Re: [Freesurfer] selxavg3-sess error

yes, or you can just

register-sess -per-session ...

that should create just the register.dof6.dat you need

doug

On 03/19/2014 03:10 PM, SHAHIN NASR wrote:

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 mailto: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
<mailto: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
<mailto: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
<mailto: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 <mailto:greve@nmr.mgh.harvard.edu>
>>>>>>> Phone Number: 617-724-2358 <tel:617-724-2358>
>>>>>>> Fax: 617-726-7422 <tel:617-726-7422>
>>>>>>>
>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://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 <mailto:greve@nmr.mgh.harvard.edu>
>>>>> Phone Number: 617-724-2358 <tel:617-724-2358>
>>>>> Fax: 617-726-7422 <tel:617-726-7422>
>>>>>
>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://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 <mailto:greve@nmr.mgh.harvard.edu>
>>> Phone Number: 617-724-2358 <tel:617-724-2358>
>>> Fax: 617-726-7422 <tel:617-726-7422>
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://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 <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://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