Here is the last subject - coronal view.. This is where I started
scaling/stretching :(
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sudhin A. Shah
[sut2...@med.cornell.edu]
Sent: Monday, February 25, 2013 1:29 PM
To: Douglas N Greve
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Registration & segmentation with FSL -
obtaining correlation matrix..
Here is another example registration (different subject). Here I cannot extract
values for label 1006 and 2006..
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sudhin A. Shah
[sut2...@med.cornell.edu]
Sent: Monday, February 25, 2013 12:49 PM
To: Douglas N Greve
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Registration & segmentation with FSL -
obtaining correlation matrix..
Sorry - this doesn't look bad. Still I cannot extract values for the ROI label
2013..
On Feb 25, 2013, at 12:43 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
wrote:
>
> 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
>>>>>>>> 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
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>>>>>>>> dispose of the e-mail.
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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
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>>>>>>>> Compliance HelpLine at
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>>>>>>>> _______________________________________________
>>>>>>>> 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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