Hi John and Jim, Thank you very much. I have been able to map both the beta*.hdr and con*.hdr after setting NaN values to zero. However, a substantial variation in activation patterns seems to be present for the results as obtained from SPM and that observed in Caret. I shall have to look into this.
Best regards, Uma --- Jim Thompson <[EMAIL PROTECTED]> wrote: > Hi John, Uma > This should do it: > > taken from > http://www.sph.umich.edu/~nichols/JohnsGems.html#Gem2 > in matlab type (with adjusted filenames): > > VI = spm_vol('original_beta.img'); > VO = VI; > VO.fname = 'patched_beta.img'; > VO = spm_create_image(VO); > for i=1:VI.dim(3), > img = spm_slice_vol(VI,spm_matrix([0 0 > i]),VI.dim(1:2),0); > tmp = find(isnan(img)); > img(tmp) = 0; > VO = spm_write_plane(VO,img,i); > end; > > Jim > > ------------------------------------------------------------------------ > James C. Thompson, PhD > Research Associate > Center for Advanced Imaging > Department of Radiology > West Virginia University > Robert C Byrd Health Sciences Center South > PO Box 9235 > Morgantown WV 26506-9235 > USA > Tel: +1 304 293 5050 > Fax: +1 304 293 4287 > > email: [EMAIL PROTECTED] > ------------------------------------------------------------------------ > >>> [EMAIL PROTECTED] 07/25/05 4:44 PM >>> > Hi Uma, > > I am not familiar with the "beta" and "con" volumes. > However, when I > searched google, I found a couple of web pages that > state that in the > "beta" and "con" volumes, voxels outside the brain > are set to Nan (not > a number). > > The web page > "http://psyphz.psych.wisc.edu/~oakes/spm/spm_how_tos.html"; > > states " One caveat which you may know if you've > followed the list, is > that the con**.img and beta*.img images have the > areas outside the > brain values set > to NaN". > > Something similar to this is posted on the SPM99 web > site > "http://www.fil.ion.ucl.ac.uk/spm/software/spm99/"; > that voxels outside > the brain are set to 0 or Nan. > > Caret5 expects all voxels in a volume to have valid > numerical values. > You will need to find a way to convert the NaN > voxels to zeros in your > volumes. > > ---------------------------------------------------------- > John Harwell > [EMAIL PROTECTED] > 314-362-3467 > > Department of Anatomy and Neurobiology > Washington University School of Medicine > 660 S. Euclid Ave. Box 8108 > St. Louis, MO 63110 USA > > On Jul 25, 2005, at 1:08 PM, Uma Sreekumar wrote: > > > Hi all, > > > > I am new to Caret. I am trying to map results of > my > > group level analysis performed in SPM99 onto the > PALS > > atlas in Caret 5.3. > > > > While I am able to map the spmT*.hdr for the > > functional volume (as per the online documentation > > provided), I am unable to map the con*.hdr or > > beta*.hdr. Following around 80% processing, > wherein > > both the scaling and descaling ranges are read as > -NaN > > -NaN, the programme crashes with the message > > sqrt: domain error. > > > > All required settings (voxel size etc) seem to be > > correct. I have gone through the previous mails in > the > > list. Shouldnt it be possible to map any SPM *.hdr > > file through Caret? Help of any kind would be > highly > > appreciated. > > > > Best regards, > > Uma Sreekumar > > > > > > > > ----------------------------- > > Y. Uma Sreekumar > > NMR Research Centre, > > Institute of Nuclear Medicine and Allied Sciences, > > Delhi- 110 054, INDIA > > > > > > > > > > > _______________________________________________________ > > Too much spam in your inbox? Yahoo! Mail gives you > the best spam > > protection for FREE! http://in.mail.yahoo.com > > _______________________________________________ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > > http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://pulvinar.wustl.edu/mailman/listinfo/caret-users > ----------------------------- Y. Uma Sreekumar NMR Research Centre, Institute of Nuclear Medicine and Allied Sciences, Delhi- 110 054, INDIA __________________________________________________________ Free antispam, antivirus and 1GB to save all your messages Only in Yahoo! Mail: http://in.mail.yahoo.com
