Re: [Freesurfer] freesurfer selxavg3-sess error

[Greve, Douglas N.,Ph.D.]

Can you include the command line and full terminal output? From what you 
have below, it says it is only finding one non-null condition, so double 
check your par files

On 11/12/2018 04:58 PM, Francesca Strappini wrote:
>
> External Email - Use Caution
>
> Thank you!
> I changed the event file and re-run the analysis. I got an error 
> message when creating the contrast:
>
> mkanalysis-sess -analysis FF-MonkeyCassis-event.sm03.lh -surface 
> MonkeyCassis lh -fwhm 3 -fsd bold -per-run -event-related -paradigm 
> FF.par -TR 2 -nconditions 2 -refeventdur 16 -spmhrf
> mkcontrast-sess -analysis FF-MonkeyCassis-event.sm03.lh -contrast 
> coherent-v-random -a 1 -c 2
>
> @: Missing file name.
> INFO: Found 1 Non-Null Conditions
> INFO: Found  Delays
> ERROR: Condition ID 2 out of range (0:1)
>
>
> 2    1    16    1    coherent
> 16    2    16    1    random
> 32    1    16    1    coherent
> 48    2    16    1    random
> 64    1    16    1    coherent
> 82    2    16    1    random
> 96    1    16    1    coherent
> 112    2    16    1    random
> 128    1    16    1    coherent
> 144    2    16    1    random
> 162    1    16    1    coherent
> 176    2    16    1    random
> 192    1    16    1    coherent
> 228    2    16    1    random
> 224    1    16    1    coherent
> 242    2    16    1    random
>
>
> Thanks a lot for the help!
> Best
> Francesca
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] freesurfer selxavg3-sess error

[Francesca Strappini]

External Email - Use Caution

Thank you!
I changed the event file and re-run the analysis. I got an error message
when creating the contrast:

mkanalysis-sess -analysis FF-MonkeyCassis-event.sm03.lh -surface
MonkeyCassis lh -fwhm 3 -fsd bold -per-run -event-related -paradigm FF.par
-TR 2 -nconditions 2 -refeventdur 16 -spmhrf
mkcontrast-sess -analysis FF-MonkeyCassis-event.sm03.lh -contrast
coherent-v-random -a 1 -c 2

@: Missing file name.
INFO: Found 1 Non-Null Conditions
INFO: Found  Delays
ERROR: Condition ID 2 out of range (0:1)


21161coherent
162161random
321161coherent
482161random
641161coherent
822161random
961161coherent
1122161random
1281161coherent
1442161random
1621161coherent
1762161random
1921161coherent
2282161random
2241161coherent
2422161random


Thanks a lot for the help!
Best
Francesca
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] freesurfer selxavg3-sess error

[Greve, Douglas N.,Ph.D.]

When you ran mkanalysis-sess, did you specify two event types? You only 
have one non-null event in your paradigm file.

On 10/28/2018 08:57 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
>
> Thanks! Now it's loading correctly my event file.
> However, when I run selxavg3-sess I get this error message:
>
> selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF -no-con-ok
>
> outanadir = 
> /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF/bold/FF-MonkeyCassis.sm03.lh
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> parfiles condition id list:  1
> ERROR: found 1 non-null conditions, expected 2
> --
> ERROR: fast_selxavg3() failed\n
>
> This is my even file:
>
> 0    1    32    1    ON
> 32    0    32    1    OFF
> 64    1    32    1    ON
> 96    0    32    1    OFF
> 128    1    32    1    ON
> 160    0    32    1    OFF
> 192    1    32    1    ON
> 224    0    32    1    OFF
>
> Thanks for the help!
> Best
> Francesca
>
> Il giorno gio 3 mag 2018 alle ore 00:49 Douglas N. Greve 
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>
> oops, sorry. Looks like it is having a problem loading your paradigm
> file. Check that. If the error does not pop out to you then send
> it to me.
>
>
> On 05/02/2018 10:06 AM, Francesca Strappini wrote:
> > Hi, sorry, maybe my last email got lost. Is there anything I can
> try
> > to fix this problem with selxavg3-sess?
> >
> > Thanks!
> > Best
> > Francesca
> >
> > 2018-04-24 20:35 GMT+03:00 Francesca Strappini
> >  
>  >>:
> >
> >     Thank you for the reply!
> >     I deleted the contrasts and run this command line:
> >
> >     selxavg3-sess -a FF-MonkeyCassis.sm03.rh -s MonkeyCassis-FF
> -no-con-ok
> >
> >
> >     --- matlab output 
> >     MATLAB is selecting SOFTWARE OPENGL rendering.
> >
> >     < M A T L A B (R) >
> >       Copyright 1984-2016 The MathWorks, Inc.
> >        R2016b (9.1.0.441655) 64-bit (glnxa64)
> >      September 7, 2016
> >
> >
> >     To get started, type one of these: helpwin, helpdesk, or demo.
> >     For product information, visit www.mathworks.com
> 
> >     .
> >
> >     >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> >     >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> >     >> /usr/local/freesurfer/matlab/MRIread.m
> >     >> >> >> starting fast_selxavg3b
> >
> >
> >     #@# MonkeyCassis-FF ###
> >     /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF
> >     -
> >     $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
> >     -
> >     outtop = /usr/local/freesurfer/fsfast/Monkeys
> >     Extension format = nii.gz
> >     INFO: key nSliceGroups unrecognized, line 11, skipping
> >     Subscripted assignment dimension mismatch.
> >
> >     Error in fast_ldpar4 (line 97)
> >       par4(nthrow,1) = tonset;
> >
> >     Error in flac_customize (line 121)
> >     [par partype] = fast_ldpar4(parpath);
> >
> >     Error in fast_selxavg3b (line 129)
> >     flac0 = flac_customize(flac0);
> >
> >     >> --
> >     ERROR: fast_selxavg3() failed\n
> >
> >
> >     2018-04-24 20:27 GMT+03:00 Douglas Greve
> mailto:dgr...@mgh.harvard.edu>
> >      >>:
> >
> >         Try deleting the contrasts (.mat files) and rerunning
> >
> >
> >         On 4/24/18 5:48 AM, Francesca Strappini wrote:
> >>
> >>
> >>         Dear FreeSurfer experts,
> >>
> >>         I'm trying to analyze some monkey functional data. I
> got this
> >>         error message with selxavg3-sess.
> >>
> >>         I run the following commands:
> >>
> >>         mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast
> >>         ON-vs-OFF -a 1 -c 0
> >>         mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast
> >>         ON-vs-OFF -a 1 -c 0
> >>         preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s
> >>         MonkeyCassis-FF -fsd bold -per-session
> >>         selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF
> >>
> >>
> >>         --- matlab output 

Re: [Freesurfer] freesurfer selxavg3-sess error

[Francesca Strappini]

External Email - Use Caution

Thanks! Now it's loading correctly my event file.
However, when I run selxavg3-sess I get this error message:

selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF -no-con-ok

outanadir =
/usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF/bold/FF-MonkeyCassis.sm03.lh
Excluding 2 points
Excluding 2 points
Excluding 2 points
Excluding 2 points
Excluding 2 points
Excluding 2 points
Excluding 2 points
Excluding 2 points
Excluding 2 points
Excluding 2 points
parfiles condition id list:  1
ERROR: found 1 non-null conditions, expected 2
--
ERROR: fast_selxavg3() failed\n

This is my even file:

01321ON
320321OFF
641321ON
960321OFF
1281321ON
1600321OFF
1921321ON
2240321OFF

Thanks for the help!
Best
Francesca

Il giorno gio 3 mag 2018 alle ore 00:49 Douglas N. Greve <
dgr...@mgh.harvard.edu> ha scritto:

> oops, sorry. Looks like it is having a problem loading your paradigm
> file. Check that. If the error does not pop out to you then send it to me.
>
>
> On 05/02/2018 10:06 AM, Francesca Strappini wrote:
> > Hi, sorry, maybe my last email got lost. Is there anything I can try
> > to fix this problem with selxavg3-sess?
> >
> > Thanks!
> > Best
> > Francesca
> >
> > 2018-04-24 20:35 GMT+03:00 Francesca Strappini
> > mailto:francescastrapp...@gmail.com>>:
> >
> > Thank you for the reply!
> > I deleted the contrasts and run this command line:
> >
> > selxavg3-sess -a FF-MonkeyCassis.sm03.rh -s MonkeyCassis-FF
> -no-con-ok
> >
> >
> > --- matlab output 
> > MATLAB is selecting SOFTWARE OPENGL rendering.
> >
> > < M A T L A B (R) >
> >   Copyright 1984-2016 The MathWorks, Inc.
> >R2016b (9.1.0.441655) 64-bit (glnxa64)
> >  September 7, 2016
> >
> >
> > To get started, type one of these: helpwin, helpdesk, or demo.
> > For product information, visit www.mathworks.com
> > .
> >
> > >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> > >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> > >> /usr/local/freesurfer/matlab/MRIread.m
> > >> >> >> starting fast_selxavg3b
> >
> >
> > #@# MonkeyCassis-FF ###
> > /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF
> > -
> > $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
> > -
> > outtop = /usr/local/freesurfer/fsfast/Monkeys
> > Extension format = nii.gz
> > INFO: key nSliceGroups unrecognized, line 11, skipping
> > Subscripted assignment dimension mismatch.
> >
> > Error in fast_ldpar4 (line 97)
> >   par4(nthrow,1) = tonset;
> >
> > Error in flac_customize (line 121)
> > [par partype] = fast_ldpar4(parpath);
> >
> > Error in fast_selxavg3b (line 129)
> > flac0 = flac_customize(flac0);
> >
> > >> --
> > ERROR: fast_selxavg3() failed\n
> >
> >
> > 2018-04-24 20:27 GMT+03:00 Douglas Greve  > >:
> >
> > Try deleting the contrasts (.mat files) and rerunning
> >
> >
> > On 4/24/18 5:48 AM, Francesca Strappini wrote:
> >>
> >>
> >> Dear FreeSurfer experts,
> >>
> >> I'm trying to analyze some monkey functional data. I got this
> >> error message with selxavg3-sess.
> >>
> >> I run the following commands:
> >>
> >> mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast
> >> ON-vs-OFF -a 1 -c 0
> >> mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast
> >> ON-vs-OFF -a 1 -c 0
> >> preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s
> >> MonkeyCassis-FF -fsd bold -per-session
> >> selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF
> >>
> >>
> >> --- matlab output 
> >> MATLAB is selecting SOFTWARE OPENGL rendering.
> >>
> >> < M A T L A B (R) >
> >>   Copyright 1984-2016 The MathWorks, Inc.
> >>R2016b (9.1.0.441655) 64-bit (glnxa64)
> >> September 7, 2016
> >>
> >>
> >> To get started, type one of these: helpwin, helpdesk, or demo.
> >> For product information, visit www.mathworks.com
> >> .
> >>
> >> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> >> >> /usr/local/freesurfer/matlab/MRIread.m
> >> >> >> >> starting fast_selxavg3b
> >>
> >>
> >> #@# MonkeyCassis-FF #

Re: [Freesurfer] freesurfer selxavg3-sess error

[Douglas N. Greve]

oops, sorry. Looks like it is having a problem loading your paradigm 
file. Check that. If the error does not pop out to you then send it to me.


On 05/02/2018 10:06 AM, Francesca Strappini wrote:
> Hi, sorry, maybe my last email got lost. Is there anything I can try 
> to fix this problem with selxavg3-sess?
>
> Thanks!
> Best
> Francesca
>
> 2018-04-24 20:35 GMT+03:00 Francesca Strappini 
> mailto:francescastrapp...@gmail.com>>:
>
> Thank you for the reply!
> I deleted the contrasts and run this command line:
>
> selxavg3-sess -a FF-MonkeyCassis.sm03.rh -s MonkeyCassis-FF -no-con-ok
>
>
> --- matlab output 
> MATLAB is selecting SOFTWARE OPENGL rendering.
>
>     < M A T L A B (R) >
>   Copyright 1984-2016 The MathWorks, Inc.
>    R2016b (9.1.0.441655) 64-bit (glnxa64)
>  September 7, 2016
>
>
> To get started, type one of these: helpwin, helpdesk, or demo.
> For product information, visit www.mathworks.com
> .
>
> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> >> /usr/local/freesurfer/matlab/MRIread.m
> >> >> >> starting fast_selxavg3b
>
>
> #@# MonkeyCassis-FF ###
> /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF
> -
> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
> -
> outtop = /usr/local/freesurfer/fsfast/Monkeys
> Extension format = nii.gz
> INFO: key nSliceGroups unrecognized, line 11, skipping
> Subscripted assignment dimension mismatch.
>
> Error in fast_ldpar4 (line 97)
>   par4(nthrow,1) = tonset;
>
> Error in flac_customize (line 121)
>     [par partype] = fast_ldpar4(parpath);
>
> Error in fast_selxavg3b (line 129)
> flac0 = flac_customize(flac0);
>
> >> --
> ERROR: fast_selxavg3() failed\n
>
>
> 2018-04-24 20:27 GMT+03:00 Douglas Greve  >:
>
> Try deleting the contrasts (.mat files) and rerunning
>
>
> On 4/24/18 5:48 AM, Francesca Strappini wrote:
>>
>>
>> Dear FreeSurfer experts,
>>
>> I'm trying to analyze some monkey functional data. I got this
>> error message with selxavg3-sess.
>>
>> I run the following commands:
>>
>> mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast
>> ON-vs-OFF -a 1 -c 0
>> mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast
>> ON-vs-OFF -a 1 -c 0
>> preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s
>> MonkeyCassis-FF -fsd bold -per-session
>> selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF
>>
>>
>> --- matlab output 
>> MATLAB is selecting SOFTWARE OPENGL rendering.
>>
>>     < M A T L A B (R) >
>>   Copyright 1984-2016 The MathWorks, Inc.
>>    R2016b (9.1.0.441655) 64-bit (glnxa64)
>> September 7, 2016
>>
>>
>> To get started, type one of these: helpwin, helpdesk, or demo.
>> For product information, visit www.mathworks.com
>> .
>>
>> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
>> >> /usr/local/freesurfer/matlab/MRIread.m
>> >> >> >> starting fast_selxavg3b
>>
>>
>> #@# MonkeyCassis-FF ###
>> /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF
>> -
>> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
>> -
>> outtop = /usr/local/freesurfer/fsfast/Monkeys
>> Extension format = nii.gz
>> INFO: key nSliceGroups unrecognized, line 11, skipping
>>  1 ON-vs-OFF.mat
>> Subscripted assignment dimension mismatch.
>>
>> Error in fast_ldpar4 (line 97)
>>   par4(nthrow,1) = tonset;
>>
>> Error in flac_customize (line 121)
>>     [par partype] = fast_ldpar4(parpath);
>>
>> Error in fast_selxavg3b (line 129)
>> flac0 = flac_customize(flac0);
>>
>> >> --
>> ERROR: fast_selxavg3() failed\n
>>
>> Thank you!
>> Best
>>
>> Francesca
>>
>> -- 
>> Francesca Strappini, Ph.D.
>> Neurobiology Department
>> Weizmann Institute of Science
>> 234 Herzl Street, Rehovot 7610001 Israel
>> Tel.: +972 58 444 2584
>> E-mail: francesca.strapp...@weizmann.ac.il
>> 
>>
>>
>>   

Re: [Freesurfer] freesurfer selxavg3-sess error

[Francesca Strappini]

External Email - Use Caution

Hi, sorry, maybe my last email got lost. Is there anything I can try to fix
this problem with selxavg3-sess?

Thanks!
Best
Francesca

2018-04-24 20:35 GMT+03:00 Francesca Strappini :

> Thank you for the reply!
> I deleted the contrasts and run this command line:
>
> selxavg3-sess -a FF-MonkeyCassis.sm03.rh -s MonkeyCassis-FF -no-con-ok
>
>
> --- matlab output 
> MATLAB is selecting SOFTWARE OPENGL rendering.
>
> < M A T L A B (R) >
>   Copyright 1984-2016 The MathWorks, Inc.
>R2016b (9.1.0.441655) 64-bit (glnxa64)
>  September 7, 2016
>
>
> To get started, type one of these: helpwin, helpdesk, or demo.
> For product information, visit www.mathworks.com.
>
> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> >> /usr/local/freesurfer/matlab/MRIread.m
> >> >> >> starting fast_selxavg3b
>
>
> #@# MonkeyCassis-FF ###
> /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF
> -
> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
> -
> outtop = /usr/local/freesurfer/fsfast/Monkeys
> Extension format = nii.gz
> INFO: key nSliceGroups unrecognized, line 11, skipping
> Subscripted assignment dimension mismatch.
>
> Error in fast_ldpar4 (line 97)
>   par4(nthrow,1) = tonset;
>
> Error in flac_customize (line 121)
> [par partype] = fast_ldpar4(parpath);
>
> Error in fast_selxavg3b (line 129)
> flac0 = flac_customize(flac0);
>
> >> --
> ERROR: fast_selxavg3() failed\n
>
>
> 2018-04-24 20:27 GMT+03:00 Douglas Greve :
>
>> Try deleting the contrasts (.mat files) and rerunning
>>
>> On 4/24/18 5:48 AM, Francesca Strappini wrote:
>>
>>
>> Dear FreeSurfer experts,
>>
>> I'm trying to analyze some monkey functional data. I got this error
>> message with selxavg3-sess.
>>
>> I run the following commands:
>>
>> mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast ON-vs-OFF -a
>> 1 -c 0
>> mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast ON-vs-OFF -a
>> 1 -c 0
>> preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s MonkeyCassis-FF -fsd
>> bold -per-session
>> selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF
>>
>>
>> --- matlab output 
>> MATLAB is selecting SOFTWARE OPENGL rendering.
>>
>> < M A T L A B (R) >
>>   Copyright 1984-2016 The MathWorks, Inc.
>>R2016b (9.1.0.441655) 64-bit (glnxa64)
>>  September 7, 2016
>>
>>
>> To get started, type one of these: helpwin, helpdesk, or demo.
>> For product information, visit www.mathworks.com.
>>
>> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
>> >> /usr/local/freesurfer/matlab/MRIread.m
>> >> >> >> starting fast_selxavg3b
>>
>>
>> #@# MonkeyCassis-FF ###
>> /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF
>> -
>> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
>> -
>> outtop = /usr/local/freesurfer/fsfast/Monkeys
>> Extension format = nii.gz
>> INFO: key nSliceGroups unrecognized, line 11, skipping
>>  1 ON-vs-OFF.mat
>> Subscripted assignment dimension mismatch.
>>
>> Error in fast_ldpar4 (line 97)
>>   par4(nthrow,1) = tonset;
>>
>> Error in flac_customize (line 121)
>> [par partype] = fast_ldpar4(parpath);
>>
>> Error in fast_selxavg3b (line 129)
>> flac0 = flac_customize(flac0);
>>
>> >> --
>> ERROR: fast_selxavg3() failed\n
>>
>> Thank you!
>> Best
>>
>> Francesca
>>
>> --
>> Francesca Strappini, Ph.D.
>> Neurobiology Department
>> Weizmann Institute of Science
>> 234 Herzl Street, Rehovot 7610001 Israel
>> Tel.: +972 58 444 2584
>> E-mail: francesca.strapp...@weizmann.ac.il
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Instit

Re: [Freesurfer] freesurfer selxavg3-sess error

[Francesca Strappini]

External Email - Use Caution

Thank you for the reply!
I deleted the contrasts and run this command line:

selxavg3-sess -a FF-MonkeyCassis.sm03.rh -s MonkeyCassis-FF -no-con-ok


--- matlab output 
MATLAB is selecting SOFTWARE OPENGL rendering.

< M A T L A B (R) >
  Copyright 1984-2016 The MathWorks, Inc.
   R2016b (9.1.0.441655) 64-bit (glnxa64)
 September 7, 2016


To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.

>> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
>> /usr/local/freesurfer/matlab/MRIread.m
>> >> >> starting fast_selxavg3b


#@# MonkeyCassis-FF ###
/usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF
-
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
-
outtop = /usr/local/freesurfer/fsfast/Monkeys
Extension format = nii.gz
INFO: key nSliceGroups unrecognized, line 11, skipping
Subscripted assignment dimension mismatch.

