Hello!
So, my first problem was that I wasn't able to load my new mgh files into qdec. I tried to follow this procedure:
1. Convert a curv file from you subject into mgh: mri_convert lh.curv lh.curv.mgh 2. Load in the mgh file to matlab lhcurv = MRIread('lh.curv.mgh'); 3. Replace the pixel data with your data: lhcurv.vol = myvector; 4. Write the result back out: MRIwrite(lhcurv,'lh.myvector.mgh'); 5. Do this for each subject 6. Run mris_preproc with --meas myvector --srcfmt mgh 7. Then run mri_glmfit
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03761.html
My first question was that I wasn't sure if I needed to use preproc or not because all I want to do is replace my lhcurv.vol information and use that in qdec but I received the following errors:
ninputs = 319 Checking inputs ERROR: dimension mismatch between /Volumes/Macintosh_Griffon_2/ParkHippoBrains/612/surf/lh.curv.fwhm5.fsaverage.mgh and /Volumes/Macintosh_Griffon_2/ParkHippoBrains/1165/surf/lh.curv.fwhm5.fsaverage.mgh Error in Analyze: command failed: mri_concat
Followed by a list of all my files.
So then I found this post: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-August/005918.htm...
They had the same problem and the solution was that there had been too much separation between run recon-all qcache. I don't think this is my problem because I ran them all in 3 days, which I'm assuming isn't significant enough to cause such a problem. On that I'm wondering if I'm completely wrong and qcache is the problem.
However, if that isn't the problem, I tried running mris_preproc and this is what happens
[b417w74-196:/Volumes/KingRAID/ParkHippoBrains] kinglab% mris_preproc --target fsaverage --hemi lh --f list.txt --meas curv --srcfmt mgh --out lh.curv.fwhm5.fsaverage.mgh nsubjects = 321 tmpdir is ./tmp.mris_preproc.26297 /Volumes/KingRAID/ParkHippoBrains Thu Jun 2 16:44:03 MDT 2011 /Volumes/KingRAID/ParkHippoBrains --target fsaverage --hemi lh --f list.txt --meas curv --srcfmt mgh --out lh.curv.fwhm5.fsaverage.mgh Darwin b417w74-196.med.utah.edu 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 setenv SUBJECTS_DIR /Volumes/KingRAID/ParkHippoBrains tmpdir is ./tmp.mris_preproc.26297 \n\n --------------------------------------------------- #@# 1/321 155 Thu Jun 2 16:44:03 MDT 2011 -------------- ----------------------- mri_surf2surf --hemi lh --srcsubject 155 --surfreg sphere.reg --sval /Volumes/KingRAID/ParkHippoBrains/155/surf/lh.curv --sfmt mgh --trgsubject fsaverage --tval ./tmp.mris_preproc.26297/155.1.mgh --noreshape mghRead(/Volumes/KingRAID/ParkHippoBrains/155/surf/lh.curv, -1): could not open file. Filename extension must be .mgh, .mgh.gz or .mgz Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 155 srcval = /Volumes/KingRAID/ParkHippoBrains/155/surf/lh.curv srctype = mgh trgsubject = fsaverage trgval = ./tmp.mris_preproc.26297/155.1.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) Reading source surface reg /Volumes/KingRAID/ParkHippoBrains/155/surf/lh.sphere.reg Loading source data No such file or directory ERROR: could not read /Volumes/KingRAID/ParkHippoBrains/155/surf/lh.curv as type 3
I wasn't able to find any solution to this online and I'm not sure where to go from here!
Thanks,
Jeanette