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Hi Mark, Reading your email on the inconsistencies between qform and sform I got concern about the orientation of our DTI images. We acquired these images on a Phillips scanner and we used r2agui, a matlab script written from someone at John Hopkins, to transform them into nifti format. the q form is like this xorient R to L yorient A to P z orient S to I and the sform has the y and z flipped xorient R to L yorient P to A z orient I to S According to the forum, the bottom one reflects radiological convention. We have not got any warnings and the images viewed in fslview are not flipped in the y and z direction. Should we change the q form? thanks! v Our DTI images, which we converted using an applet called m 2010/6/15 Mark Jenkinson <[log in to unmask]> > Dear Clark, > > I am sorry that the FAQ was out of date on this. > I have just modified the FAQ to adjust it for FSL4.1. > Basically, it no longer matters whether the storage is > "neurological" or "radiological" as the FSL tools will > work correctly with either, or even with a mix of them. > This did not use to be the case but it is now. > > As for your inconsistent qform and sform - THIS IS > EXTREMELY BAD! You should convert your images > again from the original DICOM, as if you have such > inconsistent information then there is NO WAY of > knowing which is the correct left or right in the image, > since the qform information says one thing and the > sform information says another. This is why we have > the warnings. We also use dcm2nii for our conversions > but have not noticed this problem. However, we do not > use the "reoriented" images. So check whether the other > images have consistent information in the qform and sform > (the sign of the determinant of these matrices needs to be > the same). Just running fslorient will tell you what the > situation is. > > With respect to FSLView, it is the case that it tries to display > the images in a "radiological display" although this doesn't > have an obvious meaning for images that are differently > oriented to the standard MNI152. It is not a problem for > any of the tools how things are shown in FSLView, as all > tools will work correctly for any storage type now. If you > do wish to see the images in the same orientation as the > MNI152 template images then you should run the command: > > fslswapdim invol RL PA IS outvol > and if it gives you the message > > Cannot perform requested swap (NERUOLOGICAL/RADIOLOGICAL storage inverted) >> Try the following command instead >> Fslswapdim o_dcm2nii_Output.nii.gz LR PA IS tmp >> > then simply do as it says and run the command with LR PA IS instead. > > I'm sorry that this is not simpler, but having both qform and sform > in the nifti standard makes some things complicated. I am > intending to overhaul the section relating to this and provide > a small script that reorients images to match the MNI152 > orientation, as that seems to be what people generally want to do. > It is not important that this is done - it is simply a preference that > people have in order to look at their data. It is only the display > which is now affected by this - all tools process correctly as long > as the qform and sform are consistent and correct. You should > ideally be able to tell if they are correct by looking at the labels > that FSLView attaches to the image. If they are correct and the > qform and sform are consistent then that is enough for all tools > to work. If you also want to see the image in the same orientation > as the MNI152 then perform the fslswapdim commands as shown > above. > > I hope this helps to clarify things and make things a little less > "blackbox". > Being able to store two different sets of orientation information > and this being somewhat separate from how they are displayed does > make it hard to follow, and I've tried to minimise the amount that > people need to worry about this. > > All the best, > Mark > > > > > > > > On 14 Jun 2010, at 23:53, Clark Johnson wrote: > > Mark -- We use dcm2nii for conversion to NIFTI -- As Chunhui Chen >> mentioned as this thread began -- this program's output includes an image >> that has been reoriented -- in my case from a SAG acquisition to what >> appears in FSLVIEW to be Radiologic. >> >> When viewed in FSLVIEW it "looks" like LAS -- the axial image has the left >> side of the brain on the right side of the image. But, when you increment >> the "x" index -- FSLVIEW moves to the right side of the brain. This seems >> to suggest that FSLVIEW is presenting in LAS -- but the byte order is >> actually RAS. >> >> If you request the HDR information for this file (fslhd) you get the error >> >> Inconsistent left-right order