Error in fast_ldpar4 (line 97)
  par4(nthrow,1) = tonset;

Error in flac_customize (line 121)
[par partype] = fast_ldpar4(parpath);

Error in fast_selxavg3b (line 129)
flac0 = flac_customize(flac0);

>> --
ERROR: fast_selxavg3() failed\n


2018-04-24 20:27 GMT+03:00 Douglas Greve :

> Try deleting the contrasts (.mat files) and rerunning
>
> On 4/24/18 5:48 AM, Francesca Strappini wrote:
>
>
> Dear FreeSurfer experts,
>
> I'm trying to analyze some monkey functional data. I got this error
> message with selxavg3-sess.
>
> I run the following commands:
>
> mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast ON-vs-OFF -a 1
> -c 0
> mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast ON-vs-OFF -a 1
> -c 0
> preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s MonkeyCassis-FF -fsd
> bold -per-session
> selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF
>
>
> --- matlab output 
> MATLAB is selecting SOFTWARE OPENGL rendering.
>
> < M A T L A B (R) >
>   Copyright 1984-2016 The MathWorks, Inc.
>R2016b (9.1.0.441655) 64-bit (glnxa64)
>  September 7, 2016
>
>
> To get started, type one of these: helpwin, helpdesk, or demo.
> For product information, visit www.mathworks.com.
>
> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> >> /usr/local/freesurfer/matlab/MRIread.m
> >> >> >> starting fast_selxavg3b
>
>
> #@# MonkeyCassis-FF ###
> /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF
> -
> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
> -
> outtop = /usr/local/freesurfer/fsfast/Monkeys
> Extension format = nii.gz
> INFO: key nSliceGroups unrecognized, line 11, skipping
>  1 ON-vs-OFF.mat
> Subscripted assignment dimension mismatch.
>
> Error in fast_ldpar4 (line 97)
>   par4(nthrow,1) = tonset;
>
> Error in flac_customize (line 121)
> [par partype] = fast_ldpar4(parpath);
>
> Error in fast_selxavg3b (line 129)
> flac0 = flac_customize(flac0);
>
> >> --
> ERROR: fast_selxavg3() failed\n
>
> Thank you!
> Best
>
> Francesca
>
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strapp...@weizmann.ac.il
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. 

Re: [Freesurfer] freesurfer selxavg3-sess error

[Douglas Greve]

Try deleting the contrasts (.mat files) and rerunning


On 4/24/18 5:48 AM, Francesca Strappini wrote:



Dear FreeSurfer experts,

I'm trying to analyze some monkey functional data. I got this error 
message with selxavg3-sess.


I run the following commands:

mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast ON-vs-OFF 
-a 1 -c 0
mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast ON-vs-OFF 
-a 1 -c 0
preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s MonkeyCassis-FF 
-fsd bold -per-session

selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF


--- matlab output 
MATLAB is selecting SOFTWARE OPENGL rendering.

    < M A T L A B (R) >
  Copyright 1984-2016 The MathWorks, Inc.
   R2016b (9.1.0.441655) 64-bit (glnxa64)
 September 7, 2016


To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com 
.


>> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
>> /usr/local/freesurfer/matlab/MRIread.m
>> >> >> starting fast_selxavg3b


#@# MonkeyCassis-FF ###
/usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF
-
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
-
outtop = /usr/local/freesurfer/fsfast/Monkeys
Extension format = nii.gz
INFO: key nSliceGroups unrecognized, line 11, skipping
 1 ON-vs-OFF.mat
Subscripted assignment dimension mismatch.

Error in fast_ldpar4 (line 97)
  par4(nthrow,1) = tonset;

Error in flac_customize (line 121)
    [par partype] = fast_ldpar4(parpath);

Error in fast_selxavg3b (line 129)
flac0 = flac_customize(flac0);

>> --
ERROR: fast_selxavg3() failed\n

Thank you!
Best

Francesca

--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il 




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] freesurfer selxavg3-sess error

[Francesca Strappini]

External Email - Use Caution

Dear FreeSurfer experts,

I'm trying to analyze some monkey functional data. I got this error message
with selxavg3-sess.

I run the following commands:

mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast ON-vs-OFF -a 1
-c 0
mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast ON-vs-OFF -a 1
-c 0
preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s MonkeyCassis-FF -fsd
bold -per-session
selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF


--- matlab output 
MATLAB is selecting SOFTWARE OPENGL rendering.

< M A T L A B (R) >
  Copyright 1984-2016 The MathWorks, Inc.
   R2016b (9.1.0.441655) 64-bit (glnxa64)
 September 7, 2016


To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.

>> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
>> /usr/local/freesurfer/matlab/MRIread.m
>> >> >> starting fast_selxavg3b


#@# MonkeyCassis-FF ###
/usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF
-
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
-
outtop = /usr/local/freesurfer/fsfast/Monkeys
Extension format = nii.gz
INFO: key nSliceGroups unrecognized, line 11, skipping
 1 ON-vs-OFF.mat
Subscripted assignment dimension mismatch.

Error in fast_ldpar4 (line 97)
  par4(nthrow,1) = tonset;

Error in flac_customize (line 121)
[par partype] = fast_ldpar4(parpath);

Error in fast_selxavg3b (line 129)
flac0 = flac_customize(flac0);

>> --
ERROR: fast_selxavg3() failed\n

Thank you!
Best

Francesca

-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[Douglas Greve]

not sure what is going on. Is the script stem2fname in your path? If so, 
run selxavg3-sess with -debug as the first option and send the terminal 
output



On 5/16/17 3:08 AM, std...@virgilio.it wrote:

Hi list,
this error occurs during selxavg3-sess in FS-FAST fcMRI

meanval --i stem2fname stem Looks for stem.fmt where fmt is mgh mgz 
nii nii.gz bhdr img w, then returns stem.fmt. See also stem2fmt, 
fname2stem The file needs to exist on disk. --m 
001/masks/brain.e3.nii.gz --o 001/global.meanval.dat --avgwf 
001/global.waveform.dat

ERROR: cannot find stem2fname

I have already run for this folder other seed. The error occurs only 
on it (amygdala).


Thanks

Stefano


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] selxavg3-sess error

[stdp82]

Hi list, this error occurs during selxavg3-sess in FS-FAST fcMRI
meanval --i stem2fname stem Looks for stem.fmt where fmt is mgh mgz nii nii.gz 
bhdr img w, then returns stem.fmt. See also stem2fmt, fname2stem The file needs 
to exist on disk. --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.dat 
--avgwf 001/global.waveform.datERROR: cannot find stem2fname
I have already run for this folder other seed. The error occurs only on it 
(amygdala).
Thanks
Stefano___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[Francesca Strappini]

Thank you, I'll try!

Best
Francesca

On Wednesday, June 15, 2016, Douglas N Greve 
wrote:

> Sorry for the delay. Do you have polar angle data? Unfortunately, FSFAST
> needs both. If you don't have polar, just copy the eccen data and call
> it polar. for what you want to do it won't make much difference.
>
> On 06/08/2016 09:55 AM, Francesca Strappini wrote:
> > I have only something similar in the temporal dynamics to the
> > eccentricity data. I attached the Xtmp.mat file.
> > Thank you!
> >
> > Francesca
> >
> > 2016-06-08 15:44 GMT+02:00 Douglas Greve  
> > >:
> >
> > Do you have both polar and eccen data? If so, can you send the
> > Xtmp.mat file?
> >
> >
> > On 6/8/16 6:08 AM, Francesca Strappini wrote:
> >> Hi Freesurfer experts,
> >>
> >> I'm re-posting this message because I think it got lost.
> >>
> >> I'm trying to analyze some phase-encoded data with the eccentricity
> >> protocol for retinotopic data and I'm having troubles with
> >> selxavg3-sess.
> >>
> >> I run the following commands:
> >>
> >> mkanalysis-sess -analysis OrderDisorder.idsubj.lh -surface idsubj
> >> lh -TR 2
> >> -retinotopy 24 -paradigm rtopy.par -fwhm 0 -per-run -nskip 5 -fsd
> >> bold
> >>
> >> selxavg3-sess -a OrderDisorder.idsubj.lh -s
> >> idsubj_OrderDisorder_continous
> >>
> >> and I got this error message:
> >>
> >> Found 122573/130829 (93.7) voxels in mask
> >> Creating Design Matrix
> >>  ... creation time =  0.019 sec
> >> DoMCFit = 1
> >> ntptot = 875, nX = 80, DOF = 795
> >> Saving X matrix to
> >>
>  
> /usr/local/freesurfer/fsfast/OrderDisorder_new/MK_OrderDisorder_continous/bold/OrderDisorder.MishaK.lh/Xtmp.mat
> >> Error using svd
> >> Input to SVD must not contain NaN or Inf.
> >>
> >> Error in cond (line 35)
> >> s = svd(A);
> >>
> >> Error in fast_selxavg3 (line 279)
> >>   XCond = cond(XtX);
> >>
> >> Thanks!
> >> Best
> >> Francesca
> >>
> >>
> >>
> >> --
> >> Francesca Strappini, Ph.D.
> >> Neurobiology Department
> >> Weizmann Institute of Science
> >> 234 Herzl Street, Rehovot 7610001 Israel
> >> Tel.: +972 58 444 2584 
> >> E-mail: francesca.strapp...@weizmann.ac.il 
> >> 
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu 
> >> 
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu   Freesurfer@nmr.mgh.harvard.edu >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in error and
> > the e-mail
> > contains patient information, please contact the Partners
> > Compliance HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to
> > you in error
> > but does not contain patient information, please contact the
> > sender and properly
> > dispose of the e-mail.
> >
> >
> >
> >
> > --
> > Francesca Strappini, Ph.D.
> > Neurobiology Department
> > Weizmann Institute of Science
> > 234 Herzl Street, Rehovot 7610001 Israel
> > Tel.: +972 58 444 2584
> > E-mail: francesca.strapp...@weizmann.ac.il 
> > 
> >
> >
> > ___
> > 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
> 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/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>


-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://ww

Re: [Freesurfer] selxavg3-sess error

[Douglas N Greve]

Sorry for the delay. Do you have polar angle data? Unfortunately, FSFAST 
needs both. If you don't have polar, just copy the eccen data and call 
it polar. for what you want to do it won't make much difference.

On 06/08/2016 09:55 AM, Francesca Strappini wrote:
> I have only something similar in the temporal dynamics to the 
> eccentricity data. I attached the Xtmp.mat file.
> Thank you!
>
> Francesca
>
> 2016-06-08 15:44 GMT+02:00 Douglas Greve  >:
>
> Do you have both polar and eccen data? If so, can you send the
> Xtmp.mat file?
>
>
> On 6/8/16 6:08 AM, Francesca Strappini wrote:
>> Hi Freesurfer experts,
>>
>> I'm re-posting this message because I think it got lost.
>>
>> I'm trying to analyze some phase-encoded data with the eccentricity
>> protocol for retinotopic data and I'm having troubles with
>> selxavg3-sess.
>>
>> I run the following commands:
>>
>> mkanalysis-sess -analysis OrderDisorder.idsubj.lh -surface idsubj
>> lh -TR 2
>> -retinotopy 24 -paradigm rtopy.par -fwhm 0 -per-run -nskip 5 -fsd
>> bold
>>
>> selxavg3-sess -a OrderDisorder.idsubj.lh -s
>> idsubj_OrderDisorder_continous
>>
>> and I got this error message:
>>
>> Found 122573/130829 (93.7) voxels in mask
>> Creating Design Matrix
>>  ... creation time =  0.019 sec
>> DoMCFit = 1
>> ntptot = 875, nX = 80, DOF = 795
>> Saving X matrix to
>> 
>> /usr/local/freesurfer/fsfast/OrderDisorder_new/MK_OrderDisorder_continous/bold/OrderDisorder.MishaK.lh/Xtmp.mat
>> Error using svd
>> Input to SVD must not contain NaN or Inf.
>>
>> Error in cond (line 35)
>> s = svd(A);
>>
>> Error in fast_selxavg3 (line 279)
>>   XCond = cond(XtX);
>>
>> Thanks!
>> Best
>> Francesca
>>
>>
>>
>> --
>> Francesca Strappini, Ph.D.
>> Neurobiology Department
>> Weizmann Institute of Science
>> 234 Herzl Street, Rehovot 7610001 Israel
>> Tel.: +972 58 444 2584 
>> E-mail: francesca.strapp...@weizmann.ac.il
>> 
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
> -- 
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strapp...@weizmann.ac.il 
> 
>
>
> ___
> 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
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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] selxavg3-sess error

[Francesca Strappini]

Hi Doug, it looks like my email with attached the Xtmp.mat file didn't
arrive.
How can I send it to you?

Thanks!
Francesca

2016-06-08 15:44 GMT+02:00 Douglas Greve :

> Do you have both polar and eccen data? If so, can you send the Xtmp.mat
> file?
>
>
> On 6/8/16 6:08 AM, Francesca Strappini wrote:
>
> Hi Freesurfer experts,
>
> I'm re-posting this message because I think it got lost.
>
> I'm trying to analyze some phase-encoded data with the eccentricity
> protocol for retinotopic data and I'm having troubles with selxavg3-sess.
>
> I run the following commands:
>
> mkanalysis-sess -analysis OrderDisorder.idsubj.lh -surface idsubj lh -TR 2
> -retinotopy 24 -paradigm rtopy.par -fwhm 0 -per-run -nskip 5 -fsd bold
>
> selxavg3-sess -a OrderDisorder.idsubj.lh -s idsubj_OrderDisorder_continous
>
> and I got this error message:
>
> Found 122573/130829 (93.7) voxels in mask
> Creating Design Matrix
>  ... creation time =  0.019 sec
> DoMCFit = 1
> ntptot = 875, nX = 80, DOF = 795
> Saving X matrix to
>
> /usr/local/freesurfer/fsfast/OrderDisorder_new/MK_OrderDisorder_continous/bold/OrderDisorder.MishaK.lh/Xtmp.mat
> Error using svd
> Input to SVD must not contain NaN or Inf.
>
> Error in cond (line 35)
> s = svd(A);
>
> Error in fast_selxavg3 (line 279)
>   XCond = cond(XtX);
>
> Thanks!
> Best
> Francesca
>
>
>
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strapp...@weizmann.ac.il
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[Douglas Greve]

Do you have both polar and eccen data? If so, can you send the Xtmp.mat 
file?


On 6/8/16 6:08 AM, Francesca Strappini wrote:

Hi Freesurfer experts,

I'm re-posting this message because I think it got lost.

I'm trying to analyze some phase-encoded data with the eccentricity
protocol for retinotopic data and I'm having troubles with selxavg3-sess.

I run the following commands:

mkanalysis-sess -analysis OrderDisorder.idsubj.lh -surface idsubj lh -TR 2
-retinotopy 24 -paradigm rtopy.par -fwhm 0 -per-run -nskip 5 -fsd bold

selxavg3-sess -a OrderDisorder.idsubj.lh -s idsubj_OrderDisorder_continous

and I got this error message:

Found 122573/130829 (93.7) voxels in mask
Creating Design Matrix
 ... creation time =  0.019 sec
DoMCFit = 1
ntptot = 875, nX = 80, DOF = 795
Saving X matrix to
/usr/local/freesurfer/fsfast/OrderDisorder_new/MK_OrderDisorder_continous/bold/OrderDisorder.MishaK.lh/Xtmp.mat
Error using svd
Input to SVD must not contain NaN or Inf.

Error in cond (line 35)
s = svd(A);

Error in fast_selxavg3 (line 279)
  XCond = cond(XtX);

Thanks!
Best
Francesca



--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il 




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] selxavg3-sess error

[Francesca Strappini]

Hi Freesurfer experts,

I'm re-posting this message because I think it got lost.

I'm trying to analyze some phase-encoded data with the eccentricity
protocol for retinotopic data and I'm having troubles with selxavg3-sess.

I run the following commands:

mkanalysis-sess -analysis OrderDisorder.idsubj.lh -surface idsubj lh -TR 2
-retinotopy 24 -paradigm rtopy.par -fwhm 0 -per-run -nskip 5 -fsd bold

selxavg3-sess -a OrderDisorder.idsubj.lh -s idsubj_OrderDisorder_continous

and I got this error message:

Found 122573/130829 (93.7) voxels in mask
Creating Design Matrix
 ... creation time =  0.019 sec
DoMCFit = 1
ntptot = 875, nX = 80, DOF = 795
Saving X matrix to
/usr/local/freesurfer/fsfast/OrderDisorder_new/MK_OrderDisorder_continous/bold/OrderDisorder.MishaK.lh/Xtmp.mat
Error using svd
Input to SVD must not contain NaN or Inf.

Error in cond (line 35)
s = svd(A);

Error in fast_selxavg3 (line 279)
  XCond = cond(XtX);

Thanks!
Best
Francesca



--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] selxavg3-sess error with phase-encoded data

[Francesca Strappini]

Hi Freesurfer experts,

I'm trying to analyze some phase-encoded data with the eccentricity
protocol for retinotopic data and I'm having troubles with selxavg3-sess.

I run the following commands:

mkanalysis-sess -analysis OrderDisorder.idsubj.lh -surface idsubj lh -TR 2
-retinotopy 24 -paradigm rtopy.par -fwhm 0 -per-run -nskip 5 -fsd bold

selxavg3-sess -a OrderDisorder.idsubj.lh -s idsubj_OrderDisorder_continous

and I got this error message:

Found 122573/130829 (93.7) voxels in mask
Creating Design Matrix
 ... creation time =  0.019 sec
DoMCFit = 1
ntptot = 875, nX = 80, DOF = 795
Saving X matrix to
/usr/local/freesurfer/fsfast/OrderDisorder_new/MK_OrderDisorder_continous/bold/OrderDisorder.MishaK.lh/Xtmp.mat
Error using svd
Input to SVD must not contain NaN or Inf.

Error in cond (line 35)
s = svd(A);

Error in fast_selxavg3 (line 279)
  XCond = cond(XtX);

I attached the Xtmp.mat file from the output folder in case is needed.

Thank you!
Best
Francesca

-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il


Xtmp.mat
Description: Binary data
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess ERROR

[Christina Pressl]

I see, here is a copy of my paradigm

0. 2
11.100 0
21.100 3
32.200 0
42.200 2
53.300 0
63.300 2
74.400 0
84.400  1
95.500  0
105.500 1
116.600 0
126.600 3
137.700 0
147.700 3
158.800 0
168.800 1
179.900 0

I don’t see how this setup reflects one of the two potential errors you 
outlined.

.par files are located separately in each run directory which are located in 
the bold directory.


thank you.

On Dec 9, 2015, at 2:22 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

That means that your design matrix is ill-conditioned.

This error means one of two things is wrong with your .par file (located
in each run of each subject’s bold directory): 1) there are not two or
more occurrences of one of your conditions; or 2) there is a pattern to
your conditions (for example condition 3 always follows condition 4).
You can avoid this error message for the sake of analysis by 1)
replacing other conditions with occurrences of your missing condition,
so that each condition is represented at least twice; or 2) by changing
your conditions so that they break the pattern at least twice. Even
though the effect of this change is quite small, you should distribute
the added conditions evenly across the other conditions. Ideally,
however, you would alter your stimuli so that you do not get this error
in the first place.


On 12/09/2015 02:19 PM, Christina Pressl wrote:
hi doug,

thank you so much for your quick reply.
yes - I saw this error after I sent you the error log.
I checked the paradigm file, corrected it and rerun everything.

now this error is gone but I still get the following:

   Error using svd
   Input to SVD must not contain NaN or Inf.
   Error in cond (line 36)
s = svd(A);

   Error in fast_selxavg3 (line254)
XCond  = cond(XtX);

- - - - - — - - — - - — - — -

   EROOR: fast_selxavg3() failed\n



Your help is much appreciated



On Dec 9, 2015, at 1:57 PM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu> 
> wrote:


Did you see the error description:

ERROR:
/space/mdeh5/1/halgdev/projects/christina/FSFAST/Project/NC211_fmri_060515/Sess01/bold/004/oddeven.par
is not correctly formatted. Line 19 only has 0 items

did you check this file?


On 12/09/2015 12:38 PM, Christina Pressl wrote:
Dear Freesurfer Experts,

I am having trouble with selxavg3-sess and was wondering if you could
maybe help me resolving the issue (error log attached)


I ran

#preproc-sess –s Sess01 –surface fsaverage lhrh –mni305 –fwhm 5 –per-run

and the following commands for lh, rh and mni305

#mkanalysis-sess –fsd bold –stc up -surface fsaverage lh -fwhm 5
-event-related  -paradigm oddeven.par -nconditions 3  -spmhrf 0 -TR 2
-refeventdur 10.750 -nskip 4 –mcextreg -polyfit 2  -analysis
oddeven.sm5.lh

#mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-object –a
1 –c 2 –c 3

#mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-fix  –a
1 –c 0



Thank you very much.

Christina






___
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
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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu 

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.



___
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
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: 
surfer.nmr.mgh.harvard.edu/fswiki/BugReporti

Re: [Freesurfer] selxavg3-sess ERROR

[Douglas N Greve]

That means that your design matrix is ill-conditioned.

This error means one of two things is wrong with your .par file (located 
in each run of each subject’s bold directory): 1) there are not two or 
more occurrences of one of your conditions; or 2) there is a pattern to 
your conditions (for example condition 3 always follows condition 4). 
You can avoid this error message for the sake of analysis by 1) 
replacing other conditions with occurrences of your missing condition, 
so that each condition is represented at least twice; or 2) by changing 
your conditions so that they break the pattern at least twice. Even 
though the effect of this change is quite small, you should distribute 
the added conditions evenly across the other conditions. Ideally, 
however, you would alter your stimuli so that you do not get this error 
in the first place.


