to
>>>>>> whom it is
>>>>>> addressed. If you believe this e-mail was sent to you in error and
>>>>>> the e-mail
>>>>>> contains patient information, please contact the Partners
>>>>>> Compliance HelpLine at
>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>> you in error
>>>>>> but does not contain patient information, please contact the sender
>>>>>> and properly
>>>>>> dispose of the e-mail.
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> The information in this e-mail is intended only for the person to
>>>>>> whom it is
>>>>>> addressed. If you believe this e-mail was sent to you in error and
>>>>>> the e-mail
>>>>>> contains patient information, please contact the Partners
>>>>>> Compliance HelpLine at
>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>> you in error
>>>>>> but does not contain patient information, please contact the sender
>>>>>> and properly
>>>>>> dispose of the e-mail.
>>>>
>> --
>> 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/
>
>
--
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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