Improving... now selxavg-sess finishes without error, and even mkcontrast-sess and stxgrinder-sess seem to work (see below for command lines). The output seems to be in .nii format though, which is something of a problem for the rest of our custom analysis stream (our matlab routines can only read and write the previous .bhdr/.bfloat). However, as a more fundamental problem, now the analysis crashes at func2sph-sess (again, the same commands worked in April):

mkcontrast-sess -analysis group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat -rmprestim -contrast A1-REST -a 1 -c 0 (etc. - more contrasts)

stxgrinder-sess -analysis group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat -all -sf sessid7 -df sesspar

ERROR:

[cuzco:avml_fmri_mctogether] (nmr-dev-env) func2sph-sess -analysis group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat -sf sessid7 -df sesspar -trgsubject fsaverage -projfrac 0.3 ---------------------------------------------------------- func2sph-sess logfile is /autofs/space/cuzco_014/users/raij/avml_fmri_mctogether/log/func2sph-sess.log ---------------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- Session: avml10_session_BRISI04 1/7 Mon Oct 8 02:00:29 EDT 2007 Mon Oct 8 02:00:29 EDT 2007 Filesystem 1K-blocks Used Available Use% Mounted on /local_mount/space/cuzco/14 100115936 63345920 36770016 64% /autofs/space/cuzco_014 Using Float2Int = round ------------------------------------------------ /autofs/space/cuzco_014/users/raij/avml_fmri_mctogether/avml10_session_BRISI04/bold mri_vol2surf --srcvol group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/h --src_type bfloat --srcreg register.dat --trgsubject fsaverage --mapmethod nnfr --hemi lh --surf white --surfreg sphere.reg --out /autofs/space/cuzco_014/users/raij/avml_fmri_mctogether/avml10_session_BRISI04/bold/group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/sph/h-lh --out_type bfloat --float2int round --interp nearest --projfrac 0.3 ------------------------------------------------ can't find file group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/h_000.hdr (last resort);bailing out on read srcvol = group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/h srctype = bfloat srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.3 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 ERROR: could not read group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/h as type 9 ERROR (/autofs/space/cuzco_014/users/raij/avml_fmri_mctogether/avml10_session_BRISI04): vol2surf failed [cuzco:avml_fmri_mctogether] (nmr-dev-env)

Thanks for your help in adavance, Doug!

-Tommi

This should be fixed in both dev and stable on the next update

raij@nmr.mgh.harvard.edu wrote:

...

Hi Doug,

selxavg-sess -analysis group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat -sf sessid7 -df sesspar -noomnibus

exits with the error:

... Saving offset to group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/h-offset_000.bfloat Slice 1, 77.2438 -------------- ??? Error using ==> minus Matrix dimensions must agree.

Error in ==> fast_selxavg at 439 extreg = extreg - repmat(mean(extreg), [ntrs 1]);

...

...

??? Undefined function or variable 'r'.

...

...

quiting matlab

---

ERROR: fast_selxavg() failed\n ERROR (/autofs/space/cuzco_014/users/raij/avml_fmri_mctogether/avml10_session_BRISI04): selxavg failed

I suspect this may have to do that, for each of the seven subjects, there are three runs with an unequal number of TRs.

Oddly enough, the same analysis worked in March 07. Is there a way to make this analysis work again? I am only interested in BOLD% signal change (FIR waveforms) so comparing runs with different numbers of TRs should be legal. What I would like to do is to calculate a single fixed effects group analysis where each of the three run types is output as its own category (the paradigm files are coded to allow that). Only runs that have the same number of TRs are collapsed across subjects.

(Running three separate analyses, one for each run type, would not help, as we need the output to be in a single block with multiple categories, just as in our earlier analysis)

Or maybe the error has to do with something else... my matlab setup.m should be fine to my knowledge.

machine: cuzco nmr-dev-env (same error with the standard edition) cd /space/cuzco/14/users/raij/avml_fmri_mctogether setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT fsaverage

Thanks!!!

-Tommi

---

Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. _______________________________________________ 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

--- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.