On 12/09/2015 02:19 PM, Christina Pressl wrote:
> hi doug,
>
> thank you so much for your quick reply.
> yes - I saw this error after I sent you the error log.
> I checked the paradigm file, corrected it and rerun everything.
>
> now this error is gone but I still get the following:
>
> Error using svd
> Input to SVD must not contain NaN or Inf.
> Error in cond (line 36)
>  s = svd(A);
>
> Error in fast_selxavg3 (line254)
>  XCond  = cond(XtX);
>
> >> - - - - - — - - — - - — - — -
>
> EROOR: fast_selxavg3() failed\n
>
>
>
> Your help is much appreciated
>
>
>
>> On Dec 9, 2015, at 1:57 PM, Douglas N Greve 
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>>
>> Did you see the error description:
>>
>> ERROR:
>> /space/mdeh5/1/halgdev/projects/christina/FSFAST/Project/NC211_fmri_060515/Sess01/bold/004/oddeven.par
>> is not correctly formatted. Line 19 only has 0 items
>>
>> did you check this file?
>>
>>
>> On 12/09/2015 12:38 PM, Christina Pressl wrote:
>>> Dear Freesurfer Experts,
>>>
>>> I am having trouble with selxavg3-sess and was wondering if you could
>>> maybe help me resolving the issue (error log attached)
>>>
>>>
>>> I ran
>>>
>>> #preproc-sess –s Sess01 –surface fsaverage lhrh –mni305 –fwhm 5 –per-run
>>>
>>> and the following commands for lh, rh and mni305
>>>
>>> #mkanalysis-sess –fsd bold –stc up -surface fsaverage lh -fwhm 5
>>> -event-related  -paradigm oddeven.par -nconditions 3  -spmhrf 0 -TR 2
>>> -refeventdur 10.750 -nskip 4 –mcextreg -polyfit 2  -analysis
>>> oddeven.sm5.lh
>>>
>>> #mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-object –a
>>> 1 –c 2 –c 3
>>>
>>> #mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-fix  –a 
>>> 1 –c 0
>>>
>>>
>>>
>>> Thank you very much.
>>>
>>> Christina
>>>
>>>
>>>
>>>
>>>
>>>
>>> ___
>>> 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
>> 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/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to 
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and 
>> the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to 
>> you in error
>> but does not contain patient information, please contact the sender 
>> and properly
>> dispose of the e-mail.
>
>
>
> ___
> 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
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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] selxavg3-sess ERROR

[Christina Pressl]

hi doug,

thank you so much for your quick reply.

yes - I saw this error after I sent you the error log.
I checked the paradigm file, corrected it and rerun everything.

now this error is gone but I still get the following:

Error using svd
Input to SVD must not contain NaN or Inf.

Error in cond (line 36)
 s = svd(A);

Error in fast_selxavg3 (line254)
 XCond  = cond(XtX);

>> - - - - - — - - — - - — - — -

EROOR: fast_selxavg3() failed\n


Your help is much appreciated



On Dec 9, 2015, at 1:57 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


Did you see the error description:

ERROR:
/space/mdeh5/1/halgdev/projects/christina/FSFAST/Project/NC211_fmri_060515/Sess01/bold/004/oddeven.par
is not correctly formatted. Line 19 only has 0 items

did you check this file?


On 12/09/2015 12:38 PM, Christina Pressl wrote:
Dear Freesurfer Experts,

I am having trouble with selxavg3-sess and was wondering if you could
maybe help me resolving the issue (error log attached)


I ran

#preproc-sess –s Sess01 –surface fsaverage lhrh –mni305 –fwhm 5 –per-run

and the following commands for lh, rh and mni305

#mkanalysis-sess –fsd bold –stc up -surface fsaverage lh -fwhm 5
-event-related  -paradigm oddeven.par -nconditions 3  -spmhrf 0 -TR 2
-refeventdur 10.750 -nskip 4 –mcextreg -polyfit 2  -analysis
oddeven.sm5.lh

#mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-object –a
1 –c 2 –c 3

#mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-fix  –a 1 –c 0



Thank you very much.

Christina






___
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
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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess ERROR

[Douglas N Greve]

Did you see the error description:

ERROR: 
/space/mdeh5/1/halgdev/projects/christina/FSFAST/Project/NC211_fmri_060515/Sess01/bold/004/oddeven.par
 
is not correctly formatted. Line 19 only has 0 items

did you check this file?


On 12/09/2015 12:38 PM, Christina Pressl wrote:
> Dear Freesurfer Experts,
>
> I am having trouble with selxavg3-sess and was wondering if you could 
> maybe help me resolving the issue (error log attached)
>
>
> I ran
>
> #preproc-sess –s Sess01 –surface fsaverage lhrh –mni305 –fwhm 5 –per-run
>
> and the following commands for lh, rh and mni305
>
> #mkanalysis-sess –fsd bold –stc up -surface fsaverage lh -fwhm 5 
> -event-related  -paradigm oddeven.par -nconditions 3  -spmhrf 0 -TR 2 
> -refeventdur 10.750 -nskip 4 –mcextreg -polyfit 2  -analysis 
> oddeven.sm5.lh
>
> #mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-object –a 
> 1 –c 2 –c 3
>
> #mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-fix  –a 1 –c 0
>
>
>
> Thank you very much.
>
> Christina
>
>
>
>
>
>
> ___
> 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
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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] selxavg3-sess ERROR

[Christina Pressl]

Dear Freesurfer Experts,

I am having trouble with selxavg3-sess and was wondering if you could maybe 
help me resolving the issue (error log attached)


I ran

#preproc-sess –s Sess01 –surface fsaverage lhrh –mni305 –fwhm 5 –per-run

and the following commands for lh, rh and mni305

#mkanalysis-sess –fsd bold –stc up -surface fsaverage lh -fwhm 5 -event-related 
 -paradigm oddeven.par -nconditions 3   -spmhrf 0 -TR 2 -refeventdur 10.750 
-nskip 4 –mcextreg -polyfit 2  -analysis oddeven.sm5.lh

#mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-object –a 1 –c 2 –c 
3

#mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-fix  –a 1 –c 0



Thank you very much.

Christina





doug.log
Description: doug.log
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error empty conditions in paradigm file

[Douglas Greve]

On 11/19/15 9:53 AM, Danielle Miller wrote:
> Hi Doug,
>
> Thanks for your response. So you are saying to rename a correctly 
> identified condition as the empty condition? That is if I have a 
> correct trial, rename it to an incorrect trial? Won't this pull onset 
> times from the wrong conditions?
This is what I'm suggesting. Not sure what you mean by onset times from 
wrong condition.
>
> When you say it should have little effects on the final results, are 
> you only thinking about this in terms of one or two subjects? What if 
> there are more subjects in this situation?
If you have many corrects, then it will not affect the estimation of the 
HRF for the  "correct" condition regardless of the number of subjects. 
If you plan to study the incorrects or some contrast that includes the 
incorrects, then  you won't be able to use these subjects anyway.

doug

ps. please remember to post to the FS list and not to us personally. thanks!
>
> Thanks,
> Danielle
>
> -- 
> Ph.D. Program in Behavioral Neuroscience
> Boston University School of Medicine L-815
> 72 E. Concord St
> Boston, MA 02118
>
>
> VA Boston Healthcare System Jamaica Plain
> Memory Disorders Research Center
> 150 South Huntington Ave  D11-103
> Boston, MA 02130
> OFFICE:(857) 364-2130
>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error empty conditions in paradigm file

[Douglas N Greve]

There is not a way to model empty conditions. The easiest thing to do is 
to just change another condition to say it is the missing condition. It 
should have little effect on the final results.

On 11/18/2015 02:06 PM, Danielle Miller wrote:
> Hello Freesurfer Experts,
>
> I am reposting this as this has not come up on the mail archive thread.
> I keep running into the following error (see below) when selxavg3-sess gets
> to my third subject. I am assuming this is because this subject does not
> have all of the conditions modeled (that is, this particular subject does
> not have any incorrect responses). Is there a way to model an empty
> condition to get around this? I want a general contrast of Incorrect >
> Correct, but some subjects do not make any errors and therefore would not
> have this condition in their paradigm files.
> Any advice would be greatly appreciated.
>
>
> #@# CC_003_recon ###
> /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon
> -
> $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $
> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m
> /Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> /Applications/freesurfer-5.3/matlab/MRIread.m
> -
> outtop = /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST
> Extension format = nii.gz
> INFO: key PerSession unrecognized, line 6, skipping
> INFO: key ApplySubCortMask unrecognized, line 12, skipping
>   1 Correct-v-Incorrect.mat
>   2 Incorrect-v-base.mat
> nruns = 4
> autostimdur =
>
>
> outanadir =
> /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon/Bold1/correct.sm15.mni305
> Found 57600/537168 (10.7) voxels in mask
> Creating Design Matrix
>   ... creation time =  0.008 sec
> DoMCFit = 1
> ntptot = 740, nX = 27, DOF = 713
> Saving X matrix to
> /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon/Bold1/correct.sm15.mni305/Xtmp.mat
> ??? Error using ==> svd
> Input to SVD must not contain NaN or Inf.
>
> Error in ==> cond at 39
> s = svd(A);
>
> Error in ==> fast_selxavg3 at 254
>XCond = cond(XtX);
>
> >> --
> ERROR: fast_selxavg3() failed\n
>
> Thanks,
> Danielle
>
> -- 
> Ph.D. Program in Behavioral Neuroscience
> Boston University School of Medicine L-815
> 72 E. Concord St
> Boston, MA 02118
>
>
> VA Boston Healthcare System Jamaica Plain
> Memory Disorders Research Center
> 150 South Huntington Ave  D11-103
> Boston, MA 02130
> OFFICE:(857) 364-2130
>
>
>
> ___
> 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
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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] selxavg3-sess error empty conditions in paradigm file

[Danielle Miller]

Hello Freesurfer Experts,

I am reposting this as this has not come up on the mail archive thread.

I keep running into the following error (see below) when selxavg3-sess gets
to my third subject. I am assuming this is because this subject does not
have all of the conditions modeled (that is, this particular subject does
not have any incorrect responses). Is there a way to model an empty
condition to get around this? I want a general contrast of Incorrect >
Correct, but some subjects do not make any errors and therefore would not
have this condition in their paradigm files.

Any advice would be greatly appreciated.


#@# CC_003_recon ###
/Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon
-
$Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $
/Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m
/Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m
/Applications/freesurfer-5.3/matlab/MRIread.m
-
outtop = /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST
Extension format = nii.gz
INFO: key PerSession unrecognized, line 6, skipping
INFO: key ApplySubCortMask unrecognized, line 12, skipping
 1 Correct-v-Incorrect.mat
 2 Incorrect-v-base.mat
nruns = 4
autostimdur =


outanadir =
/Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon/Bold1/correct.sm15.mni305
Found 57600/537168 (10.7) voxels in mask
Creating Design Matrix
 ... creation time =  0.008 sec
DoMCFit = 1
ntptot = 740, nX = 27, DOF = 713
Saving X matrix to
/Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon/Bold1/correct.sm15.mni305/Xtmp.mat
??? Error using ==> svd
Input to SVD must not contain NaN or Inf.

Error in ==> cond at 39
   s = svd(A);

Error in ==> fast_selxavg3 at 254
  XCond = cond(XtX);

>> --
ERROR: fast_selxavg3() failed\n

Thanks,
Danielle


-- 
Ph.D. Program in Behavioral Neuroscience
Boston University School of Medicine L-815
72 E. Concord St
Boston, MA 02118


VA Boston Healthcare System Jamaica Plain
Memory Disorders Research Center
150 South Huntington Ave  D11-103
Boston, MA 02130
OFFICE:(857) 364-2130
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] selxavg3-sess error

[Danielle Miller]

Hello Freesurfer Experts,

I keep running into the following error (see below) when selxavg3-sess gets
to my third subject. I am assuming this is because this subject does not
have all of the conditions modeled (that is, this particular subject does
not have any incorrect responses). Is there a way to model an empty
condition to get around this? I want a general contrast of Incorrect >
Correct, but some subjects do not make any errors and therefore would not
have this condition in their paradigm files.

Any advice would be greatly appreciated.


#@# CC_003_recon ###
/Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon
-
$Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $
/Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m
/Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m
/Applications/freesurfer-5.3/matlab/MRIread.m
-
outtop = /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST
Extension format = nii.gz
INFO: key PerSession unrecognized, line 6, skipping
INFO: key ApplySubCortMask unrecognized, line 12, skipping
 1 Correct-v-Incorrect.mat
 2 Incorrect-v-base.mat
nruns = 4
autostimdur =


outanadir =
/Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon/Bold1/correct.sm15.mni305
Found 57600/537168 (10.7) voxels in mask
Creating Design Matrix
 ... creation time =  0.008 sec
DoMCFit = 1
ntptot = 740, nX = 27, DOF = 713
Saving X matrix to
/Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon/Bold1/correct.sm15.mni305/Xtmp.mat
??? Error using ==> svd
Input to SVD must not contain NaN or Inf.

Error in ==> cond at 39
   s = svd(A);

Error in ==> fast_selxavg3 at 254
  XCond = cond(XtX);

>> --
ERROR: fast_selxavg3() failed\n

Thanks,
Danielle

-- 
Ph.D. Program in Behavioral Neuroscience
Boston University School of Medicine L-815
72 E. Concord St
Boston, MA 02118


VA Boston Healthcare System Jamaica Plain
Memory Disorders Research Center
150 South Huntington Ave  D11-103
Boston, MA 02130
OFFICE:(857) 364-2130
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[Rodriguez-Thompson, Anais]

Hi Doug, 

Sorry I wasn't clear. That was a separate issue. I was using a different 
analysis (SIRP_LoadRegression_Stable5_050514) that uses an old per-session file 
that was generated in 5.0 (fmc.sm5.nii). For the current analysis 
(SIRP_LoadRegression_Stable5_072915), I want to run the analysis per-run. 
Running preproc I get an fmcpr.nii.gz file, but I don't get the 
fmcpr.sm5.nii.gz file, which the analysis looks for. 

Best,
Anais

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, August 21, 2015 1:46 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess error

I thought this problem was fixed when you eliminated the multiple
formats (?)

On 8/20/15 12:03 PM, Rodriguez-Thompson, Anais wrote:
> Hi Doug,
>
> I sent a message a while back about a problem I was having running selxavg3 
> (I've attached the thread below this email). Selxavg3 is looking for a file 
> that was not generated during preprocessing (fmcpr.sm5.nii.gz).
>
> The commands I was using were
> preproc-sess -s (subject) -d $SUBJECTS_DIR -fsd bold -fwhm 5 -per-run
> mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_072915 -TR 2 -paradigm 
> slopepar -event-related -fsd bold -runlistfile runlistfile -tpef 
> tpef_1.5mm.txt -native -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 
> 1.25 -refeventdur 2 -fwhm 5 -per-run
>
> I sent you a couple of logs, but did not hear back about how I can generate 
> the fmcpr.sm5.nii file. In the meantime I haven't been able to run any first 
> level analyses on my subjects. Is there any update to this issue?
>
> Any insight into the problem would be greatly appreciated!
>
> Thanks,
> Anais
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rodriguez-Thompson, 
> Anais [arodriguez-thomp...@mgh.harvard.edu]
> Sent: Thursday, July 30, 2015 6:34 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] selxavg3-sess error
>
> Hi Doug,
>
> Attached is doug2.log.
>
> Thanks,
> Anais
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, July 30, 2015 4:29 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] selxavg3-sess error
>
> ok, still not sure what is happening. Can you try
>
> preproc-sess -debug -s GDDA001 -d
> /autofs/cluster/roffman/users/Stable5_PerRun -a
> SIRP_LoadRegression_Stable5_072915 |& tee doug2.log
>
> and send me doug2.log
>
>
> On 07/30/2015 12:54 PM, Rodriguez-Thompson, Anais wrote:
>> Hi Doug,
>>
>> Below are the contents of doug.log:
>>
>> set echo = 1 ;
>> breaksw
>> breaksw
>>
>> end
>> end
>> while ( $#argv != 0 )
>> while ( 0 != 0 )
>> goto parse_args_return ;
>> goto parse_args_return
>>
>> foreach grp ( $grpdefs )
>> foreach grp ( )
>>
>> goto check_params ;
>> goto check_params
>>
>> if ( $#SessList == 0 ) then
>> if ( 1 == 0 ) then
>>
>> if ( $#SearchPathList == 0 ) then
>> if ( 0 == 0 ) then
>> set SearchPathList = "." ;
>> set SearchPathList = .
>> endif
>> endif
>>
>> goto check_params_return ;
>> goto check_params_return
>>
>>
>> set UniqueList = ( ) ;
>> set UniqueList = ( )
>> foreach d ( $SearchPathList )
>> foreach d ( . )
>> if ( ! -e $d ) then
>> if ( ! -e . ) then
>>
>> set IsUnique = 1 ;
>> set IsUnique = 1
>> foreach u ( $UniqueList )
>> foreach u ( )
>> if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;
>> if ( 1 ) set UniqueList = ( . )
>> set UniqueList = ( . )
>> end
>> end
>>
>> set SearchPathList = ( $UniqueList ) ;
>> set SearchPathList = ( . )
>>
>> set errs = 0 ;
>> set errs = 0
>>
>>
>> set SessPath = ( ) ;
>> set SessPath = ( )
>> foreach sess ( $SessList )
>> foreach sess ( GDDA001 )
>> set tmp = ( ) ;
>> set tmp = ( )
>> foreach d ( $SearchPathList )
>> foreach d ( . )
>> set stst = $d/$sess
>> set stst = ./GDDA001
>> if ( -d $stst ) then
>> if ( -d ./GDDA001 ) then
>> if ( ! -r $stst ) then
>> if ( ! -r ./GDDA001 ) then
>> pushd $stst > /dev/null ;
>> pushd ./GDDA001
>> set tmp = ( $tmp `$PWDCMD` ) ;
>> set tmp = ( `$PWDCMD` )
>> pwd
>> popd > /dev/null ;
>> popd
&g

Re: [Freesurfer] selxavg3-sess error

[Douglas Greve]

I thought this problem was fixed when you eliminated the multiple 
formats (?)

On 8/20/15 12:03 PM, Rodriguez-Thompson, Anais wrote:
> Hi Doug,
>
> I sent a message a while back about a problem I was having running selxavg3 
> (I've attached the thread below this email). Selxavg3 is looking for a file 
> that was not generated during preprocessing (fmcpr.sm5.nii.gz).
>
> The commands I was using were
> preproc-sess -s (subject) -d $SUBJECTS_DIR -fsd bold -fwhm 5 -per-run
> mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_072915 -TR 2 -paradigm 
> slopepar -event-related -fsd bold -runlistfile runlistfile -tpef 
> tpef_1.5mm.txt -native -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 
> 1.25 -refeventdur 2 -fwhm 5 -per-run
>
> I sent you a couple of logs, but did not hear back about how I can generate 
> the fmcpr.sm5.nii file. In the meantime I haven't been able to run any first 
> level analyses on my subjects. Is there any update to this issue?
>
> Any insight into the problem would be greatly appreciated!
>
> Thanks,
> Anais
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rodriguez-Thompson, 
> Anais [arodriguez-thomp...@mgh.harvard.edu]
> Sent: Thursday, July 30, 2015 6:34 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] selxavg3-sess error
>
> Hi Doug,
>
> Attached is doug2.log.
>
> Thanks,
> Anais
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, July 30, 2015 4:29 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] selxavg3-sess error
>
> ok, still not sure what is happening. Can you try
>
> preproc-sess -debug -s GDDA001 -d
> /autofs/cluster/roffman/users/Stable5_PerRun -a
> SIRP_LoadRegression_Stable5_072915 |& tee doug2.log
>
> and send me doug2.log
>
>
> On 07/30/2015 12:54 PM, Rodriguez-Thompson, Anais wrote:
>> Hi Doug,
>>
>> Below are the contents of doug.log:
>>
>> set echo = 1 ;
>> breaksw
>> breaksw
>>
>> end
>> end
>> while ( $#argv != 0 )
>> while ( 0 != 0 )
>> goto parse_args_return ;
>> goto parse_args_return
>>
>> foreach grp ( $grpdefs )
>> foreach grp ( )
>>
>> goto check_params ;
>> goto check_params
>>
>> if ( $#SessList == 0 ) then
>> if ( 1 == 0 ) then
>>
>> if ( $#SearchPathList == 0 ) then
>> if ( 0 == 0 ) then
>> set SearchPathList = "." ;
>> set SearchPathList = .
>> endif
>> endif
>>
>> goto check_params_return ;
>> goto check_params_return
>>
>>
>> set UniqueList = ( ) ;
>> set UniqueList = ( )
>> foreach d ( $SearchPathList )
>> foreach d ( . )
>> if ( ! -e $d ) then
>> if ( ! -e . ) then
>>
>> set IsUnique = 1 ;
>> set IsUnique = 1
>> foreach u ( $UniqueList )
>> foreach u ( )
>> if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;
>> if ( 1 ) set UniqueList = ( . )
>> set UniqueList = ( . )
>> end
>> end
>>
>> set SearchPathList = ( $UniqueList ) ;
>> set SearchPathList = ( . )
>>
>> set errs = 0 ;
>> set errs = 0
>>
>>
>> set SessPath = ( ) ;
>> set SessPath = ( )
>> foreach sess ( $SessList )
>> foreach sess ( GDDA001 )
>> set tmp = ( ) ;
>> set tmp = ( )
>> foreach d ( $SearchPathList )
>> foreach d ( . )
>> set stst = $d/$sess
>> set stst = ./GDDA001
>> if ( -d $stst ) then
>> if ( -d ./GDDA001 ) then
>> if ( ! -r $stst ) then
>> if ( ! -r ./GDDA001 ) then
>> pushd $stst > /dev/null ;
>> pushd ./GDDA001
>> set tmp = ( $tmp `$PWDCMD` ) ;
>> set tmp = ( `$PWDCMD` )
>> pwd
>> popd > /dev/null ;
>> popd
>> endif
>> endif
>> end
>> end
>> set nfound = ( $#tmp ) ;
>> set nfound = ( 1 )
>> if ( $nfound == 0 ) then
>> if ( 1 == 0 ) then
>> if ( $nfound > 1 ) then
>> if ( 1 > 1 ) then
>> set SessPath = ( $SessPath $tmp ) ;
>> set SessPath = ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 )
>> end
>> end
>>
>>
>> set UniqueList = ( ) ;
>> set UniqueList = ( )
>> foreach s ( $SessPath )
>> foreach s ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 )
>> set IsUnique = 1 ;
>> set IsUnique = 1
>> foreach u ( $UniqueList )
>> foreach u ( )
>> if ( ! $IsUnique && ! $AllowRedundant

[Freesurfer] selxavg3-sess error

[Rodriguez-Thompson, Anais]

Hi Doug,

I sent a message a while back about a problem I was having running selxavg3 
(I've attached the thread below this email). Selxavg3 is looking for a file 
that was not generated during preprocessing (fmcpr.sm5.nii.gz). 

