Hi! It turns out the 3T scans have a lot of susceptibility artifact so it might not be the registration failing but more of the signal :( Unfortunately I will just leave out those ROIs for my analysis.. ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, February 25, 2013 3:28 PM To: Sudhin A. Shah Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Registration & segmentation with FSL - obtaining correlation matrix..
It may be that there is a lot of T2* decay around the edge of the brain. See slide 13 from this presentation: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fs.multimodal-integration.ppt To check your data, turn off the intensity normalization by clicking in the image window and hitting 'i'. In the control window, increase the value of "fmov" to brighten the image. It may be that there is actually tissue outside of those areas but they are very dark. Adjusting the fmov will also allow you to get better contrast which may help to evaluate whether the surfaces inside the brain are correct. doug ps. what was your TE and echo spacing? Is this at 3T? On 02/25/2013 02:52 PM, Sudhin A. Shah wrote: > w/attachment > ________________________________________ > From: Sudhin A. Shah > Sent: Monday, February 25, 2013 2:52 PM > To: Douglas N Greve > Cc: Freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] Registration & segmentation with FSL - > obtaining correlation matrix.. > > 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 >>>>>>>>> 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. >>>>>>>>> _______________________________________________ >>>>>>>>> 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/ >> > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
