does /home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh exist? doug
Linda Zhang wrote: > Dear all, > > I think I figured out the contrasts (I'm using [0 0 0 0 0.5 0.5 0 > 0]...is that correct?) but I've come across an error when trying to do > the next step in the tutorial. > > I didn't cache the data during recon-all, so I ran the following: > > mris_preproc --fsgd MMSE-AD.fsgd --target fsaverage --hemi lh --meas > thickness --out lh.MMSE-AD.thickness.00.mgh > > It seemed to run smoothly (I've attached the log below) so I ran the > next step: > > mri_surf2surf --hemi lh --s fsaverage --sval > lh.MMSE-AD.thickness.00.mgh --fwhm 10 --cortex --tval > lh.MMSE-AD.thickness.10.mgh > > I got the following error: > > Reading source surface reg > /home/virtualuser/freesurfer/subjects/fsaverage/surf/lh.sphere.reg > Loading source data > mghRead(/home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh, > -1): could not open file > ERROR: could not read lh.MMSE-AD.thickness.00.mgh as type 3 > > Can anyone tell me where the problem is? Thanks! > > Cheers, > Linda > > The log for mris_preproc (truncated to the last subject and last line): > > --------------------------------------------------- > #@# 12/12 avo1249 Fri Dec 2 18:20:04 HKT 2011 -------------- > ----------------------- > mri_surf2surf --srcsubject avo1249 --srchemi lh --srcsurfreg > sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg > --tval ./tmp.mris_preproc.18275/avo1249.12.mgh --sval > /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.thickness --sfmt > curv --noreshape --no-cortex > Source registration surface changed to sphere.reg > Target registration surface changed to sphere.reg > srcsubject = avo1249 > srcval = > /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.thickness > srctype = curv > trgsubject = fsaverage > trgval = ./tmp.mris_preproc.18275/avo1249.12.mgh > trgtype = > srcsurfreg = sphere.reg > trgsurfreg = sphere.reg > srchemi = lh > trghemi = lh > frame = 0 > fwhm-in = 0 > fwhm-out = 0 > label-src = (null) > label-trg = (null) > OKToRevFaceOrder = 1 > Reading source surface reg > /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.sphere.reg > Loading source data > Reading curvature file > /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.thickness > Reading target surface reg > /home/virtualuser/freesurfer/subjects/fsaverage/surf/lh.sphere.reg > Done > Mapping Source Volume onto Source Subject Surface > surf2surf_nnfr: building source hash (res=16). > Surf2Surf: Forward Loop (163842) > > surf2surf_nnfr: building target hash (res=16). > Surf2Surf: Reverse Loop (121128) > Reverse Loop had 15750 hits > Surf2Surf: Dividing by number of hits (163842) > INFO: nSrcLost = 0 > nTrg121 = 151248, nTrgMulti = 12594, MnTrgMultiHits = 2.2506 > nSrc121 = 78171, nSrcLost = 0, nSrcMulti = 42957, MnSrcMultiHits = > 2.36099 > Saving target data > Saving to ./tmp.mris_preproc.18275/avo1249.12.mgh > > > > ----------------------- > mri_concat ./tmp.mris_preproc.18275/avo0015.1.mgh > ./tmp.mris_preproc.18275/avo0260.2.mgh > ./tmp.mris_preproc.18275/avo0403.3.mgh > ./tmp.mris_preproc.18275/avo0441.4.mgh > ./tmp.mris_preproc.18275/avo0493.5.mgh > ./tmp.mris_preproc.18275/avo0622.6.mgh > ./tmp.mris_preproc.18275/avo0677.7.mgh > ./tmp.mris_preproc.18275/avo0920.8.mgh > ./tmp.mris_preproc.18275/avo1086.9.mgh > ./tmp.mris_preproc.18275/avo1206.10.mgh > ./tmp.mris_preproc.18275/avo1241.11.mgh > ./tmp.mris_preproc.18275/avo1249.12.mgh --o lh.MMSE-AD.thickness.00.mgh > > > > On 2 December 2011 11:42, Linda Zhang <lzhan...@gmail.com > <mailto:lzhan...@gmail.com>> wrote: > > Dear all, > > I have a bit of an amateur question. I've read the slides and > tutorial for group analysis, but I'm still confused about the > contrasts. I made my fsgd file, which contains two groups: M and > F. I also have three continuous variables: Age, MMSE, Education. > I would like to test whether thickness is correlated with MMSE > scores, after controlling for gender, age, and education. What > should my contrast file be in this case? > > Thanks for the help! > > Cheers, > Linda > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 _______________________________________________ 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.