The commands I was using were
preproc-sess -s (subject) -d $SUBJECTS_DIR -fsd bold -fwhm 5 -per-run
mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_072915 -TR 2 -paradigm 
slopepar -event-related -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt 
-native -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 
-fwhm 5 -per-run

I sent you a couple of logs, but did not hear back about how I can generate the 
fmcpr.sm5.nii file. In the meantime I haven't been able to run any first level 
analyses on my subjects. Is there any update to this issue?

Any insight into the problem would be greatly appreciated!

Thanks,
Anais


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rodriguez-Thompson, Anais 
[arodriguez-thomp...@mgh.harvard.edu]
Sent: Thursday, July 30, 2015 6:34 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] selxavg3-sess error

Hi Doug,

Attached is doug2.log.

Thanks,
Anais

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, July 30, 2015 4:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess error

ok, still not sure what is happening. Can you try

preproc-sess -debug -s GDDA001 -d
/autofs/cluster/roffman/users/Stable5_PerRun -a
SIRP_LoadRegression_Stable5_072915 |& tee doug2.log

and send me doug2.log


On 07/30/2015 12:54 PM, Rodriguez-Thompson, Anais wrote:
> Hi Doug,
>
> Below are the contents of doug.log:
>
> set echo = 1 ;
> breaksw
> breaksw
>
> end
> end
> while ( $#argv != 0 )
> while ( 0 != 0 )
> goto parse_args_return ;
> goto parse_args_return
>
> foreach grp ( $grpdefs )
> foreach grp ( )
>
> goto check_params ;
> goto check_params
>
> if ( $#SessList == 0 ) then
> if ( 1 == 0 ) then
>
> if ( $#SearchPathList == 0 ) then
> if ( 0 == 0 ) then
> set SearchPathList = "." ;
> set SearchPathList = .
> endif
> endif
>
> goto check_params_return ;
> goto check_params_return
>
>
> set UniqueList = ( ) ;
> set UniqueList = ( )
> foreach d ( $SearchPathList )
> foreach d ( . )
> if ( ! -e $d ) then
> if ( ! -e . ) then
>
> set IsUnique = 1 ;
> set IsUnique = 1
> foreach u ( $UniqueList )
> foreach u ( )
> if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;
> if ( 1 ) set UniqueList = ( . )
> set UniqueList = ( . )
> end
> end
>
> set SearchPathList = ( $UniqueList ) ;
> set SearchPathList = ( . )
>
> set errs = 0 ;
> set errs = 0
>
>
> set SessPath = ( ) ;
> set SessPath = ( )
> foreach sess ( $SessList )
> foreach sess ( GDDA001 )
> set tmp = ( ) ;
> set tmp = ( )
> foreach d ( $SearchPathList )
> foreach d ( . )
> set stst = $d/$sess
> set stst = ./GDDA001
> if ( -d $stst ) then
> if ( -d ./GDDA001 ) then
> if ( ! -r $stst ) then
> if ( ! -r ./GDDA001 ) then
> pushd $stst > /dev/null ;
> pushd ./GDDA001
> set tmp = ( $tmp `$PWDCMD` ) ;
> set tmp = ( `$PWDCMD` )
> pwd
> popd > /dev/null ;
> popd
> endif
> endif
> end
> end
> set nfound = ( $#tmp ) ;
> set nfound = ( 1 )
> if ( $nfound == 0 ) then
> if ( 1 == 0 ) then
> if ( $nfound > 1 ) then
> if ( 1 > 1 ) then
> set SessPath = ( $SessPath $tmp ) ;
> set SessPath = ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 )
> end
> end
>
>
> set UniqueList = ( ) ;
> set UniqueList = ( )
> foreach s ( $SessPath )
> foreach s ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 )
> set IsUnique = 1 ;
> set IsUnique = 1
> foreach u ( $UniqueList )
> foreach u ( )
> if ( ! $IsUnique && ! $AllowRedundant ) then
> if ( ! 1 && ! 0 ) then
>
> set UniqueList = ( $UniqueList $s ) ;
> set UniqueList = ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 )
> endif
> endif
> end
> end
>
>
> echo $SessPath
> echo /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001
>
> exit $errs ;
> exit 0
> set echo = 1 ;
> breaksw
> breaksw
>
> end
> end
> while ( $#argv != 0 )
> while ( 0 != 0 )
>
> goto parse_args_return ;
> goto parse_args_return
>
> goto check_params ;
> goto check_params
>
> if ( $#SessList == 0 ) then
> if ( 1 == 0 ) then
> if ( $#analysis == 0 && $flacfile == 0 ) then
> if ( 1 == 0 && == 0 ) then
> if ( $#analysis != 0 ) then
> if ( 1 != 0 ) then
> if ( ! -d $analys

[Freesurfer] selxavg3-sess error

[Rodriguez-Thompson, Anais]

Sorry, disregard my previous email! I just realized that I should have created 
a new message thread. 

Below is the previous email thread. Given this issue, could I rename the 
preproc-sess output volume (fmcpr.nii.gz) to fmcpr.sm5.nii.gz in order to run 
the command? Given preproc-sess at -fwhm 5, this volume should be smoothed at 5 
and should be the input for analysis, correct?

Thanks,
Anais

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, July 30, 2015 4:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess error

ok, still not sure what is happening. Can you try

preproc-sess -debug -s GDDA001 -d
/autofs/cluster/roffman/users/Stable5_PerRun -a
SIRP_LoadRegression_Stable5_072915 |& tee doug2.log

and send me doug2.log


On 07/30/2015 12:54 PM, Rodriguez-Thompson, Anais wrote:
> Hi Doug,
>
> Below are the contents of doug.log:
>
> set echo = 1 ;
> breaksw
> breaksw
>
> end
> end
> while ( $#argv != 0 )
> while ( 0 != 0 )
> goto parse_args_return ;
> goto parse_args_return
>
> foreach grp ( $grpdefs )
> foreach grp ( )
>
> goto check_params ;
> goto check_params
>
> if ( $#SessList == 0 ) then
> if ( 1 == 0 ) then
>
> if ( $#SearchPathList == 0 ) then
> if ( 0 == 0 ) then
> set SearchPathList = "." ;
> set SearchPathList = .
> endif
> endif
>
> goto check_params_return ;
> goto check_params_return
>
>
> set UniqueList = ( ) ;
> set UniqueList = ( )
> foreach d ( $SearchPathList )
> foreach d ( . )
> if ( ! -e $d ) then
> if ( ! -e . ) then
>
> set IsUnique = 1 ;
> set IsUnique = 1
> foreach u ( $UniqueList )
> foreach u ( )
> if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;
> if ( 1 ) set UniqueList = ( . )
> set UniqueList = ( . )
> end
> end
>
> set SearchPathList = ( $UniqueList ) ;
> set SearchPathList = ( . )
>
> set errs = 0 ;
> set errs = 0
>
>
> set SessPath = ( ) ;
> set SessPath = ( )
> foreach sess ( $SessList )
> foreach sess ( GDDA001 )
> set tmp = ( ) ;
> set tmp = ( )
> foreach d ( $SearchPathList )
> foreach d ( . )
> set stst = $d/$sess
> set stst = ./GDDA001
> if ( -d $stst ) then
> if ( -d ./GDDA001 ) then
> if ( ! -r $stst ) then
> if ( ! -r ./GDDA001 ) then
> pushd $stst > /dev/null ;
> pushd ./GDDA001
> set tmp = ( $tmp `$PWDCMD` ) ;
> set tmp = ( `$PWDCMD` )
> pwd
> popd > /dev/null ;
> popd
> endif
> endif
> end
> end
> set nfound = ( $#tmp ) ;
> set nfound = ( 1 )
> if ( $nfound == 0 ) then
> if ( 1 == 0 ) then
> if ( $nfound > 1 ) then
> if ( 1 > 1 ) then
> set SessPath = ( $SessPath $tmp ) ;
> set SessPath = ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 )
> end
> end
>
>
> set UniqueList = ( ) ;
> set UniqueList = ( )
> foreach s ( $SessPath )
> foreach s ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 )
> set IsUnique = 1 ;
> set IsUnique = 1
> foreach u ( $UniqueList )
> foreach u ( )
> if ( ! $IsUnique && ! $AllowRedundant ) then
> if ( ! 1 && ! 0 ) then
>
> set UniqueList = ( $UniqueList $s ) ;
> set UniqueList = ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 )
> endif
> endif
> end
> end
>
>
> echo $SessPath
> echo /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001
>
> exit $errs ;
> exit 0
> set echo = 1 ;
> breaksw
> breaksw
>
> end
> end
> while ( $#argv != 0 )
> while ( 0 != 0 )
>
> goto parse_args_return ;
> goto parse_args_return
>
> goto check_params ;
> goto check_params
>
> if ( $#SessList == 0 ) then
> if ( 1 == 0 ) then
> if ( $#analysis == 0 && $flacfile == 0 ) then
> if ( 1 == 0 && == 0 ) then
> if ( $#analysis != 0 ) then
> if ( 1 != 0 ) then
> if ( ! -d $analysis ) then
> if ( ! -d SIRP_LoadRegression_Stable5_072915 ) then
> if ( ! -e $analysis/analysis.info ) then
> if ( ! -e SIRP_LoadRegression_Stable5_072915/analysis.info ) then
> endif
> endif
> if ( $#flacfile != 0 ) then
> if ( 0 != 0 ) then
> if ( $perrun && $jkrun ) then
> if ( 0 && 0 ) then
>
> if ( $UseOctave ) then
> if ( 0 ) then
>
> goto check_params_return ;
> goto check_params_return
>
> set StudyDir = `pwd` ;
> set StudyDir = `pwd`
> pwd
>
> if ( $#analysis ) then
> if ( 1 ) then
>
> set analysisname = $analysis
> set analysisname = SIRP_LoadRegression_Stable5_072915
> set fsd = `getana -a $analysis -t fsd` ;
> set fsd = `getana -a $analysis -t fsd`
> getana -a SIRP_LoadRegression_Stable5_072915 -t fsd
> set PerSession = `getana -a $analysis

Re: [Freesurfer] selxavg3-sess error

[Rodriguez-Thompson, Anais]

Hi Doug,

Is there any update on this issue?

Thanks,
Anais

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rodriguez-Thompson, Anais 
[arodriguez-thomp...@mgh.harvard.edu]
Sent: Thursday, July 30, 2015 6:34 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] selxavg3-sess error

Hi Doug,

Attached is doug2.log.

Thanks,
Anais

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, July 30, 2015 4:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess error

ok, still not sure what is happening. Can you try

preproc-sess -debug -s GDDA001 -d
/autofs/cluster/roffman/users/Stable5_PerRun -a
SIRP_LoadRegression_Stable5_072915 |& tee doug2.log

and send me doug2.log


On 07/30/2015 12:54 PM, Rodriguez-Thompson, Anais wrote:
> Hi Doug,
>
> Below are the contents of doug.log:
>
> set echo = 1 ;
> breaksw
> breaksw
>
> end
> end
> while ( $#argv != 0 )
> while ( 0 != 0 )
> goto parse_args_return ;
> goto parse_args_return
>
> foreach grp ( $grpdefs )
> foreach grp ( )
>
> goto check_params ;
> goto check_params
>
> if ( $#SessList == 0 ) then
> if ( 1 == 0 ) then
>
> if ( $#SearchPathList == 0 ) then
> if ( 0 == 0 ) then
> set SearchPathList = "." ;
> set SearchPathList = .
> endif
> endif
>
> goto check_params_return ;
> goto check_params_return
>
>
> set UniqueList = ( ) ;
> set UniqueList = ( )
> foreach d ( $SearchPathList )
> foreach d ( . )
> if ( ! -e $d ) then
> if ( ! -e . ) then
>
> set IsUnique = 1 ;
> set IsUnique = 1
> foreach u ( $UniqueList )
> foreach u ( )
> if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;
> if ( 1 ) set UniqueList = ( . )
> set UniqueList = ( . )
> end
> end
>
> set SearchPathList = ( $UniqueList ) ;
> set SearchPathList = ( . )
>
> set errs = 0 ;
> set errs = 0
>
>
> set SessPath = ( ) ;
> set SessPath = ( )
> foreach sess ( $SessList )
> foreach sess ( GDDA001 )
> set tmp = ( ) ;
> set tmp = ( )
> foreach d ( $SearchPathList )
> foreach d ( . )
> set stst = $d/$sess
> set stst = ./GDDA001
> if ( -d $stst ) then
> if ( -d ./GDDA001 ) then
> if ( ! -r $stst ) then
> if ( ! -r ./GDDA001 ) then
> pushd $stst > /dev/null ;
> pushd ./GDDA001
> set tmp = ( $tmp `$PWDCMD` ) ;
> set tmp = ( `$PWDCMD` )
> pwd
> popd > /dev/null ;
> popd
> endif
> endif
> end
> end
> set nfound = ( $#tmp ) ;
> set nfound = ( 1 )
> if ( $nfound == 0 ) then
> if ( 1 == 0 ) then
> if ( $nfound > 1 ) then
> if ( 1 > 1 ) then
> set SessPath = ( $SessPath $tmp ) ;
> set SessPath = ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 )
> end
> end
>
>
> set UniqueList = ( ) ;
> set UniqueList = ( )
> foreach s ( $SessPath )
> foreach s ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 )
> set IsUnique = 1 ;
> set IsUnique = 1
> foreach u ( $UniqueList )
> foreach u ( )
> if ( ! $IsUnique && ! $AllowRedundant ) then
> if ( ! 1 && ! 0 ) then
>
> set UniqueList = ( $UniqueList $s ) ;
> set UniqueList = ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 )
> endif
> endif
> end
> end
>
>
> echo $SessPath
> echo /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001
>
> exit $errs ;
> exit 0
> set echo = 1 ;
> breaksw
> breaksw
>
> end
> end
> while ( $#argv != 0 )
> while ( 0 != 0 )
>
> goto parse_args_return ;
> goto parse_args_return
>
> goto check_params ;
> goto check_params
>
> if ( $#SessList == 0 ) then
> if ( 1 == 0 ) then
> if ( $#analysis == 0 && $flacfile == 0 ) then
> if ( 1 == 0 && == 0 ) then
> if ( $#analysis != 0 ) then
> if ( 1 != 0 ) then
> if ( ! -d $analysis ) then
> if ( ! -d SIRP_LoadRegression_Stable5_072915 ) then
> if ( ! -e $analysis/analysis.info ) then
> if ( ! -e SIRP_LoadRegression_Stable5_072915/analysis.info ) then
> endif
> endif
> if ( $#flacfile != 0 ) then
> if ( 0 != 0 ) then
> if ( $perrun && $jkrun ) then
> if ( 0 && 0 ) then
>
> if ( $UseOctave ) then
> if ( 0 ) then
>
> goto check_params_return ;
> goto check_params_return
>
> set StudyDir = `pwd` ;
> set StudyDir = `pwd`
> pwd
>
> if ( $#analysis ) then
> if ( 1 ) then
>
> set analysisname = $analysis
> set analysisname = SIRP_LoadRegression_Stable5_072915
> set fsd = `getana -a $analysis -t fsd` ;
> set fsd = `getana -a $analysis -t fsd`
> getana -a SIRP_LoadRegression_S

Re: [Freesurfer] selxavg3-sess error

[Rodriguez-Thompson, Anais]

Hi Doug, 

Attached is doug2.log. 

Thanks,
Anais

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, July 30, 2015 4:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess error

ok, still not sure what is happening. Can you try

preproc-sess -debug -s GDDA001 -d
/autofs/cluster/roffman/users/Stable5_PerRun -a
SIRP_LoadRegression_Stable5_072915 |& tee doug2.log

and send me doug2.log


On 07/30/2015 12:54 PM, Rodriguez-Thompson, Anais wrote:
> Hi Doug,
>
> Below are the contents of doug.log:
>
> set echo = 1 ;
> breaksw
> breaksw
>
> end
> end
> while ( $#argv != 0 )
> while ( 0 != 0 )
> goto parse_args_return ;
> goto parse_args_return
>
> foreach grp ( $grpdefs )
> foreach grp ( )
>
> goto check_params ;
> goto check_params
>
> if ( $#SessList == 0 ) then
> if ( 1 == 0 ) then
>
> if ( $#SearchPathList == 0 ) then
> if ( 0 == 0 ) then
> set SearchPathList = "." ;
> set SearchPathList = .
> endif
> endif
>
> goto check_params_return ;
> goto check_params_return
>
>
> set UniqueList = ( ) ;
> set UniqueList = ( )
> foreach d ( $SearchPathList )
> foreach d ( . )
> if ( ! -e $d ) then
> if ( ! -e . ) then
>
> set IsUnique = 1 ;
> set IsUnique = 1
> foreach u ( $UniqueList )
> foreach u ( )
> if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;
> if ( 1 ) set UniqueList = ( . )
> set UniqueList = ( . )
> end
> end
>
> set SearchPathList = ( $UniqueList ) ;
> set SearchPathList = ( . )
>
> set errs = 0 ;
> set errs = 0
>
>
> set SessPath = ( ) ;
> set SessPath = ( )
> foreach sess ( $SessList )
> foreach sess ( GDDA001 )
> set tmp = ( ) ;
> set tmp = ( )
> foreach d ( $SearchPathList )
> foreach d ( . )
> set stst = $d/$sess
> set stst = ./GDDA001
> if ( -d $stst ) then
> if ( -d ./GDDA001 ) then
> if ( ! -r $stst ) then
> if ( ! -r ./GDDA001 ) then
> pushd $stst > /dev/null ;
> pushd ./GDDA001
> set tmp = ( $tmp `$PWDCMD` ) ;
> set tmp = ( `$PWDCMD` )
> pwd
> popd > /dev/null ;
> popd
> endif
> endif
> end
> end
> set nfound = ( $#tmp ) ;
> set nfound = ( 1 )
> if ( $nfound == 0 ) then
> if ( 1 == 0 ) then
> if ( $nfound > 1 ) then
> if ( 1 > 1 ) then
> set SessPath = ( $SessPath $tmp ) ;
> set SessPath = ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 )
> end
> end
>
>
> set UniqueList = ( ) ;
> set UniqueList = ( )
> foreach s ( $SessPath )
> foreach s ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 )
> set IsUnique = 1 ;
> set IsUnique = 1
> foreach u ( $UniqueList )
> foreach u ( )
> if ( ! $IsUnique && ! $AllowRedundant ) then
> if ( ! 1 && ! 0 ) then
>
> set UniqueList = ( $UniqueList $s ) ;
> set UniqueList = ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 )
> endif
> endif
> end
> end
>
>
> echo $SessPath
> echo /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001
>
> exit $errs ;
> exit 0
> set echo = 1 ;
> breaksw
> breaksw
>
> end
> end
> while ( $#argv != 0 )
> while ( 0 != 0 )
>
> goto parse_args_return ;
> goto parse_args_return
>
> goto check_params ;
> goto check_params
>
> if ( $#SessList == 0 ) then
> if ( 1 == 0 ) then
> if ( $#analysis == 0 && $flacfile == 0 ) then
> if ( 1 == 0 && == 0 ) then
> if ( $#analysis != 0 ) then
> if ( 1 != 0 ) then
> if ( ! -d $analysis ) then
> if ( ! -d SIRP_LoadRegression_Stable5_072915 ) then
> if ( ! -e $analysis/analysis.info ) then
> if ( ! -e SIRP_LoadRegression_Stable5_072915/analysis.info ) then
> endif
> endif
> if ( $#flacfile != 0 ) then
> if ( 0 != 0 ) then
> if ( $perrun && $jkrun ) then
> if ( 0 && 0 ) then
>
> if ( $UseOctave ) then
> if ( 0 ) then
>
> goto check_params_return ;
> goto check_params_return
>
> set StudyDir = `pwd` ;
> set StudyDir = `pwd`
> pwd
>
> if ( $#analysis ) then
> if ( 1 ) then
>
> set analysisname = $analysis
> set analysisname = SIRP_LoadRegression_Stable5_072915
> set fsd = `getana -a $analysis -t fsd` ;
> set fsd = `getana -a $analysis -t fsd`
> getana -a SIRP_LoadRegression_Stable5_072915 -t fsd
> set PerSession = `getana -a $analysis -t IsPerSession`
> set PerSession = `getana -a $analysis -t IsPerSession`
> getana -a SIRP_LoadRegression_Stable5_072915 -t IsPerSession
> set IsNative = `getana -a $analysis -t IsNative`
> set IsNative = `getana -a $analysis -t IsNative`
> getana -a SIRP_LoadRegression_Stable5_072915 -t IsNative

