Hopefully this is the last problem with per-run analysis (in native space) but as far as I see, preproc-sess and selxavg3-sess do not generate
/autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/register.dof6.dat Because of that, when I use tksurfer-sess it faces an error: ERROR: cannot find /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/register.dof6.dat I can use bbregister to register /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/template.nii.gz to the subject's anatomical scan and then use the register.dof.dat file for tksurfer. But is this the correct thing to do? On Wed, Mar 19, 2014 at 11:41 AM, <sha...@nmr.mgh.harvard.edu> wrote: > YES! Started to work. > > Thanks Doug! > > > use > > -nuisreg mcprextreg 3 > > > > On 03/19/2014 11:34 AM, sha...@nmr.mgh.harvard.edu wrote: > >> I used "-nuisreg mcprextreg" in mkanalysis-sess. Got this error: > >> > >> Error: -nuisreg requires two arguments" > >> > >> > >> > >>> -nuisreg > >>> > >>> On 03/19/2014 11:24 AM, sha...@nmr.mgh.harvard.edu wrote: > >>>> Does not accept "-nuis" flag. I changed my mkanalysis-sess to this: > >>>> > >>>> mkanalysis-sess -analysis ColorPrj_TR4_1p5mm_PR_ANOVA -fwhm 1.5 > >>>> -paradigm > >>>> Conds.par -native -event-related -polyfit 2 -gammafit 2.25 1.25 -nuis > >>>> mcprextreg -TR 4 -nconditions 8 -refeventdur 14 -force -fsd bold_Color > >>>> -per-run > >>>> > >>>> and got this error: > >>>> > >>>> ERROR: Flag -nuis unrecognized. > >>>> > >>>> > >>>> > >>>>> I think it is just confused because it expects native to be > >>>>> per-session. > >>>>> One way around this is to just specify -nuis mcprextreg instead of > >>>>> -mcprextreg > >>>>> doug > >>>>> > >>>>> > >>>>> On 03/19/2014 11:15 AM, sha...@nmr.mgh.harvard.edu wrote: > >>>>>> But this is a per-run analysis and preproc-sess is -per-run (in > >>>>>> native > >>>>>> space). I assumed that I have to change my mkanalysis-sess to this: > >>>>>> > >>>>>> mkanalysis-sess -analysis ColorPrj_TR4_1p5mm_PR_ANOVA -fwhm 1.5 > >>>>>> -paradigm > >>>>>> Conds.par -native -event-related -polyfit 2 -gammafit 2.25 1.25 > >>>>>> -mcprextreg -TR 4 -nconditions 8 -refeventdur 14 -force -fsd > >>>>>> bold_Color > >>>>>> -per-run > >>>>>> > >>>>>> > >>>>>> But using -mcprextreg flag generates an error. Is it a bug? > >>>>>> > >>>>>> > >>>>>>> There is not an mcextreg file there. There is mcprextreg file. I > >>>>>>> think > >>>>>>> you need to run preproc with -per-session to get the mcextreg file > >>>>>>> doug > >>>>>>> > >>>>>>> On 03/18/2014 02:34 PM, SHAHIN NASR wrote: > >>>>>>>> Hi, > >>>>>>>> When I run selxavg3-sess, I face this error: > >>>>>>>> > >>>>>>>> ERROR: cannot find volume matching > >>>>>>>> > /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg > >>>>>>>> ERROR: loading nonpar reg > >>>>>>>> > /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg > >>>>>>>> ------------------------------------------ > >>>>>>>> ERROR: fast_selxavg3() failed\n > >>>>>>>> > >>>>>>>> I repeated the preproc-sess from scratch and it worked fine, > >>>>>>>> finished without any problem and I still get the same error. I > >>>>>>>> even > >>>>>>>> check the registration in this run and it fine. > >>>>>>>> > >>>>>>>> Now I am wondering why do I see this error for this subjects > >>>>>>>> (and > >>>>>>>> why I don't see it for the other subjects)? > >>>>>>>> > >>>>>>>> Regards > >>>>>>>> -- > >>>>>>>> Shahin Nasr > >>>>>>>> > >>>>>>>> PhD in Cognitive Neuroscience > >>>>>>>> Martinos Imaging Center, MGH > >>>>>>>> Harvard Medical School > >>>>>>> -- > >>>>>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > >>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >>>>>>> Outgoing: > >>>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >>>>>>> > >>>>>>> > >>>>>>> > >>>>> -- > >>>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > >>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >>>>> Outgoing: > >>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >>>>> > >>>>> > >>>>> > >>> -- > >>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >>> Outgoing: > >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >>> > >>> > >>> > >> > > > > -- > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > > > > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School
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