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Thank you so much!! -Dianne On Fri, Aug 17, 2018 at 2:03 AM paul mccarthy <[log in to unmask]> wrote: > Hi Dianne, > > Your image likely just contains a few nans - fslstats and fslmaths are > not able to work with images that have any nan values. > > You can use fslmaths -nan to replace all of the nans with 0. > > Cheers, > > Paul > > On 17 August 2018 at 03:05, Dianne Patterson <[log in to unmask]> > wrote: > >> Dear SPM and FSL experts, >> >> I am comparing various options for normalization of lesioned brains >> across ants, fsl and spm12, and I am confused by the following result: >> >> All of the warped images (w*) that spm12 generates are not interpretable >> by fslstats (although you can view the image in fsleyes and see the brain >> and range of values). What I mean by "not interpretable" is that >> fslstats is reporting all the values in the image are nan. fslmaths also >> cannot operate on these images as it thinks they are all nans. >> >> FSL does understand the values in the deformation field and the >> segmentation images, just not the warped images...I have bolded the results >> below for all the spm images... >> >> I have linked to a brain image: >> https://arizona.box.com/s/8kxixwhpo97dmg7et96hw6llgyfbkbic so you can >> see the problem: it can be viewed with fsleyes but fslstats and >> fslmaths think it contains only nans. >> >> I am working with Matlab 2016b, spm12 and Mac OSX Sierra. Any insights >> would be greatly appreciated! >> Thanks, >> >> Dianne >> >> T1w.nii >> 1.191157 622.975098 >> T1w_brain.nii >> 0.000000 438.224121 >> *c1T1w_brain.nii* >> *0.000000 0.993000* >> *c2T1w_brain.nii* >> *0.000000 0.993000* >> *c3T1w_brain.nii* >> *0.000000 0.953463* >> *c4T1w_brain.nii* >> *0.000000 0.463200* >> *c5T1w_brain.nii* >> *0.000000 1.000000* >> lesionmask.nii >> 0.000000 1.000000 >> lesionmaskinv.nii >> 0.000000 1.000000 >> sub-001_T1w.nii >> 1.191157 622.975098 >> sub-001_T1w_brain.nii >> 0.000000 438.224121 >> sub-001_T1w_lesioninv.nii >> 0.000000 1.000000 >> sub-001_brain_mask.nii >> 0.000000 1.000000 >> *wT1w.nii* >> *nan nan* >> *wT1w_brain.nii* >> *nan nan* >> *wlesionmask.nii* >> *nan nan* >> *y_T1w_brain.nii* >> *-86.839539 106.838730* >> >> >> >> >> -- >> Dianne Patterson, Ph.D. >> Research Scientist >> [log in to unmask] <[log in to unmask]> >> or >> [log in to unmask] >> University of Arizona >> Speech and Hearing Science 314 >> 1131 E 2nd Street, Building #71 >> (Just East of Harvill) >> ============== >> If you don't hear back from me (and you expected to), >> I blame the University's new SPAM filter. >> Please write to my gmail account. >> ============== >> Antipiphany: That moment when you realize how little you actually know >> ============== >> >> ------------------------------ >> >> To unsubscribe from the FSL list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >> > > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1