Re: [Freesurfer] selxavg3-sess error

[Douglas N Greve]

gz
> GDDA001 017 Update not needed
> WARNING: multiple formats found for 018/template
>USING: 018/template.nii.gz
> GDDA001 018 Update not needed
>
>
> Thu Jul 30 12:52:19 EDT 2015
> mc-sess completed SUCCESSFULLY
> 
> Started at Thu Jul 30 12:52:18 EDT 2015
> Ended   at Thu Jul 30 12:52:19 EDT 2015
> preproc-sess done
> if ( $status ) exit 1 ;
> if ( 0 ) exit 1
> end
> end
> endif
> endif
>
> if ( $#MLF == 0 ) set MLF = /tmp/selxavg3-sess-$$.m
> if ( 0 == 0 ) set MLF = /tmp/selxavg3-sess-30587.m
> set MLF = /tmp/selxavg3-sess-30587.m
> rm -f $MLF
> rm -f /tmp/selxavg3-sess-30587.m
> echo "% `date`  " >> $MLF
> echo % `date`
> date
> echo "% `pwd`  " >> $MLF
> echo % `pwd`
> pwd
> echo "% $flacfile $analysis  " >> $MLF
> echo %  SIRP_LoadRegression_Stable5_072915
> echo "  " >> $MLF
> echo
> echo "  " >> $MLF
> echo
>
> set okfile = /tmp/selxavg3-sess-$$.ok
> set okfile = /tmp/selxavg3-sess-30587.ok
> rm -f $okfile
> rm -f /tmp/selxavg3-sess-30587.ok
>
> set parname = `getana -a $analysis -t parname`
> set parname = `getana -a $analysis -t parname`
> getana -a SIRP_LoadRegression_Stable5_072915 -t parname
> set funcstem = `getana -a $analysis -t funcstem`
> set funcstem = `getana -a $analysis -t funcstem`
> getana -a SIRP_LoadRegression_Stable5_072915 -t funcstem
> set rlf = `getana -a $analysis -t runlistfile`
> set rlf = `getana -a $analysis -t runlistfile`
> getana -a SIRP_LoadRegression_Stable5_072915 -t runlistfile
> set ConList = `getana -a $analysis -t contrasts`
> set ConList = `getana -a $analysis -t contrasts`
> getana -a SIRP_LoadRegression_Stable5_072915 -t contrasts
>
>
> @ nthsess = 0 ;
> @ nthsess = 0
> @ nprocs = 0 ;
> @ nprocs = 0
> foreach sess ( $SessList )
> foreach sess ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 )
> @ nthsess = $nthsess + 1 ;
> @ nthsess = 0 + 1
> set sessbase = `basename $sess` ;
> set sessbase = `basename $sess`
> basename /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001
> set sessdir = `dirname  $sess` ;
> set sessdir = `dirname  $sess`
> dirname /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001
>
> echo "---" | & tee -a $LF
> echo ---
> tee -a 
> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log
> ---
> echo "$sess " | & tee -a $LF
> echo /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001
> tee -a 
> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001
> date | & tee -a $LF
> date
> tee -a 
> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log
> Thu Jul 30 12:52:20 EDT 2015
>
> if ( ! -d $sess ) then
> if ( ! -d /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 ) then
>
> set funcdir = $sess/$fsd
> set funcdir = /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold
> set anadir = $sess/$fsd/$analysisname
> set anadir = 
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/SIRP_LoadRegression_Stable5_072915
> if ( $#OutParent == 0 ) then
> if ( 0 == 0 ) then
> set anadir = $sess/$fsd/$analysisname
> set anadir = 
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/SIRP_LoadRegression_Stable5_072915
> else
> else
> echo anadir = $anadir | tee -a $LF
> echo anadir = 
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/SIRP_LoadRegression_Stable5_072915
> tee -a 
> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log
> anadir = 
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/SIRP_LoadRegression_Stable5_072915
>
> set DoGLMFit = 0 ;
> set DoGLMFit = 0
> if ( $Overwrite || $perrun ) set DoGLMFit = 1 ;
> if ( 0 || 0 ) set DoGLMFit = 1
> set beta = `stem2fname $anadir/beta`
> set beta = `stem2fname $anadir/beta`
> stem2fname 
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/SIRP_LoadRegression_Stable5_072915/beta
> if ( $status ) set DoGLMFit = 1 ;
> if ( 0 ) set DoGLMFit = 1
> if ( $DoGLMFit == 0 ) then
> if ( 0 == 0 ) then
>
> set deplist = ( $analysis/analysis.info ) ;
> set deplist = ( SIRP_LoadRegression_Stable5_072915/analysis.info )
> set RunList = ( `getrunlist $sess/$fsd $rlf` ) ;
> set RunList = ( `getrunlist $sess/$fsd $rlf` )
> getrunlist /au

Re: [Freesurfer] selxavg3-sess error

[Rodriguez-Thompson, Anais]

915-150730125217.log
---
echo "$sess " | & tee -a $LF
echo /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 
tee -a 
/autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 
date | & tee -a $LF
date
tee -a 
/autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log
Thu Jul 30 12:52:20 EDT 2015

if ( ! -d $sess ) then
if ( ! -d /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 ) then

set funcdir = $sess/$fsd
set funcdir = /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold
set anadir = $sess/$fsd/$analysisname
set anadir = 
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/SIRP_LoadRegression_Stable5_072915
if ( $#OutParent == 0 ) then
if ( 0 == 0 ) then
set anadir = $sess/$fsd/$analysisname
set anadir = 
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/SIRP_LoadRegression_Stable5_072915
else
else
echo anadir = $anadir | tee -a $LF
echo anadir = 
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/SIRP_LoadRegression_Stable5_072915
tee -a 
/autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log
anadir = 
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/SIRP_LoadRegression_Stable5_072915

set DoGLMFit = 0 ;
set DoGLMFit = 0
if ( $Overwrite || $perrun ) set DoGLMFit = 1 ;
if ( 0 || 0 ) set DoGLMFit = 1
set beta = `stem2fname $anadir/beta`
set beta = `stem2fname $anadir/beta`
stem2fname 
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/SIRP_LoadRegression_Stable5_072915/beta
if ( $status ) set DoGLMFit = 1 ;
if ( 0 ) set DoGLMFit = 1
if ( $DoGLMFit == 0 ) then
if ( 0 == 0 ) then

set deplist = ( $analysis/analysis.info ) ;
set deplist = ( SIRP_LoadRegression_Stable5_072915/analysis.info )
set RunList = ( `getrunlist $sess/$fsd $rlf` ) ;
set RunList = ( `getrunlist $sess/$fsd $rlf` )
getrunlist /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold runlistfile
set funclist = ( )
set funclist = ( )
foreach Run ( $RunList )
foreach Run ( 016 017 018 )
set funcstempath = $sess/$fsd/$Run/$funcstem ;
set funcstempath = 
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/016/fmcpr.sm5
set func = `stem2fname $funcstempath` ;
set func = `stem2fname $funcstempath`
stem2fname 
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/016/fmcpr.sm5
if ( $status ) then
if ( 1 ) then
echo "ERROR: cannot find $funcstempath"
echo ERROR: cannot find 
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/016/fmcpr.sm5
ERROR: cannot find 
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/016/fmcpr.sm5
exit 1 ;
exit 1



Thanks,
Anais

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, July 30, 2015 12:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess error

those look ok. Can you run your selxavg3-sess command with -debug and
capture the output in a log file? Eg,

selxavg3-sess -s sess -a SIRP_LoadRegression_Stable5_072915 -debug |&
tee doug.log

and send me doug.log



On 07/30/2015 12:09 PM, Rodriguez-Thompson, Anais wrote:
> My preproc-sess command is preproc-sess -s (subject) -d $SUBJECTS_DIR -fsd 
> bold -fwhm 5 -per-run
>
> My mkanalysis command is mkanalysis-sess -analysis 
> SIRP_LoadRegression_Stable5_072915 -TR 2 -paradigm slopepar -event-related 
> -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt -native -timewindow 
> 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 -fwhm 5 -per-run
>
> Thanks,
> Anais
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, July 30, 2015 12:02 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] selxavg3-sess error
>
> What is your preproc-sess command and your mkanalysis-sess command?
>
>
> On 07/30/2015 12:00 PM, Rodriguez-Thompson, Anais wrote:
>> Hi Freesurfer experts,
>>
>> I'm having trouble running selxavg3-sess in 5.3 because it is looking for a 
>> file that does not exist (fmcpr.sm5.nii.gz). I read in another freesurfer 
>> mail thread that this issue can be fixed by preprocessing the subject. 
>> However, even after re-preprocessing my subjects at fwhm= 5, this file is 
>> still not generated. My subjects do have a fmcpr.nii.gz file. Should I 
>> remake my analysis with fwhm=0 so that it uses this file, or is there a way 
>> to generate fmcpr.sm5?
>>
>> Thanks for your help,
>> Anais

Re: [Freesurfer] selxavg3-sess error

[Douglas N Greve]

those look ok. Can you run your selxavg3-sess command with -debug and 
capture the output in a log file? Eg,

selxavg3-sess -s sess -a SIRP_LoadRegression_Stable5_072915 -debug |& 
tee doug.log

and send me doug.log



On 07/30/2015 12:09 PM, Rodriguez-Thompson, Anais wrote:
> My preproc-sess command is preproc-sess -s (subject) -d $SUBJECTS_DIR -fsd 
> bold -fwhm 5 -per-run
>
> My mkanalysis command is mkanalysis-sess -analysis 
> SIRP_LoadRegression_Stable5_072915 -TR 2 -paradigm slopepar -event-related 
> -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt -native -timewindow 
> 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 -fwhm 5 -per-run
>
> Thanks,
> Anais
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, July 30, 2015 12:02 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] selxavg3-sess error
>
> What is your preproc-sess command and your mkanalysis-sess command?
>
>
> On 07/30/2015 12:00 PM, Rodriguez-Thompson, Anais wrote:
>> Hi Freesurfer experts,
>>
>> I'm having trouble running selxavg3-sess in 5.3 because it is looking for a 
>> file that does not exist (fmcpr.sm5.nii.gz). I read in another freesurfer 
>> mail thread that this issue can be fixed by preprocessing the subject. 
>> However, even after re-preprocessing my subjects at fwhm= 5, this file is 
>> still not generated. My subjects do have a fmcpr.nii.gz file. Should I 
>> remake my analysis with fwhm=0 so that it uses this file, or is there a way 
>> to generate fmcpr.sm5?
>>
>> Thanks for your help,
>> Anais
>> ___
>> 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
> 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/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> 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
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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[Rodriguez-Thompson, Anais]

My preproc-sess command is preproc-sess -s (subject) -d $SUBJECTS_DIR -fsd bold 
-fwhm 5 -per-run

My mkanalysis command is mkanalysis-sess -analysis 
SIRP_LoadRegression_Stable5_072915 -TR 2 -paradigm slopepar -event-related -fsd 
bold -runlistfile runlistfile -tpef tpef_1.5mm.txt -native -timewindow 20 -TER 
2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 -fwhm 5 -per-run 

Thanks,
Anais

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, July 30, 2015 12:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess error

What is your preproc-sess command and your mkanalysis-sess command?


On 07/30/2015 12:00 PM, Rodriguez-Thompson, Anais wrote:
> Hi Freesurfer experts,
>
> I'm having trouble running selxavg3-sess in 5.3 because it is looking for a 
> file that does not exist (fmcpr.sm5.nii.gz). I read in another freesurfer 
> mail thread that this issue can be fixed by preprocessing the subject. 
> However, even after re-preprocessing my subjects at fwhm= 5, this file is 
> still not generated. My subjects do have a fmcpr.nii.gz file. Should I remake 
> my analysis with fwhm=0 so that it uses this file, or is there a way to 
> generate fmcpr.sm5?
>
> Thanks for your help,
> Anais
> ___
> 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
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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[Douglas N Greve]

What is your preproc-sess command and your mkanalysis-sess command?


On 07/30/2015 12:00 PM, Rodriguez-Thompson, Anais wrote:
> Hi Freesurfer experts,
>
> I'm having trouble running selxavg3-sess in 5.3 because it is looking for a 
> file that does not exist (fmcpr.sm5.nii.gz). I read in another freesurfer 
> mail thread that this issue can be fixed by preprocessing the subject. 
> However, even after re-preprocessing my subjects at fwhm= 5, this file is 
> still not generated. My subjects do have a fmcpr.nii.gz file. Should I remake 
> my analysis with fwhm=0 so that it uses this file, or is there a way to 
> generate fmcpr.sm5?
>
> Thanks for your help,
> Anais
> ___
> 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
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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] selxavg3-sess error

[Rodriguez-Thompson, Anais]

Hi Freesurfer experts,

I'm having trouble running selxavg3-sess in 5.3 because it is looking for a 
file that does not exist (fmcpr.sm5.nii.gz). I read in another freesurfer mail 
thread that this issue can be fixed by preprocessing the subject. However, even 
after re-preprocessing my subjects at fwhm= 5, this file is still not 
generated. My subjects do have a fmcpr.nii.gz file. Should I remake my analysis 
with fwhm=0 so that it uses this file, or is there a way to generate fmcpr.sm5?

Thanks for your help,
Anais
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[Douglas N Greve]

The problem is that you are doing it in native space, and the native 
space differs from one run to the next. If you do it in surface space or 
mni305, then this problem will go away. You cannot use native space when 
the native space differs from one run to the next
doug
On 03/09/2015 03:11 PM, Eryilmaz, H. Hamdi wrote:
> We use 'preproc-sess' before a single subject analysis. Here are the 
> commands we run:
>
> >> preproc-sess -s SUBJECT_ID -fwhm 5 -per-run
>
> >> mkanalysis-sess -analysis FT_TEST -TR 1.9 -paradigm FT.par 
> -event-related -runlistfile runlistFT -native -fwhm 5 -mcextreg 
> -nconditions 10 -gammafit 2.25 1.25 -refeventdur 2 -force
>
>
> 'preproc-sess' is run for all runs by default. Do you think we should 
> run a separate 'preproc-sess' for each run?
>
> Thanks!
> Hamdi
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> *Sent:* Monday, March 09, 2015 2:49 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] selxavg3-sess error
>
>
> What is your mris_preproc command? And your mkanalysis-sess command?
>
>
> On 3/9/15 2:41 PM, Eryilmaz, H. Hamdi wrote:
>> Hi Doug,
>>
>> Yes, that's correct. Images in runs 015,016,017 have 37 slices, those 
>> in run 018 have 35.
>>
>> Hamdi
>>
>>
>> 
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> *Sent:* Monday, March 09, 2015 2:38 PM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* Re: [Freesurfer] selxavg3-sess error
>>
>>
>> It looks like different runs have different number of slices. Is that 
>> right?
>>
>> On 3/9/15 1:13 PM, Eryilmaz, H. Hamdi wrote:
>>> Dear FS experts,
>>>
>>> I got an error while running selxavg3-sess for a single subject. The 
>>> log (attached) says the following:
>>>
>>> *
>>> ** Input 018/tmp.mc-afni2.7515/invol.nii.gz and base 
>>> 018/tmp.mc-afni2.7515/tempvol.nii.gz don't have same dimensions!
>>>Input: nx=64  ny=64  nz=35
>>>Base:  nx=64  ny=64  nz=37
>>> ** FATAL ERROR: perhaps you could make your datasets match?
>>> ERROR: 3dvolreg
>>> *
>>>
>>> I am wondering which 'template.nii' file the script reads to create 
>>> tempvol.nii.gz. We have different functional runs (with different 
>>> TRs) under the subject's bold directory and for the run '/018' the 
>>> TR should be 1900 ms. It looks like the script is reading from a 
>>> 'template.nii' located elsewhere for which the TR is 2000 ms.
>>>
>>> *
>>> reading from template.nii...
>>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>>> i_ras = (-0.998769, -0.00721698, 0.0490727)
>>> j_ras = (-1.73634e-08, -0.989358, -0.145502)
>>> k_ras = (0.0496006, -0.145323, 0.98814)
>>> changing data type from short to float (noscale = 0)...
>>> writing to 018/tmp.mc-afni2.7515/tempvol.nii.gz...
>>> *
>>>
>>> Many thanks for your help!
>>> Hamdi
>>>
>>>
>>> --
>>>
>>> Hamdi Eryilmaz, PhD
>>>
>>> Massachusetts General Hospital
>>> A.A. Martinos Center for Biomedical Imaging
>>> Psychiatric Neuroimaging Division
>>> 149 13th St, Charlestown, MA 02129
>>> Phone: +1 617 643 7462
>>> Email:hamdi.eryil...@mgh.harvard.edu <mailto:heryil...@partners.org>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard

Re: [Freesurfer] selxavg3-sess error

[Eryilmaz, H. Hamdi]

We use 'preproc-sess' before a single subject analysis. Here are the commands 
we run:

>> preproc-sess -s SUBJECT_ID -fwhm 5 -per-run

>> mkanalysis-sess -analysis FT_TEST -TR 1.9 -paradigm FT.par -event-related 
>> -runlistfile runlistFT -native -fwhm 5 -mcextreg -nconditions 10 -gammafit 
>> 2.25 1.25 -refeventdur 2 -force


'preproc-sess' is run for all runs by default. Do you think we should run a 
separate 'preproc-sess' for each run?

Thanks!
Hamdi



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, March 09, 2015 2:49 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess error


What is your mris_preproc command? And your mkanalysis-sess command?


On 3/9/15 2:41 PM, Eryilmaz, H. Hamdi wrote:
Hi Doug,

Yes, that's correct. Images in runs 015,016,017 have 37 slices, those in run 
018 have 35.

Hamdi



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>]
Sent: Monday, March 09, 2015 2:38 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] selxavg3-sess error


It looks like different runs have different number of slices. Is that right?

On 3/9/15 1:13 PM, Eryilmaz, H. Hamdi wrote:
Dear FS experts,

I got an error while running selxavg3-sess for a single subject. The log 
(attached) says the following:

*
** Input 018/tmp.mc-afni2.7515/invol.nii.gz and base 
018/tmp.mc-afni2.7515/tempvol.nii.gz don't have same dimensions!
   Input: nx=64  ny=64  nz=35
   Base:  nx=64  ny=64  nz=37
** FATAL ERROR: perhaps you could make your datasets match?
ERROR: 3dvolreg
*

I am wondering which 'template.nii' file the script reads to create 
tempvol.nii.gz. We have different functional runs (with different TRs) under 
the subject's bold directory and for the run '/018' the TR should be 1900 ms. 
It looks like the script is reading from a 'template.nii' located elsewhere for 
which the TR is 2000 ms.

*
reading from template.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998769, -0.00721698, 0.0490727)
j_ras = (-1.73634e-08, -0.989358, -0.145502)
k_ras = (0.0496006, -0.145323, 0.98814)
changing data type from short to float (noscale = 0)...
writing to 018/tmp.mc-afni2.7515/tempvol.nii.gz...
*

Many thanks for your help!
Hamdi


--

Hamdi Eryilmaz, PhD

Massachusetts General Hospital
A.A. Martinos Center for Biomedical Imaging
Psychiatric Neuroimaging Division
149 13th St, Charlestown, MA 02129
Phone: +1 617 643 7462
Email: hamdi.eryil...@mgh.harvard.edu<mailto:heryil...@partners.org>



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[Douglas Greve]

What is your mris_preproc command? And your mkanalysis-sess command?


On 3/9/15 2:41 PM, Eryilmaz, H. Hamdi wrote:

Hi Doug,

Yes, that's correct. Images in runs 015,016,017 have 37 slices, those 
in run 018 have 35.


Hamdi



*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]

*Sent:* Monday, March 09, 2015 2:38 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] selxavg3-sess error


It looks like different runs have different number of slices. Is that 
right?


On 3/9/15 1:13 PM, Eryilmaz, H. Hamdi wrote:

Dear FS experts,

I got an error while running selxavg3-sess for a single subject. The 
log (attached) says the following:


*
** Input 018/tmp.mc-afni2.7515/invol.nii.gz and base 
018/tmp.mc-afni2.7515/tempvol.nii.gz don't have same dimensions!

   Input: nx=64  ny=64  nz=35
   Base:  nx=64  ny=64  nz=37
** FATAL ERROR: perhaps you could make your datasets match?
ERROR: 3dvolreg
*

I am wondering which 'template.nii' file the script reads to create 
tempvol.nii.gz. We have different functional runs (with different 
TRs) under the subject's bold directory and for the run '/018' the TR 
should be 1900 ms. It looks like the script is reading from a 
'template.nii' located elsewhere for which the TR is 2000 ms.


