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
>
> [EMAIL PROTECTED] 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
> [EMAIL PROTECTED]
> 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.
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