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/
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/
-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 (andwhy 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/
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/
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/
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/
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/
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
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
SHAHIN NASR -
shahin＠nmr.mgh.harvard.edu