*
reading from template.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998769, -0.00721698, 0.0490727)
j_ras = (-1.73634e-08, -0.989358, -0.145502)
k_ras = (0.0496006, -0.145323, 0.98814)
changing data type from short to float (noscale = 0)...
writing to 018/tmp.mc-afni2.7515/tempvol.nii.gz...
*

Many thanks for your help!
Hamdi


--

Hamdi Eryilmaz, PhD

Massachusetts General Hospital
A.A. Martinos Center for Biomedical Imaging
Psychiatric Neuroimaging Division
149 13th St, Charlestown, MA 02129
Phone: +1 617 643 7462
Email:hamdi.eryil...@mgh.harvard.edu <mailto:heryil...@partners.org>


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[Eryilmaz, H. Hamdi]

Hi Doug,

Yes, that's correct. Images in runs 015,016,017 have 37 slices, those in run 
018 have 35.

Hamdi



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, March 09, 2015 2:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess error


It looks like different runs have different number of slices. Is that right?

On 3/9/15 1:13 PM, Eryilmaz, H. Hamdi wrote:
Dear FS experts,

I got an error while running selxavg3-sess for a single subject. The log 
(attached) says the following:

*
** Input 018/tmp.mc-afni2.7515/invol.nii.gz and base 
018/tmp.mc-afni2.7515/tempvol.nii.gz don't have same dimensions!
   Input: nx=64  ny=64  nz=35
   Base:  nx=64  ny=64  nz=37
** FATAL ERROR: perhaps you could make your datasets match?
ERROR: 3dvolreg
*

I am wondering which 'template.nii' file the script reads to create 
tempvol.nii.gz. We have different functional runs (with different TRs) under 
the subject's bold directory and for the run '/018' the TR should be 1900 ms. 
It looks like the script is reading from a 'template.nii' located elsewhere for 
which the TR is 2000 ms.

*
reading from template.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998769, -0.00721698, 0.0490727)
j_ras = (-1.73634e-08, -0.989358, -0.145502)
k_ras = (0.0496006, -0.145323, 0.98814)
changing data type from short to float (noscale = 0)...
writing to 018/tmp.mc-afni2.7515/tempvol.nii.gz...
*

Many thanks for your help!
Hamdi


--

Hamdi Eryilmaz, PhD

Massachusetts General Hospital
A.A. Martinos Center for Biomedical Imaging
Psychiatric Neuroimaging Division
149 13th St, Charlestown, MA 02129
Phone: +1 617 643 7462
Email: hamdi.eryil...@mgh.harvard.edu<mailto:heryil...@partners.org>



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[Douglas Greve]

It looks like different runs have different number of slices. Is that right?

On 3/9/15 1:13 PM, Eryilmaz, H. Hamdi wrote:

Dear FS experts,

I got an error while running selxavg3-sess for a single subject. The 
log (attached) says the following:


*
** Input 018/tmp.mc-afni2.7515/invol.nii.gz and base 
018/tmp.mc-afni2.7515/tempvol.nii.gz don't have same dimensions!

   Input: nx=64  ny=64  nz=35
   Base:  nx=64  ny=64  nz=37
** FATAL ERROR: perhaps you could make your datasets match?
ERROR: 3dvolreg
*

I am wondering which 'template.nii' file the script reads to create 
tempvol.nii.gz. We have different functional runs (with different TRs) 
under the subject's bold directory and for the run '/018' the TR 
should be 1900 ms. It looks like the script is reading from a 
'template.nii' located elsewhere for which the TR is 2000 ms.


*
reading from template.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998769, -0.00721698, 0.0490727)
j_ras = (-1.73634e-08, -0.989358, -0.145502)
k_ras = (0.0496006, -0.145323, 0.98814)
changing data type from short to float (noscale = 0)...
writing to 018/tmp.mc-afni2.7515/tempvol.nii.gz...
*

Many thanks for your help!
Hamdi


--

Hamdi Eryilmaz, PhD

Massachusetts General Hospital
A.A. Martinos Center for Biomedical Imaging
Psychiatric Neuroimaging Division
149 13th St, Charlestown, MA 02129
Phone: +1 617 643 7462
Email:hamdi.eryil...@mgh.harvard.edu 


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] selxavg3-sess error

[Eryilmaz, H. Hamdi]

Dear FS experts,

I got an error while running selxavg3-sess for a single subject. The log 
(attached) says the following:

*
** Input 018/tmp.mc-afni2.7515/invol.nii.gz and base 
018/tmp.mc-afni2.7515/tempvol.nii.gz don't have same dimensions!
   Input: nx=64  ny=64  nz=35
   Base:  nx=64  ny=64  nz=37
** FATAL ERROR: perhaps you could make your datasets match?
ERROR: 3dvolreg
*

I am wondering which 'template.nii' file the script reads to create 
tempvol.nii.gz. We have different functional runs (with different TRs) under 
the subject's bold directory and for the run '/018' the TR should be 1900 ms. 
It looks like the script is reading from a 'template.nii' located elsewhere for 
which the TR is 2000 ms.

*
reading from template.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998769, -0.00721698, 0.0490727)
j_ras = (-1.73634e-08, -0.989358, -0.145502)
k_ras = (0.0496006, -0.145323, 0.98814)
changing data type from short to float (noscale = 0)...
writing to 018/tmp.mc-afni2.7515/tempvol.nii.gz...
*

Many thanks for your help!
Hamdi


--

Hamdi Eryilmaz, PhD

Massachusetts General Hospital
A.A. Martinos Center for Biomedical Imaging
Psychiatric Neuroimaging Division
149 13th St, Charlestown, MA 02129
Phone: +1 617 643 7462
Email: hamdi.eryil...@mgh.harvard.edu
selxavg3-sess log file
/usr/local/freesurfer/stable5_0_0/fsfast/bin/selxavg3-sess
-sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/FruitTask_030815 -analysis FT_TEST -overwrite
$Id: selxavg3-sess,v 1.52.2.5 2010/08/25 19:07:37 greve Exp $
uid=3429288(hhe0) gid=3429288(hhe0) groups=3429288(hhe0),1506(roffmagp)
/autofs/cluster/roffman/users/Stable5_PerRun
Linux audrey 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Sun Mar  8 18:17:22 EDT 2015
preproc-sess -s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -a FT_TEST -nolog
--
preproc-sess logfile is /dev/null
--
$Id: preproc-sess,v 1.31.2.6 2011/01/10 17:05:53 greve Exp $
hhe0
setenv FREESURFER_HOME /usr/local/freesurfer/stable5_0_0
setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun
Linux audrey 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
/autofs/cluster/roffman/users/Stable5_PerRun
/usr/local/freesurfer/stable5_0_0/fsfast/bin/preproc-sess
-s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -a FT_TEST -nolog
Sun Mar  8 18:17:22 EDT 2015
instem   f 
mc   1 f fmc 
stc  0 fmc
sm   1 fmc fmc.sm5 
mask 1   brain
GDDA074 Template -
mktemplate-sess -s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -rlf runlistFT -nolog -update
 
Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA074 
Sun Mar  8 18:17:22 EDT 2015
Detected input format at nii
GDDA074 Update not needed
  Run: 018 
  Sun Mar  8 18:17:22 EDT 2015
  GDDA074 018 Update not needed
Sun Mar  8 18:17:22 EDT 2015
mktemplate-sess completed 
GDDA074 Mask 
mkbrainmask-sess -maskstem brain -fsd bold -s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -rlf runlistFT -nolog -update

/autofs/cluster/roffman/users/Stable5_PerRun/GDDA074 
Sun Mar  8 18:17:22 EDT 2015
GDDA074 Update not needed for session-level mask
GDDA074 Update not needed for run 018 mask
GDDA074 Update not needed for run 018 meanval
Sun Mar  8 18:17:22 EDT 2015
mkbrainmask-sess done
GDDA074 Registration -
register-sess -s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf runlistFT -per-session -nolog -update
--
register-sess logfile is /dev/null
--
Sun Mar  8 18:17:23 EDT 2015

setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun
cd /autofs/cluster/roffman/users/Stable5_PerRun
/usr/local/freesurfer/stable5_0_0/fsfast/bin/register-sess -s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf runlistFT -per-session -nolog -update

freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319
Linux audrey 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
 
Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA074 
Sun Mar  8 18:17:23 EDT 2015
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA074
Sun Mar  8 18:17:23 EDT 2015
register-sess completed 
GDDA074 MC -
mc-sess -fstem f -fmcstem fmc -s GDDA074 -d /autofs/cluster/ro

Re: [Freesurfer] selxavg3-sess error

[Francesca Strappini]

Thank you, now it works!

Best
Francesca

2014-09-08 15:24 GMT+03:00 Douglas Greve :
> It is not looking for fmc.sm5.DM.lh.nii.gz but rather fmcsm5.nii.gz in
>
> /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001
>
> does that file exist? Have you run preproc-sess?
> doug
>
> On 8/28/14 9:49 AM, Francesca Strappini wrote:
>> Dear all,
>>
>> I've run selxavg3-sess and I got this error message when it tried to
>> read the fmcsm file (fmc.sm5.DM.lh.nii.gz).
>>
>> Thank you for your help,
>> Francesca
>>
>>
>> shalim-ubuntu:/usr/local/freesurfer/fsfast/MeytalRetinotopy>
>> selxavg3-sess -a rtopy.DM.lh -s SUBJ01
>> Surface data DM lh
>> --
>> selxavg3-sess logfile is
>> /usr/local/freesurfer/fsfast/MeytalRetinotopy/log/selxavg3-sess-bold-rtopy.DM.lh-140828163352.log
>> --
>> ---
>> /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01
>> Thu Aug 28 16:33:53 IDT 2014
>> anadir = 
>> /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh
>> DoGLMFit = 1
>> DoContrasts = 1
>> UpdateNeeded = 1
>> --
>> --- matlab output 
>> No window system found.  Java option 'MWT' ignored.
>> Warning: Unable to open display 'iconic'.  You will not be able to
>> display graphics on the screen.
>> Warning: No window system found.  Java option 'MWT' ignored.
>>
>>  < M A T L A B (R) >
>>Copyright 1984-2013 The MathWorks, Inc.
>>  R2013b (8.2.0.701) 64-bit (glnxa64)
>>August 13, 2013
>>
>>
>> To get started, type one of these: helpwin, helpdesk, or demo.
>> For product information, visit www.mathworks.com.
>>
>> sxa3pwd =
>>
>> /usr/local/freesurfer/fsfast/MeytalRetinotopy
>>
>> sxa3cmd =
>>
>> /usr/local/freesurfer/fsfast/bin/selxavg3-sess -a rtopy.DM.lh -s SUBJ01
>>
 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> #@# SUBJ01 ###
>> /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01
>> -
>> $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
>> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
>> /usr/local/freesurfer/fsfast/MeytalRetinotopy/MRIread.m
>> -
>> outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopy
>> Extension format = nii.gz
>> ERROR: cannot determine format of
>> /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001/fmcsm5
>> ERROR: attempting to read
>> /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001/fmcsm5
>> --
>> ERROR: fast_selxavg3() failed\n
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] selxavg3-sess error

[Douglas Greve]

It is not looking for fmc.sm5.DM.lh.nii.gz but rather fmcsm5.nii.gz in

/usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001

does that file exist? Have you run preproc-sess?
doug

On 8/28/14 9:49 AM, Francesca Strappini wrote:
> Dear all,
>
> I've run selxavg3-sess and I got this error message when it tried to
> read the fmcsm file (fmc.sm5.DM.lh.nii.gz).
>
> Thank you for your help,
> Francesca
>
>
> shalim-ubuntu:/usr/local/freesurfer/fsfast/MeytalRetinotopy>
> selxavg3-sess -a rtopy.DM.lh -s SUBJ01
> Surface data DM lh
> --
> selxavg3-sess logfile is
> /usr/local/freesurfer/fsfast/MeytalRetinotopy/log/selxavg3-sess-bold-rtopy.DM.lh-140828163352.log
> --
> ---
> /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01
> Thu Aug 28 16:33:53 IDT 2014
> anadir = /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh
> DoGLMFit = 1
> DoContrasts = 1
> UpdateNeeded = 1
> --
> --- matlab output 
> No window system found.  Java option 'MWT' ignored.
> Warning: Unable to open display 'iconic'.  You will not be able to
> display graphics on the screen.
> Warning: No window system found.  Java option 'MWT' ignored.
>
>  < M A T L A B (R) >
>Copyright 1984-2013 The MathWorks, Inc.
>  R2013b (8.2.0.701) 64-bit (glnxa64)
>August 13, 2013
>
>
> To get started, type one of these: helpwin, helpdesk, or demo.
> For product information, visit www.mathworks.com.
>
> sxa3pwd =
>
> /usr/local/freesurfer/fsfast/MeytalRetinotopy
>
> sxa3cmd =
>
> /usr/local/freesurfer/fsfast/bin/selxavg3-sess -a rtopy.DM.lh -s SUBJ01
>
>>> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> #@# SUBJ01 ###
> /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01
> -
> $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> /usr/local/freesurfer/fsfast/MeytalRetinotopy/MRIread.m
> -
> outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopy
> Extension format = nii.gz
> ERROR: cannot determine format of
> /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001/fmcsm5
> ERROR: attempting to read
> /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001/fmcsm5
> --
> ERROR: fast_selxavg3() failed\n
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] selxavg3-sess error

[Francesca Strappini]

Dear all,

I've run selxavg3-sess and I got this error message when it tried to
read the fmcsm file (fmc.sm5.DM.lh.nii.gz).

Thank you for your help,
Francesca


shalim-ubuntu:/usr/local/freesurfer/fsfast/MeytalRetinotopy>
selxavg3-sess -a rtopy.DM.lh -s SUBJ01
Surface data DM lh
--
selxavg3-sess logfile is
/usr/local/freesurfer/fsfast/MeytalRetinotopy/log/selxavg3-sess-bold-rtopy.DM.lh-140828163352.log
--
---
/usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01
Thu Aug 28 16:33:53 IDT 2014
anadir = /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh
DoGLMFit = 1
DoContrasts = 1
UpdateNeeded = 1
--
--- matlab output 
No window system found.  Java option 'MWT' ignored.
Warning: Unable to open display 'iconic'.  You will not be able to
display graphics on the screen.
Warning: No window system found.  Java option 'MWT' ignored.

< M A T L A B (R) >
  Copyright 1984-2013 The MathWorks, Inc.
R2013b (8.2.0.701) 64-bit (glnxa64)
  August 13, 2013


To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.

>> >> >> >> >> >> >>
sxa3pwd =

/usr/local/freesurfer/fsfast/MeytalRetinotopy

>>
sxa3cmd =

/usr/local/freesurfer/fsfast/bin/selxavg3-sess -a rtopy.DM.lh -s SUBJ01

>> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>

#@# SUBJ01 ###
/usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01
-
$Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
/usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
/usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
/usr/local/freesurfer/fsfast/MeytalRetinotopy/MRIread.m
-
outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopy
Extension format = nii.gz
ERROR: cannot determine format of
/usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001/fmcsm5
ERROR: attempting to read
/usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001/fmcsm5
--
ERROR: fast_selxavg3() failed\n
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error in ==> fast_selxavg3 at 434

[pfannmoelj]

Thank you for your Help. I figured out that it was a problem with the data 
which caused this error.





On Wed, 04 Jun 2014 12:00:08 -0400
Douglas N Greve  wrote:

> 
> This is a strange error that I cannot figure out from the terminal 
> output. What version of FS are you using? Here's something you can try:
> 
> Run selxavg3-sess with --monly sxa3.m This will return right away having 
> created sxa3.m
> 
> Start matlab and run sxa3. It will stop at the error below. Then type
> 
> flac0.inorm
> 
> gmean
> 
> Each of these will print something out to the terminal. Send the results 
> to the list
> 
> doug
> 
> 
> On 06/02/2014 06:27 AM, pfannmo...@uni-greifswald.de wrote:
> > Dear Experts,
> >
> > during an fsfast analysis an error occured after selxavg3-sess was 
> > executed. The corresponding commands were:
> >
> > mkanalysis-sess -fsd bold -surface self lh -fwhm 0 -event-related -paradigm 
> > sensory.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 8 
> > -polyfit 2 -analysis analysis.lh -delay 0 -per-run -force -mcextreg
> > mkcontrast-sess -analysis analysis.lh -contrast stim-v-base -a 1
> >
> > selxavg3-sess -s ./sessdir -analysis analysis.lh -no-preproc -force
> >
> >
> >
> > The output of selxavg3-sess was:
> >
> >
> > sxa3pwd =
> >
> > /.../evaluation
> >
> > sxa3cmd =
> >
> > /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./sessdir -analysis 
> > analysis.lh -no-preproc -force
> >
> >>> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> > #@# sessdir ###
> > /.../evaluation/sessdir
> > -
> > $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
> > /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> > /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> > /usr/local/freesurfer/matlab/MRIread.m
> > -
> > outtop = /.../evaluation
> > Extension format = nii.gz
> >   1 stim-v-base.mat
> > Excluding 8 points
> > nruns = 1
> > autostimdur =
> >
> >
> > outanadir = /.../evaluation/sessdir/bold/analysis.lh
> > Excluding 8 points
> > Found 145573/155188 (93.8) voxels in mask
> > Creating Design Matrix
> >   ... creation time =  0.008 sec
> > DoMCFit = 1
> > ntptot = 108, nX = 15, DOF = 93
> > Saving X matrix to /.../evaluation/sessdir/bold/analysis.lh/Xtmp.mat
> > XCond = 64.7067 (normalized)
> > Computing compensation for resdual AR1 bias
> >   1  -0.5  -0.468819(t=0.005249)
> >   2  -0.25  -0.252194(t=0.007053)
> >   3  0  -0.0449419(t=0.008126)
> >   4  0.25  0.149516(t=0.00935)
> >   5  0.5  0.319324(t=0.010795)
> > AR1 Correction M: 0.0749452 1.26122
> > Computing contrast matrices
> > OLS Beta Pass
> >run 1t= 0.0
> >  Global Mean
> > Global In-Mask Mean =  (0.664951)
> > ??? Error using ==> mrdivide
> > Matrix dimensions must agree.
> >
> > Error in ==> fast_selxavg3 at 434
> >  RescaleFactor = flac0.inorm/gmean;
> >
> >>> --
> > ERROR: fast_selxavg3() failed\n
> >
> >
> > Do you have an idea what went wrong?
> >
> > Sincerely yours pfannmoe
> > ___
> > 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
> 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/
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
> 


-- 
Joerg Pfannmoeller 
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] selxavg3-sess error in ==> fast_selxavg3 at 434

[Douglas N Greve]

This is a strange error that I cannot figure out from the terminal 
output. What version of FS are you using? Here's something you can try:

Run selxavg3-sess with --monly sxa3.m This will return right away having 
created sxa3.m

Start matlab and run sxa3. It will stop at the error below. Then type

flac0.inorm

gmean

Each of these will print something out to the terminal. Send the results 
to the list

doug


On 06/02/2014 06:27 AM, pfannmo...@uni-greifswald.de wrote:
> Dear Experts,
>
> during an fsfast analysis an error occured after selxavg3-sess was executed. 
> The corresponding commands were:
>
> mkanalysis-sess -fsd bold -surface self lh -fwhm 0 -event-related -paradigm 
> sensory.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 8 -polyfit 
> 2 -analysis analysis.lh -delay 0 -per-run -force -mcextreg
> mkcontrast-sess -analysis analysis.lh -contrast stim-v-base -a 1
>
> selxavg3-sess -s ./sessdir -analysis analysis.lh -no-preproc -force
>
>
>
> The output of selxavg3-sess was:
>
>
> sxa3pwd =
>
> /.../evaluation
>
> sxa3cmd =
>
> /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./sessdir -analysis 
> analysis.lh -no-preproc -force
>
>>> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> #@# sessdir ###
> /.../evaluation/sessdir
> -
> $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> /usr/local/freesurfer/matlab/MRIread.m
> -
> outtop = /.../evaluation
> Extension format = nii.gz
>   1 stim-v-base.mat
> Excluding 8 points
> nruns = 1
> autostimdur =
>
>
> outanadir = /.../evaluation/sessdir/bold/analysis.lh
> Excluding 8 points
> Found 145573/155188 (93.8) voxels in mask
> Creating Design Matrix
>   ... creation time =  0.008 sec
> DoMCFit = 1
> ntptot = 108, nX = 15, DOF = 93
> Saving X matrix to /.../evaluation/sessdir/bold/analysis.lh/Xtmp.mat
> XCond = 64.7067 (normalized)
> Computing compensation for resdual AR1 bias
>   1  -0.5  -0.468819(t=0.005249)
>   2  -0.25  -0.252194(t=0.007053)
>   3  0  -0.0449419(t=0.008126)
>   4  0.25  0.149516(t=0.00935)
>   5  0.5  0.319324(t=0.010795)
> AR1 Correction M: 0.0749452 1.26122
> Computing contrast matrices
> OLS Beta Pass
>run 1t= 0.0
>  Global Mean
> Global In-Mask Mean =  (0.664951)
> ??? Error using ==> mrdivide
> Matrix dimensions must agree.
>
> Error in ==> fast_selxavg3 at 434
>  RescaleFactor = flac0.inorm/gmean;
>
>>> --
> ERROR: fast_selxavg3() failed\n
>
>
> Do you have an idea what went wrong?
>
> Sincerely yours pfannmoe
> ___
> 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
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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] selxavg3-sess error in ==> fast_selxavg3 at 434

[pfannmoelj]

Dear Experts,

during an fsfast analysis an error occured after selxavg3-sess was executed. 
The corresponding commands were:

mkanalysis-sess -fsd bold -surface self lh -fwhm 0 -event-related -paradigm 
sensory.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 8 -polyfit 2 
-analysis analysis.lh -delay 0 -per-run -force -mcextreg
mkcontrast-sess -analysis analysis.lh -contrast stim-v-base -a 1

selxavg3-sess -s ./sessdir -analysis analysis.lh -no-preproc -force



The output of selxavg3-sess was:


>> >> >> >> >> >> >> 
sxa3pwd =

/.../evaluation

>> 
sxa3cmd =

/usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./sessdir -analysis 
analysis.lh -no-preproc -force

>> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> 

#@# sessdir ###
/.../evaluation/sessdir
-
$Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
/usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
/usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
/usr/local/freesurfer/matlab/MRIread.m
-
outtop = /.../evaluation
Extension format = nii.gz
 1 stim-v-base.mat
Excluding 8 points
nruns = 1
autostimdur = 


outanadir = /.../evaluation/sessdir/bold/analysis.lh
Excluding 8 points
Found 145573/155188 (93.8) voxels in mask
Creating Design Matrix
 ... creation time =  0.008 sec
DoMCFit = 1
ntptot = 108, nX = 15, DOF = 93
Saving X matrix to /.../evaluation/sessdir/bold/analysis.lh/Xtmp.mat
XCond = 64.7067 (normalized)
Computing compensation for resdual AR1 bias
 1  -0.5  -0.468819(t=0.005249)
 2  -0.25  -0.252194(t=0.007053)
 3  0  -0.0449419(t=0.008126)
 4  0.25  0.149516(t=0.00935)
 5  0.5  0.319324(t=0.010795)
AR1 Correction M: 0.0749452 1.26122
Computing contrast matrices
OLS Beta Pass 
  run 1t= 0.0
Global Mean 
Global In-Mask Mean =  (0.664951)
??? Error using ==> mrdivide
Matrix dimensions must agree.

