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Ah, that explains it. The NIfTI standard is quite clear that scl_slope really must be used to interpret the intensities correctly. It is rather naughty of ImageJ to display the unscaled intensities. I definitely recommend sticking with FSLView! :) All the best, Mark On 21 Jun 2010, at 22:02, Anil Krishna Vasireddi wrote: > Hm, I see what you mean. I have been looking at these images as raw > files through ImageJ since I'm reading them as raw files when > processing them. The large differences in intensity between the > input and output FLAIRs are evident in this case. When I look at > them in fslview, I see that the difference in intensities is not as > significant. > -Anil > > > > ----- Original Message ---- > From: Mark Jenkinson <[log in to unmask]> > To: [log in to unmask] > Sent: Mon, June 21, 2010 3:10:20 PM > Subject: Re: [FSL] Issues with intensity scaling when using FLIRT > > Dear Anil, > > I see no problem with any of these. > Everything seems consistent - the values in the FSLView intensity > window, the histogram generated by FSLView and the stats output > by fslstats. For example: > > ws183$ fslstats FLAIR_masked.nii -r -R > 0.000000 6163.926270 0.000000 18566.042969 1009.216190 3510.841900 > ws183$ fslstats cFLAIR_masked.nii -r -R > 0.000000 5669.895996 0.000000 17078.000000 857.194649 2773.019085 > > These differences are certainly consistent with interpolation effects. > > What version of FSL and FSLView are you using? > I am using FSL version 4.1.5 and FSLview version 3.1.5. > > I notice that the scl_slope in your nifti images is > set to non-unity values (e.g. 15.069840 in FLAIR_masked > and 3.338950 for PD_masked). These values represent > scalings of the intensities which FSL will apply to the > values stored in the non-header part of the image, as > dictated by the NIFTI format. There may have been > older versions of FSLView that did not display the > scaled intensities, in which might explain why you > quote a mean value in the original FLAIR around 130 > whereas I see values that are much bigger than this. > > If this is the problem then you can easily save > a scaled version (where the scl_slope is reset to > 1.0 and the stored values are scaled instead) by doing: > fslmaths FLAIR_masked ScaledFLAIR_masked > > I hope this helps solve the problem. > > All the best, > Mark > > > > > On 21 Jun 2010, at 20:27, Anil Krishna Vasireddi wrote: > >> The reference number is 979615. >> I have uploaded a set of three images from the same brain. The >> input FLAIR (FLAIR_masked.nii), the input PD (PD_masked.nii), and >> the output FLAIR (cFLAIR_masked.nii). >> >> Thanks again-Anil >> >> >> >> ----- Original Message ---- >> From: Mark Jenkinson <[log in to unmask]> >> To: [log in to unmask] >> Sent: Fri, June 18, 2010 10:42:43 AM >> Subject: Re: [FSL] Issues with intensity scaling when using FLIRT >> >> Him >> >> This sounds very concerning and very unusual. >> Can you please upload the relevant images to: >> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi >> and send us the reference number. >> >> Hopefully we will be able to identify the problem quickly. >> >> All the best, >> Mark >> >> >> >> On 18 Jun 2010, at 16:35, Anil Krishna Vasireddi wrote: >> >>> The resolution of the PD is higher than the resolution of the FLAIR. >>> >>> PD: 288x288x42 >>> FLAIR: 160x160x40 >>> >>> To test the increase in intensity, I look at intensities in the >>> same regions of the brain within the two volumes. To quantify the >>> degree of scaling, I compare the mean intensity of the two >>> volumes. The mean intensity within the original FLAIR typically >>> rests around 130. The mean intensity in the registered FLAIR >>> varied for different volumes, ranging from 900 to 2500. >>> >>> >>> -Anil >>> >>> >>> >>> ----- Original Message ---- >>> From: Mark Jenkinson <[log in to unmask]> >>> To: [log in to unmask] >>> Sent: Thu, June 17, 2010 4:59:57 PM >>> Subject: Re: [FSL] Issues with intensity scaling when using FLIRT >>> >>> Hi, >>> >>> There is no scaling or modification of the intensities except for >>> interpolation. Is it possible that what you are seeing are just >>> interpolation effects? If the resolution of the PD is lower than >>> the FLAIR then that will make the effects worse. >>> >>> If you still do not think it is just interpolation effects then can >>> you describe how you are testing this and give us some >>> numerical examples? >>> >>> All the best, >>> Mark >>> >>> >>> >>> >>> On 17 Jun 2010, at 22:40, Anil Vasireddi wrote: >>> >>>> Hi, >>>> >>>> I have been using FLIRT to register FLAIR volumes of a given >>>> brain to the corresponding proton density (PD) volumes. I am >>>> using the following simple command for this purpose: >>>> >>>> flirt -in <FLAIR volume> -ref <PD volume> -out <registered FLAIR >>>> volume> >>>> >>>> The input and reference volumes were similar enough for the above >>>> command to be sufficient for a successful registration. >>>> >>>> However, the I have been noticing that the image intensities of >>>> voxels in the output FLAIR volumes are considerably larger than >>>> the intensities from the input FLAIR volumes. It doesn't seem as >>>> though the intensities were simply multiplied by a scalar factor >>>> either. >>>> >>>> Is it possible to use the flirt command without altering the >>>> image intensities from the input volumes during registration? >>>> >>>> Any help would be greatly appreciated. >>>> >>>> -Anil >>>> >>> >>> >>> >>> >> >> >> >> >> > > > > >