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, shahin@nmr.mgh.harvard.edu wrote:
YES! Started to work.
Thanks Doug!
use -nuisreg mcprextreg 3
On 03/19/2014 11:34 AM, shahin@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, shahin@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, shahin@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 >> greve@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 greve@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 greve@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 greve@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/