Error in ==> fast_selxavg3 at 434
RescaleFactor = flac0.inorm/gmean;

>> --
ERROR: fast_selxavg3() failed\n


Do you have an idea what went wrong?

Sincerely yours pfannmoe
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[SHAHIN NASR]

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,  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

Re: [Freesurfer] selxavg3-sess error

[Douglas N 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,  > 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
> 

Re: [Freesurfer] selxavg3-sess error

[shahin]

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/
>
>
>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[Douglas N Greve]

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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[Douglas N Greve]

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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[shahin]

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/
>
>
>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[shahin]

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/
>
>
>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the s

Re: [Freesurfer] selxavg3-sess error

[Douglas N Greve]

-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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[Douglas N Greve]

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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error]

[shahin]

 Original Message 
Subject: Re: selxavg3-sess error
From:sha...@nmr.mgh.harvard.edu
Date:Wed, March 19, 2014 11:15 am
To:  "Douglas N Greve" 
--

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/
>
>
>


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] selxavg3-sess error

[SHAHIN NASR]

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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] selxavg3-sess error

[Sam Cartmell]

Hello,

I'm trying to run selxavg3-sess with FS v4.5 for an FIR analysis where each
trial is modeled as a separate condition.  The command works smoothly for
the majority of subjects, but for 2 different subjects, it exits with the
following error:

Saving X matrix to
/home/sam/fMRIDATA/samstudies/SoCo/SoCo10/bold/Logit/Xtmp.mat
XCond = 12220.6 (normalized)
ERROR: design is ill-conditioned
>> --
ERROR: fast_selxavg3() failed\n

details:
I do not definite any contrasts, as I'm only running this command to
generate trial specific betas for a separate analysis.  Each trial lasts 18
seconds, followed by 4 seconds of fixation.  Here is what part of a
paradigm file looks like (the paradigm files are identical for all
subjects):

4 1 18 1
22 0 4 1
26 2 18 1
44 0 4 1
48 3 18 1
66 0 4 1
70 4 18 1
88 0 4 1
92 5 18 1
110 0 4 1
114 6 18 1
132 0 4 1
136 7 18 1
154 0 4 1

here are the analysis.cfg and .info files:
analysis analysis_name
TR 2
fsdbold
funcstem   fmcsm4
tpexclude
parnameFIR_logit.par
designtype event-related
nconditions 96

-timewindow 20
-prestim 2
-acfbins 10
-fix-acf
-noautostimdur
-no-fsv3-st2fir
-no-fsv3-whiten
-polyfit 2
-TER 2
-nskip 0
-fwhm 0
-extreg mcextreg
-nextreg 3
-rescale 1000

the command which throws the error:
selxavg3-sess  -analysis analysis_name -s subject_name

The strange part for me is that this only seems to be a problem with a
couple subjects, despite the fact all the paradigm files are identical.
 After looking through the mailing archive, I tried playing around with the
prestim window, but even it if is = 0, there is 1 subject that exits with
an error when I run selxavg3-sess.  Do you know what might be going on?

Any guidance would be appreciated.

Thanks,
Sam
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess ERROR: analysis XYZ does not exist

[Michael Bannert]

Hi Doug,

Yes, that was the problem. I think Freesurfer expects that you start Matlab by 
typing "matlab" in the terminal (as opposed to "matlab2010a" which is what I 
usually do). So I created a new symbolic that takes care of that.

Now I got the error message "ERROR: TR mismatch between analysis and data"
I'm now re-running the preprocessing as suggested here 
(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-March/023012.html)

Fingers crossed! :)

Thanks for your help!
Michael

On May 25, 2012, at 3:44 PM, Douglas Greve wrote:

> yes, B is correct. The error says that it cannot find matlab. Is it in your 
> path?
> doug
> 
> On 5/25/12 9:16 AM, Michael Bannert wrote:
>> 
>> Hi Doug,
>> 
>> Thanks for your help! No, the current directory is the "Project" directory 
>> (refering to naming conventions in 
>> http://www.freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastDirStruct). It is 
>> identical to $FUNCTIONALS_DIR.
>> 
>> The rtopy.self.lh folder is in the "Sess0x" directory and contains only the 
>> file called "analysis.info".
>> 
>> I actually tried two different commands:
>> 
>> A: selxavg-sess -s ex01s05 -a rtopy.self.lh
>> B: selxavg3-sess -s ex01s05 -a rtopy.self.lh
>> 
>> I suspect that version B is the correct one. I accidentally posted the wrong 
>> code in the previous email. Sorry! I tried both with the same negative 
>> outcome.
>> 
>> I now moved the rtopy.self.lh folder into the "Project" folder and tried 
>> running the command again. (I think I have to run this command from 
>> "Project" because otherwise Freesurfer tells me that it can't find the 
>> session.) That gave me the following output:
>> 
>> >> !selxavg3-sess -s ex01s05 -a rtopy.self.lh
>> Surface data self lh
>> --
>> selxavg3-sess logfile is 
>> /Users/mbannert/experiments/freesurfer/mc_retinotopy/log/selxavg3-sess-bold-rtopy.self.lh-120524182304.log
>> --
>> ---
>> /Users/mbannert/experiments/freesurfer/mc_retinotopy/ex01s05 
>> Thu May 24 18:23:04 CEST 2012
>> anadir = 
>> /Users/mbannert/experiments/freesurfer/mc_retinotopy/ex01s05/bold/rtopy.self.lh
>> DoGLMFit = 1
>> DoContrasts = 1
>> UpdateNeeded = 1
>> --
>> --- matlab output 
>> matlab: Command not found.
>> cat: stdout: Broken pipe
>> --
>> ERROR: fast_selxavg3() failed\n
>> 
>> Btw: I'm running all these commands from inside a Matlab shell. I hope this 
>> isn't a problem.
>> 
>> Thanks for your support!
>> 
>> Best regards,
>> Michael
>> 
>> 
>> 
>> On May 24, 2012, at 4:33 PM, Douglas N Greve wrote:
>> 
>>> Hi Michael, is rtopy.self.lh in the current directory (the one that you 
>>> are running selxavg from)?
>>> doug
>>> 
>>> On 05/24/2012 07:57 AM, Michael Bannert wrote:
 Hi all,
 
 I'm trying to analyze a retinotopic mapping dataset using FsFast but 
 some things don't seem to work the way they should.
 
 When running "selxavg-sess -s ex01s05 -a rtopy.self.lh", I get the 
 following error:
 
 "ERROR: analysis rtopy.self.lh does not exist, see mkanalysis-sess"
 
 However, I checked that rtopy.self.lh does in fact exist. I also made 
 sure that the folder contains the file analysis.info 
 . Why do I still get this error message?
 
 Here is the contents of analysis.info :
 
 # FSBUILD freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
 # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.1 2011/03/22 16:58:57 greve 
 Exp $
 # MKACMD 
 /Users/mbannert/../../Applications/freesurfer/fsfast/bin/mkanalysis-sess 
 -a rtopy.self.lh -surface self lh -TR 3.12 -retinotopy 49.92 -paradigm 
 rtopy.par -funcstem fmcsurfsm5 -fsd bold -nskip 0 -force
 # DATE Thu May 24 11:50:39 CEST 2012
 
 analysis rtopy.self.lh
 mcstem fmcpr
 funcstem fmcsurfsm5
 fsd bold
 TR 3.12
 RegDOF 6
 RawSpace surface self lh
 mask brain
 RawFWHM 0
 RawSTC none
 UseB0DC 0
 inorm 100
 acfbins 0
 fixacf  1
 acffwhm 20
 acfsvd  0
 designtype retinotopy
 nskip 0
 polyfit 2
 HPFCutoffHz 0
 HeteroGCor 0
 parname rtopy.par
 period 49.92
 
 Any ideas? Thanks for your help!
 Michael
 
 --
 Michael Bannert, Dipl.-Psych.
 Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of 
 Tübingen & BCCN Tübingen
 Otfried-Müller-Str. 25, 72076 Tübingen, Germany
 Phone: +49 - (0)7071 / 29 - 89031
 
 
 
 
 
 ___
 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
>>> gr...@nmr

Re: [Freesurfer] selxavg3-sess ERROR: analysis XYZ does not exist

[Douglas Greve]

yes, B is correct. The error says that it cannot find matlab. Is it in 
your path?

doug

On 5/25/12 9:16 AM, Michael Bannert wrote:

Hi Doug,

Thanks for your help! No, the current directory is the "Project" 
directory (refering to naming conventions in 
http://www.freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastDirStruct). 
It is identical to $FUNCTIONALS_DIR.


The rtopy.self.lh folder is in the "Sess0x" directory and contains 
only the file called "analysis.info ".


I actually tried two different commands:

A: selxavg-sess -s ex01s05 -a rtopy.self.lh
B: selxavg3-sess -s ex01s05 -a rtopy.self.lh

I suspect that version B is the correct one. I accidentally posted the 
wrong code in the previous email. Sorry! I tried both with the same 
negative outcome.


I now moved the rtopy.self.lh folder into the "Project" folder and 
tried running the command again. (I think I have to run this command 
from "Project" because otherwise Freesurfer tells me that it can't 
find the session.) That gave me the following output:


>> !selxavg3-sess -s ex01s05 -a rtopy.self.lh
Surface data self lh
--
selxavg3-sess logfile is 
/Users/mbannert/experiments/freesurfer/mc_retinotopy/log/selxavg3-sess-bold-rtopy.self.lh-120524182304.log

--
---
/Users/mbannert/experiments/freesurfer/mc_retinotopy/ex01s05
Thu May 24 18:23:04 CEST 2012
anadir = 
/Users/mbannert/experiments/freesurfer/mc_retinotopy/ex01s05/bold/rtopy.self.lh

DoGLMFit = 1
DoContrasts = 1
UpdateNeeded = 1
--
--- matlab output 
matlab: Command not found.
cat: stdout: Broken pipe
--
ERROR: fast_selxavg3() failed\n

Btw: I'm running all these commands from inside a Matlab shell. I hope 
this isn't a problem.


Thanks for your support!

Best regards,
Michael



On May 24, 2012, at 4:33 PM, Douglas N Greve wrote:


Hi Michael, is rtopy.self.lh in the current directory (the one that you
are running selxavg from)?
doug

On 05/24/2012 07:57 AM, Michael Bannert wrote:

Hi all,

I'm trying to analyze a retinotopic mapping dataset using FsFast but
some things don't seem to work the way they should.

When running "selxavg-sess -s ex01s05 -a rtopy.self.lh", I get the
following error:

"ERROR: analysis rtopy.self.lh does not exist, see mkanalysis-sess"

However, I checked that rtopy.self.lh does in fact exist. I also made
sure that the folder contains the file analysis.info 


. Why do I still get this error message?

Here is the contents of analysis.info  
:


# FSBUILD freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
# MKAVERSION $Id: mkanalysis-sess,v 1.64.2.1 2011/03/22 16:58:57 greve
Exp $
# MKACMD
/Users/mbannert/../../Applications/freesurfer/fsfast/bin/mkanalysis-sess 


-a rtopy.self.lh -surface self lh -TR 3.12 -retinotopy 49.92 -paradigm
rtopy.par -funcstem fmcsurfsm5 -fsd bold -nskip 0 -force
# DATE Thu May 24 11:50:39 CEST 2012

analysis rtopy.self.lh
mcstem fmcpr
funcstem fmcsurfsm5
fsd bold
TR 3.12
RegDOF 6
RawSpace surface self lh
mask brain
RawFWHM 0
RawSTC none
UseB0DC 0
inorm 100
acfbins 0
fixacf  1
acffwhm 20
acfsvd  0
designtype retinotopy
nskip 0
polyfit 2
HPFCutoffHz 0
HeteroGCor 0
parname rtopy.par
period 49.92

Any ideas? Thanks for your help!
Michael

--
Michael Bannert, Dipl.-Psych.
Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of
Tübingen & BCCN Tübingen
Otfried-Müller-Str. 25, 72076 Tübingen, Germany
Phone: +49 - (0)7071 / 29 - 89031





___
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
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to 
whom it is
addressed. If you believe this e-mail was sent to you in error and 
the e-mail
contains patient information, please contact the Partners Compliance 
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to 
you in error
but does not contain patient information, please contact the sender 
and properly

dispose of the e-mail.




--
Michael Bannert, Dipl.-Psych.
Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of 
Tübingen & BCCN Tübingen

Otfried-Müller-Str. 25, 72076 Tübingen, Germany
Phon

Re: [Freesurfer] selxavg3-sess ERROR: analysis XYZ does not exist

[Michael Bannert]

Hi Doug,

Thanks for your help! No, the current directory is the "Project" directory 
(refering to naming conventions in 
http://www.freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastDirStruct). It is 
identical to $FUNCTIONALS_DIR.

The rtopy.self.lh folder is in the "Sess0x" directory and contains only the 
file called "analysis.info".

I actually tried two different commands:

A: selxavg-sess -s ex01s05 -a rtopy.self.lh
B: selxavg3-sess -s ex01s05 -a rtopy.self.lh

I suspect that version B is the correct one. I accidentally posted the wrong 
code in the previous email. Sorry! I tried both with the same negative outcome.

I now moved the rtopy.self.lh folder into the "Project" folder and tried 
running the command again. (I think I have to run this command from "Project" 
because otherwise Freesurfer tells me that it can't find the session.) That 
gave me the following output:

>> !selxavg3-sess -s ex01s05 -a rtopy.self.lh
Surface data self lh
--
selxavg3-sess logfile is 
/Users/mbannert/experiments/freesurfer/mc_retinotopy/log/selxavg3-sess-bold-rtopy.self.lh-120524182304.log
--
---
/Users/mbannert/experiments/freesurfer/mc_retinotopy/ex01s05 
Thu May 24 18:23:04 CEST 2012
anadir = 
/Users/mbannert/experiments/freesurfer/mc_retinotopy/ex01s05/bold/rtopy.self.lh
DoGLMFit = 1
DoContrasts = 1
UpdateNeeded = 1
--
--- matlab output 
matlab: Command not found.
cat: stdout: Broken pipe
--
ERROR: fast_selxavg3() failed\n

Btw: I'm running all these commands from inside a Matlab shell. I hope this 
isn't a problem.

Thanks for your support!

Best regards,
Michael



On May 24, 2012, at 4:33 PM, Douglas N Greve wrote:

> Hi Michael, is rtopy.self.lh in the current directory (the one that you 
> are running selxavg from)?
> doug
> 
> On 05/24/2012 07:57 AM, Michael Bannert wrote:
>> Hi all,
>> 
>> I'm trying to analyze a retinotopic mapping dataset using FsFast but 
>> some things don't seem to work the way they should.
>> 
>> When running "selxavg-sess -s ex01s05 -a rtopy.self.lh", I get the 
>> following error:
>> 
>> "ERROR: analysis rtopy.self.lh does not exist, see mkanalysis-sess"
>> 
>> However, I checked that rtopy.self.lh does in fact exist. I also made 
>> sure that the folder contains the file analysis.info 
>> . Why do I still get this error message?
>> 
>> Here is the contents of analysis.info :
>> 
>> # FSBUILD freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
>> # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.1 2011/03/22 16:58:57 greve 
>> Exp $
>> # MKACMD 
>> /Users/mbannert/../../Applications/freesurfer/fsfast/bin/mkanalysis-sess 
>> -a rtopy.self.lh -surface self lh -TR 3.12 -retinotopy 49.92 -paradigm 
>> rtopy.par -funcstem fmcsurfsm5 -fsd bold -nskip 0 -force
>> # DATE Thu May 24 11:50:39 CEST 2012
>> 
>> analysis rtopy.self.lh
>> mcstem fmcpr
>> funcstem fmcsurfsm5
>> fsd bold
>> TR 3.12
>> RegDOF 6
>> RawSpace surface self lh
>> mask brain
>> RawFWHM 0
>> RawSTC none
>> UseB0DC 0
>> inorm 100
>> acfbins 0
>> fixacf  1
>> acffwhm 20
>> acfsvd  0
>> designtype retinotopy
>> nskip 0
>> polyfit 2
>> HPFCutoffHz 0
>> HeteroGCor 0
>> parname rtopy.par
>> period 49.92
>> 
>> Any ideas? Thanks for your help!
>> Michael
>> 
>> --
>> Michael Bannert, Dipl.-Psych.
>> Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of 
>> Tübingen & BCCN Tübingen
>> Otfried-Müller-Str. 25, 72076 Tübingen, Germany
>> Phone: +49 - (0)7071 / 29 - 89031
>> 
>> 
>> 
>> 
>> 
>> ___
>> 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
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
> 


--
Michael Bannert, Dipl.-Psych.
Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen 
& BCCN Tübingen
Otfried-Müller-Str. 25, 72076 Tübingen, Germany
Phone: +49 - (0)7071 / 29 - 8

Re: [Freesurfer] selxavg3-sess ERROR: analysis XYZ does not exist

[Douglas N Greve]

Hi Michael, is rtopy.self.lh in the current directory (the one that you 
are running selxavg from)?
doug

On 05/24/2012 07:57 AM, Michael Bannert wrote:
> Hi all,
>
> I'm trying to analyze a retinotopic mapping dataset using FsFast but 
> some things don't seem to work the way they should.
>
> When running "selxavg-sess -s ex01s05 -a rtopy.self.lh", I get the 
> following error:
>
> "ERROR: analysis rtopy.self.lh does not exist, see mkanalysis-sess"
>
> However, I checked that rtopy.self.lh does in fact exist. I also made 
> sure that the folder contains the file analysis.info 
> . Why do I still get this error message?
>
> Here is the contents of analysis.info :
>
> # FSBUILD freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
> # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.1 2011/03/22 16:58:57 greve 
> Exp $
> # MKACMD 
> /Users/mbannert/../../Applications/freesurfer/fsfast/bin/mkanalysis-sess 
> -a rtopy.self.lh -surface self lh -TR 3.12 -retinotopy 49.92 -paradigm 
> rtopy.par -funcstem fmcsurfsm5 -fsd bold -nskip 0 -force
> # DATE Thu May 24 11:50:39 CEST 2012
>
> analysis rtopy.self.lh
> mcstem fmcpr
> funcstem fmcsurfsm5
> fsd bold
> TR 3.12
> RegDOF 6
> RawSpace surface self lh
> mask brain
> RawFWHM 0
> RawSTC none
> UseB0DC 0
> inorm 100
> acfbins 0
> fixacf  1
> acffwhm 20
> acfsvd  0
> designtype retinotopy
> nskip 0
> polyfit 2
> HPFCutoffHz 0
> HeteroGCor 0
> parname rtopy.par
> period 49.92
>
> Any ideas? Thanks for your help!
> Michael
>
> --
> Michael Bannert, Dipl.-Psych.
> Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of 
> Tübingen & BCCN Tübingen
> Otfried-Müller-Str. 25, 72076 Tübingen, Germany
> Phone: +49 - (0)7071 / 29 - 89031
>
>
>
>
>
> ___
> 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
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] selxavg3-sess ERROR: analysis XYZ does not exist

[Michael Bannert]

Hi all,

I'm trying to analyze a retinotopic mapping dataset using FsFast but some 
things don't seem to work the way they should.

When running "selxavg-sess -s ex01s05 -a rtopy.self.lh", I get the following 
error:

"ERROR: analysis rtopy.self.lh does not exist, see mkanalysis-sess"

However, I checked that rtopy.self.lh does in fact exist. I also made sure that 
the folder contains the file analysis.info. Why do I still get this error 
message?