stored in sform and qform in file XYZ >> Using sform instead of qform values >> >> And the output attached to this email. >> >> >> In your response on May 5th -- you indicated that FEAT / FLIRT won't have >> any problem with an RAS oriented image (though possibly we have to turn on >> "Full search" in FEAT). However, the "format and orientation conventions" >> section of the FSL documentation is still pretty unambiguous about this -- >> stating: >> >> "NIFTI allows the left-right orientation of your data to be specified but >> we do not recommend using anything but radiologically ordered images with >> this release." >> >> It is this statement in the documentation that has me confused. FSLVIEW >> is pretty clever -- but the byte order in the file does not appear to be LAS >> -- I am wondering if that means it's not "radiologically ordered". >> >> In a previous response to this issue -- >> >> >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1003&L=FSL&D=0&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=179521 >> >> you suggested >> >> "If the labels that you see in FSLView (L, R, A, P, S, I) are in >> the correct places in the image then all you need to do in order >> to reorient your images to axial is: >> fslswapdim invol RL PA IS outvol >> ..." >> >> >> In an effort to work exclusively with LAS oriented images I've tried the " >> fslswapdim invol RL PA IS outvol" approach. As noted above, the labels are >> correct -- I just want the byte order to reflect an LAS orientation as well. >> >> For this file, the suggested fslswapdim call generates several >> "inconsistent left-right" messages then stops with the following message" >> >> Cannot perform requested swap (NERUOLOGICAL/RADIOLOGICAL storage inverted) >> Try the following command instead >> Fslswapdim o_dcm2nii_Output.nii.gz LR PA IS tmp >> >> Since I think it already is RAS -- this suggested solution does not seem >> to solve the problem >> >> >> We all love FSL tools -- but sometimes they seem a little like a >> "blackbox" -- things are happening and we don't really understand all of >> the implications. I am concerned that we are not being careful enough about >> the L/R orientation of our data and am hoping you can give me some >> additional guidance >> >> Thank you for all your help. >> >> Clark >> >> >> >> >> -----Original Message----- >> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On >> Behalf Of Mark Jenkinson >> Sent: Tuesday, May 04, 2010 3:10 PM >> To: [log in to unmask] >> Subject: Re: [FSL] Should I flip L-R of images from dcm2niigui (MRIcron)? >> >> Hi, >> >> I'm not quite sure how you are defining RAS, or similar, for fslview >> *display*. >> >> Anyway, all that *really* matters is that the labels are in the >> correct places on >> the image. It doesn't really matter which way the image is >> displayed. All the >> FSL tools should work, regardless of which way the image is stored and >> displayed, as long as the labels are correct. However, if the >> different images >> are very differently oriented then you should check the registrations >> carefully >> to make sure that they all work correctly. >> >> So, in summary, I wouldn't worry about swapping anything. >> >> As for FreeSurfer problems, you should email the FreeSurfer list about >> that. >> >> All the best, >> Mark >> >> On 4 May 2010, at 09:11, chen wrote: >> >> Hello FSLers, >>> >>> I may be asking a stupid question but it really troubled me a while. >>> >>> I converted dicom files to nift using dcm2niigui (MRIcron). In >>> fslview, it displayed in RAS coordinates, but template of FSL are in >>> LAS coordinates. Should I filp L-R before doing any further analysis? >>> Besides, my structrual imagews were scanned in sagittal view, and >>> after dcm2niigui transforation, it's in PIL coordinates in fslview. >>> Should I reorient the image to LAS coordinates too? >>> But the letters L R I S A P are labled correctly (at least A-P and I－ >>> S are correct), which means FSL can read in orientation information >>> correctly. So I am confused whetehr I should reorient my data or not? >>> I also processed strucutre images with Freesurfer, and the results >>> between reoriented and not-reoriented images are different, so which >>> one is correct? >>> >>> Any help is appreciated, >>> Thanks! >>> -- >>> Chunhui Chen >>> >>> >>> 网易为中小企业免费提供企业邮箱（自主域名） >>> >> <o_dcm2nii_Output_HD.txt> >> > > -- Valeria Della-Maggiore, Ph. D Department of Physiology, School of Medicine University of Buenos Aires Paraguay 2155, Capital Federal Buenos Aires, C1121ABG Argentina phone 54 11 5 950 9500 (2132) http://www.fmed.uba.ar/depto/fisiologia/fdaction.htm ------------------------------------------------------------ being wild and disciplined at the same time....