It does not look bad to me. Why do you think it looks wrong?
On 02/25/2013 12:29 PM, Sudhin A. Shah wrote:
> Hi Doug,
>
> Here's an example view... It looks fine to me. See attached..
> ________________________________________
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, February 25, 2013 12:12 PM
> To: Sudhin A. Shah
> Cc: Freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Registration & segmentation with FSL -
> obtaining correlation matrix..
>
> 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
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>>>>>>>
>>>>>>> The information in this e-mail is intended only for the person
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>>>>>>> Freesurfer mailing list
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>>>>>>> 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/
>
--
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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