Here is the contents of analysis.info:

# FSBUILD freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
# MKAVERSION $Id: mkanalysis-sess,v 1.64.2.1 2011/03/22 16:58:57 greve Exp $
# MKACMD 
/Users/mbannert/../../Applications/freesurfer/fsfast/bin/mkanalysis-sess -a 
rtopy.self.lh -surface self lh -TR 3.12 -retinotopy 49.92 -paradigm rtopy.par 
-funcstem fmcsurfsm5 -fsd bold -nskip 0 -force
# DATE Thu May 24 11:50:39 CEST 2012

analysis rtopy.self.lh
mcstem fmcpr
funcstem fmcsurfsm5
fsd bold
TR 3.12
RegDOF 6
RawSpace surface self lh
mask brain
RawFWHM 0
RawSTC none
UseB0DC 0
inorm 100
acfbins 0
fixacf  1
acffwhm 20
acfsvd  0
designtype retinotopy
nskip 0
polyfit 2
HPFCutoffHz 0
HeteroGCor 0
parname rtopy.par
period 49.92

Any ideas? Thanks for your help!
Michael

--
Michael Bannert, Dipl.-Psych.
Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen 
& BCCN Tübingen
Otfried-Müller-Str. 25, 72076 Tübingen, Germany
Phone: +49 - (0)7071 / 29 - 89031



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[Oya, Hiroyuki (UI Health Care)]

I have not set path for afni.
After setting the correct path, that runs fine.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Oya, Hiroyuki (UI 
Health Care)
Sent: 30 March 2012 07:53
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] selxavg3-sess error

Hi

I got an error while running selxavg3-sess, "cannot find AFNI command 
3dvolreg".(In ubuntu v11.).
Any help would be appreciated.

Hiroyuki





Notice: This UI Health Care e-mail (including attachments) is covered by the 
Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and 
may be legally privileged.  If you are not the intended recipient, you are 
hereby notified that any retention, dissemination, distribution, or copying of 
this communication is strictly prohibited.  Please reply to the sender that you 
have received the message in error, then delete it.  Thank you.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] selxavg3-sess error

[Oya, Hiroyuki (UI Health Care)]

Hi

I got an error while running selxavg3-sess, "cannot find AFNI command 
3dvolreg".(In ubuntu v11.).
Any help would be appreciated.

Hiroyuki





Notice: This UI Health Care e-mail (including attachments) is covered by the 
Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and 
may be legally privileged.  If you are not the intended recipient, you are 
hereby notified that any retention, dissemination, distribution, or copying of 
this communication is strictly prohibited.  Please reply to the sender that you 
have received the message in error, then delete it.  Thank you.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error

[Douglas N Greve]

It does not look too bad to me. That is a significance map and it is 
covering most of the occipital region. If you want to see the angle,  
add -angle to your tksurfer-sess command.
doug

Daniel Cole wrote:
> I was mistaken, I only have *Polar* (Rotating wedge) not Eccentricity 
> stimuli.  
> After running selxavg3-sess I view my results with "tksurfer-sess 
> -analysis rtopy.self.lh -sf sessid".
> The retinotopic data shows up on the surface but looks incorrect... 
>  I'm new to freesurfer so I'm not sure if it's simply the viewing 
> options causing the graphics to look incorrect or if the analysis 
> failed.  Does the attached picture look correct to you?
>
> My apologies for the elementary questions.  Thanks again for all of 
> your help,
> Daniel
>
> On Thu, Feb 16, 2012 at 2:16 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> It can't create a fieldsign map from just the eccentricity.
> doug
>
> Daniel Cole wrote:
>
> Hello,
> Thanks for your reply.
> You are right, I only have eccentricity.  I reran all the
> steps and tried your suggestion which worked!  
> However, now I'm having a different problem.
> After running "mkanalysis-sess -analysis rtopy.self.lh
> -surface self lh -TR 1.2 -abblocked 38.4 -fsd bold -fwhm 5"
> followed by "selxavg3-sess -analysis rtopy.self.lh -sf
> sessid",  I try running "fieldsign-sess -a rtopy.self.lh
> -sphere -sf sessid",
>
> which gives me the error "ERROR: rtopy.self.lh is not
> retinotopy".  Will changing the analysis name for
> mkanalysis-sess fix this?
>
> Many thanks,
> Daniel
>
> On Thu, Feb 16, 2012 at 11:16 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
>Hi Daniel, sorry for the delay. Is it the case that you
> only have
>eccentricity? The retinotopy tools are designed to work
> with both
>eccen and polar. You can still do the same analysis, just use
>-abblocked instead of -retinotopy.
>doug
>
>Daniel Cole wrote:
>
>Hello Doug,
>I don't mean to rush your response, but, I was wondering if
>you found any reason for why I'm getting this error?  I've
>been busy doing other analysis but I'm going to be
> returning
>to this data today and was hoping for your insight.
>
>Thanks again for taking the time,
>Daniel
>
>On Fri, Feb 10, 2012 at 11:48 AM, Daniel Cole
>   edu >
> . edu
>
> 
>   Hi Doug,
>   Thanks for the response!
>   Here are the files you requested.
>
>   Daniel
>
>
>   On Fri, Feb 10, 2012 at 11:44 AM, Douglas N Greve
>
> >
> . edu
>
> 
>   Hi Daniel, can you send me the analysis.info
> 
>
>    and Xtmp.mat files?
>
>   doug
>
>   Daniel Cole wrote:
>
>
>   Hello Freesurfers,
>
>   I think my last email failed to send so here
> it is
>again -
>
>
>   I'm running into problems using fs-fast for
> a polar
>only,
>   retinotopic analysis.
>
>
>   The error message I get is:
>
>
>   *
>
>
>   Retinotopy dcole$ selxavg3-sess -analysis
> rtopy.self.lh
>   -sf sessid
>
>   Surface data self lh
>
>   --
>   -- --
>
>   selxavg3-sess logfile is
> /rcbiUsers/dcole/Retinotopy/
>   log/selxavg3-sess-bold-rtopy.
> self.lh-120209144554.log
>
>   --
>   

Re: [Freesurfer] selxavg3-sess error

[Douglas N Greve]

Hi Daniel, can you send me the analysis.info and Xtmp.mat files?
doug

Daniel Cole wrote:
>
> Hello Freesurfers,
>
> I think my last email failed to send so here it is again -
>
>
> I'm running into problems using fs-fast for a polar only, retinotopic 
> analysis.
>
>
> The error message I get is:
>
>
> *
>
>
> Retinotopy dcole$ selxavg3-sess -analysis rtopy.self.lh -sf sessid
>
> Surface data self lh
>
> --
>
> selxavg3-sess logfile is 
> /rcbiUsers/dcole/Retinotopy/log/selxavg3-sess-bold-rtopy.self.lh-120209144554.log
>
> --
>
> preproc-sess -s SUB01 -d /rcbiUsers/dcole/Retinotopy -a rtopy.self.lh 
> -nolog
>
> --
>
> preproc-sess logfile is /dev/null
>
> --
>
> $Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $
>
> dcole
>
> setenv FREESURFER_HOME /Volumes/RCBI/freesurfer
>
> setenv SUBJECTS_DIR /Volumes/rcbiUsers/dcole/Retinotopy/Subjects/test
>
> Darwin commissure.local 11.2.0 Darwin Kernel Version 11.2.0: Tue Aug 
>  9 20:54:00 PDT 2011; root:xnu-1699.24.8~1/RELEASE_X86_64 x86_64
>
> /rcbiUsers/dcole/Retinotopy
>
> /Volumes/RCBI/freesurfer/fsfast/bin/preproc-sess
>
> -s SUB01 -d /rcbiUsers/dcole/Retinotopy -a rtopy.self.lh -nolog
>
> Thu Feb  9 14:45:54 EST 2012
>
> instem   f 
>
> mc   1 f fmcpr 
>
> stc  0 fmcpr
>
> sm   0   
>
> mask 1   brain
>
> SUB01 Template -
>
> mktemplate-sess -s SUB01 -d /rcbiUsers/dcole/Retinotopy -fsd bold 
> -nolog -update
>
>  
>
> Session: /rcbiUsers/dcole/Retinotopy/SUB01 
>
> Thu Feb  9 14:45:54 EST 2012
>
> Detected input format at nii
>
> SUB01 Update not needed
>
>   Run: 001 
>
>   Thu Feb  9 14:45:54 EST 2012
>
>   SUB01 001 Update not needed
>
>   Run: 002 
>
>   Thu Feb  9 14:45:54 EST 2012
>
>   SUB01 002 Update not needed
>
>   Run: 003 
>
>   Thu Feb  9 14:45:55 EST 2012
>
>   SUB01 003 Update not needed
>
>   Run: 004 
>
>   Thu Feb  9 14:45:55 EST 2012
>
>   SUB01 004 Update not needed
>
>   Run: 005 
>
>   Thu Feb  9 14:45:55 EST 2012
>
>   SUB01 005 Update not needed
>
> Thu Feb  9 14:45:55 EST 2012
>
> mktemplate-sess completed 
>
> SUB01 Mask 
>
> mkbrainmask-sess -maskstem brain -fsd bold -s SUB01 -d 
> /rcbiUsers/dcole/Retinotopy -nolog -update
>
> 
>
> /rcbiUsers/dcole/Retinotopy/SUB01 
>
> Thu Feb  9 14:45:55 EST 2012
>
> SUB01 Update not needed for session-level mask
>
> SUB01 Update not needed for run 001 mask
>
> SUB01 Update not needed for run 001 meanval
>
> SUB01 Update not needed for run 002 mask
>
> SUB01 Update not needed for run 002 meanval
>
> SUB01 Update not needed for run 003 mask
>
> SUB01 Update not needed for run 003 meanval
>
> SUB01 Update not needed for run 004 mask
>
> SUB01 Update not needed for run 004 meanval
>
> SUB01 Update not needed for run 005 mask
>
> SUB01 Update not needed for run 005 meanval
>
> Thu Feb  9 14:45:55 EST 2012
>
> mkbrainmask-sess done
>
> SUB01 Registration -
>
> register-sess -s SUB01 -d /rcbiUsers/dcole/Retinotopy -fsd bold -dof 6 
> -per-run -nolog -update
>
> --
>
> register-sess logfile is /dev/null
>
> --
>
> Thu Feb  9 14:45:55 EST 2012
>
>
> setenv SUBJECTS_DIR /Volumes/rcbiUsers/dcole/Retinotopy/Subjects/test
>
> cd /rcbiUsers/dcole/Retinotopy
>
> /Volumes/RCBI/freesurfer/fsfast/bin/register-sess -s SUB01 -d 
> /rcbiUsers/dcole/Retinotopy -fsd bold -dof 6 -per-run -nolog -update
>
>
> freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
>
> Darwin commissure.local 11.2.0 Darwin Kernel Version 11.2.0: Tue Aug 
>  9 20:54:00 PDT 2011; root:xnu-1699.24.8~1/RELEASE_X86_64 x86_64
>
>  
>
> Session: /rcbiUsers/dcole/Retinotopy/SUB01 
>
> Thu Feb  9 14:45:55 EST 2012
>
>   Run: 001 
>
> Thu Feb  9 14:45:55 EST 2012
>
> Update not needed
>
>   Run: 002 
>
> Thu Feb  9 14:45:55 EST 2012
>
> Update not needed
>
>   Run: 003 
>
> Thu Feb  9 14:45:55 EST 2012
>
> Update not needed
>
>   Run: 004 
>
> Thu Feb  9 14:45:55 EST 2012
>
> Update not needed
>
>   Run: 005 
>
> Thu Feb  9 14:45:55 EST 2012
>
> Update not needed
>
> Thu Feb  9 14:45:55 EST 2012
>
> register-sess completed 
>
> SUB01 MC -
>
> mc-sess -fstem f -fmcstem fmcpr -s SUB01 -d 
> /rcbiUsers/dcole/Retinotopy -fsd bold -per-run -nolog -update
>
> Logfile is /dev/null
>
> ---
>
> /rcbiUsers/dcole/Retinotopy/SUB01 
>
> RunList: 001 002 003 004 005
>
> SUB01 001 Update not n

Re: [Freesurfer] Selxavg3-sess error

[Douglas N Greve]

Hi Reagan, I was not able to recreate this error. Can you send me the 
full terminal output?
thanks
doug

Wetherill, Reagan wrote:
> Hello FreeSurfers!
>
> I am new to FSFast and am attempting to run selxavg3-sess, but I keep 
> receiving the following errors:
>
> ERROR: model ??? In an assignment  A(:) = B, the number of elements in A and B
> must be the same.
>
> Error in ==> fast_ldanaflac at 391
>   flac.ev(nthev) = flac_ev_parse(tline);
>
> Error in ==> fast_selxavg3 at 45
>   flac0 = fast_ldanaflac(analysis);
>
>   
>>> --
>>>   
> ERROR: fast_selxavg3() failed\n
>
> Here are my commands for mkanalysis and mkcontrast
>
> # FSBUILD freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
> # MKAVERSION $Id: mkanalysis-sess,v 1.49.2.3 2010/07/30 16:51:11 greve Exp $
> # MKACMD /usr/local/freesurfer5/fsfast/bin/mkanalysis-sess -a try -mni305 2 
> -fwhm 6 -event-related -p vwm.par -TR 2 -nc 3 -spmhrf 0 -refeventdur 4 
> -polyfit 2 -hpf .08 -nskip 4 -nuisreg wm.dat 3 -nuisreg vcsfreg.dat 3 
> -nuisreg global.waveform.dat 1 -mcextreg -fsd bold
> # DATE Tue Apr 19 12:17:42 PDT 2011
>
> analysis try
> mcstem fmcpr
> fsd bold
> TR 2
> RegDOF 6
> RawSpace volume mni305 2
> mask brain
> RawFWHM 6
> RawSTC none
> inorm 100
> acfbins 30
> fixacf  1
> acffwhm 20
> acfsvd  0
> designtype event-related
> nskip 4
> polyfit 2
> HPFCutoffHz .08
> nconditions 3
> parname vwm.par
> RefEventDur 4
> timewindow 40.00
> prestim 0
> TER 0.05
> spmhrf 0
> stimulusdelay 0
> Condition 1 Condition01
> Condition 2 Condition02
> Condition 3 Condition03
> nuisreg wm.dat 3
> nuisreg vcsfreg.dat 3
> nuisreg global.waveform.dat 1
> nuisreg mcprextreg 3
>
> mkcontrast-sess -analysis try -contrast six-v-two -a 3 -c 1
>
> selxavg3-sess -sf sess_test -analysis try
>
> THANKS IN ADVANCE!!
> Reagan
>
>
>
> Reagan Wetherill, Ph.D.
> Postdoctoral Fellow
> Department of Psychiatry
> University of California, San Diego
> 8950 Villa La Jolla Drive. Suite C213
> San Diego, CA 92037-0862
> Phone: 858-822-3400
> Fax: 858-822-3933 
> ___
> 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
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Selxavg3-sess error

[Wetherill, Reagan]

Hello FreeSurfers!

I am new to FSFast and am attempting to run selxavg3-sess, but I keep receiving 
the following errors:

ERROR: model ??? In an assignment  A(:) = B, the number of elements in A and B
must be the same.

Error in ==> fast_ldanaflac at 391
  flac.ev(nthev) = flac_ev_parse(tline);

Error in ==> fast_selxavg3 at 45
  flac0 = fast_ldanaflac(analysis);

>> --
ERROR: fast_selxavg3() failed\n

Here are my commands for mkanalysis and mkcontrast

# FSBUILD freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
# MKAVERSION $Id: mkanalysis-sess,v 1.49.2.3 2010/07/30 16:51:11 greve Exp $
# MKACMD /usr/local/freesurfer5/fsfast/bin/mkanalysis-sess -a try -mni305 2 
-fwhm 6 -event-related -p vwm.par -TR 2 -nc 3 -spmhrf 0 -refeventdur 4 -polyfit 
2 -hpf .08 -nskip 4 -nuisreg wm.dat 3 -nuisreg vcsfreg.dat 3 -nuisreg 
global.waveform.dat 1 -mcextreg -fsd bold
# DATE Tue Apr 19 12:17:42 PDT 2011

analysis try
mcstem fmcpr
fsd bold
TR 2
RegDOF 6
RawSpace volume mni305 2
mask brain
RawFWHM 6
RawSTC none
inorm 100
acfbins 30
fixacf  1
acffwhm 20
acfsvd  0
designtype event-related
nskip 4
polyfit 2
HPFCutoffHz .08
nconditions 3
parname vwm.par
RefEventDur 4
timewindow 40.00
prestim 0
TER 0.05
spmhrf 0
stimulusdelay 0
Condition 1 Condition01
Condition 2 Condition02
Condition 3 Condition03
nuisreg wm.dat 3
nuisreg vcsfreg.dat 3
nuisreg global.waveform.dat 1
nuisreg mcprextreg 3

mkcontrast-sess -analysis try -contrast six-v-two -a 3 -c 1

selxavg3-sess -sf sess_test -analysis try

THANKS IN ADVANCE!!
Reagan



Reagan Wetherill, Ph.D.
Postdoctoral Fellow
Department of Psychiatry
University of California, San Diego
8950 Villa La Jolla Drive. Suite C213
San Diego, CA 92037-0862
Phone: 858-822-3400
Fax: 858-822-3933 
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error "design is ill-conditioned"

[Douglas N Greve]

try it with a prestim of 0

Ben Letham wrote:
> Yes, the paradigm came from optseq2 with a PSD window 0 19.2 0.4.
>
> Looking more into the details, it seems that the design is pretty
> ill-conditioned, cond(Xn'*Xn) is 6.2e5, and the cut-off in
> fast_selxavg3.m is 1e4.
>
> Like I said, the design came from optseq2 and the cost/efficiency is
> the same as other paradigms that have worked well (albeit with
> TER=TR). Perhaps this one was pushing it just a little too much?.
>
> Thanks!
> Ben.
>
> 2010/4/15 Douglas N Greve :
>   
>> Did you optimize the stimulus schedule with the idea that you would do
>> sub-TR FIR estimation? Eg, you would have had to have run optseq2 with this
>> in mind. If not, then you probably cannot do an FIR analysis. Instead,
>> assume a shape (eg, -gammafit 2.25 1.25)
>>
>> doug
>>
>> Ben Letham wrote:
>> 
>>> Hello,
>>>
>>> I'm trying to run selxavg3-sess for an analysis with TER < TR, and it
>>> errors with "design is ill-conditioned". I searched the mailing list
>>> archive, and the only past problem of this sort that I found was
>>> associated with a faulty tpef file, which I am not using.
>>>
>>> The details: There is only one run. TR is 1.2s, and stimuli were
>>> presented at intervals of 1/3 TR (0.4s) (the desired TER). The
>>> paradigm file reflects this, it is of the form:
>>>
>>> 0 0
>>> 0.4 1
>>> 0.8 0
>>> 1.2 2
>>> 1.6 1
>>> 2 0
>>>
>>> I loaded it into matlab and verified that the time points all have a
>>> difference of 0.4s.
>>>
>>> The analysis is,
>>> mkanalysis-sess -analysis analysis_name -TR 1.2 -TER 0.4 -paradigm
>>> 03TR.par -designtype event-related -nconditions 2 -timewindow 19.2
>>> -prestim 2.4 -mcextreg -funcstem fmcstcsm6 -polyfit 2 -runlistfile
>>> runlist_03TR -noautostimdur -force
>>>
>>> I define two contrasts,
>>>
>>> mkcontrast_sess -analysis analysis_name -rmprestim -contrast AV-REST -a 1
>>> -c 0
>>> mkcontrast_sess -analysis analysis_name -rmprestim -contrast AVT-REST -a 2
>>> -c 0
>>>
>>> And then selxavg3-sess,
>>>
>>> selxavg3-sess -analysis analysis_name -sf subjectname -df sessdir
>>> -overwrite
>>>
>>> And this errors. Like I said, the only thing I found in the mailing
>>> list was a problem with tpef, and so I left it out altogether (as
>>> above), and the problem persists. If I change TER to equal TR (1.2),
>>> then it works. So the problem has something to do with TER being less
>>> than TR. Perhaps something in the par file then? I checked it in
>>> matlab, and diff(par(:,1)) = 0.4 for all of the events.
>>>
>>> Any thoughts would be very appreciated!
>>> Ben.
>>> ___
>>> 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
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358 Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>> 
>
>
>   

-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] selxavg3-sess error "design is ill-conditioned"

[Ben Letham]

Yes, the paradigm came from optseq2 with a PSD window 0 19.2 0.4.

Looking more into the details, it seems that the design is pretty
ill-conditioned, cond(Xn'*Xn) is 6.2e5, and the cut-off in
fast_selxavg3.m is 1e4.

Like I said, the design came from optseq2 and the cost/efficiency is
the same as other paradigms that have worked well (albeit with
TER=TR). Perhaps this one was pushing it just a little too much?.

Thanks!
Ben.

2010/4/15 Douglas N Greve :
> Did you optimize the stimulus schedule with the idea that you would do
> sub-TR FIR estimation? Eg, you would have had to have run optseq2 with this
> in mind. If not, then you probably cannot do an FIR analysis. Instead,
> assume a shape (eg, -gammafit 2.25 1.25)
>
> doug
>
> Ben Letham wrote:
>>
>> Hello,
>>
>> I'm trying to run selxavg3-sess for an analysis with TER < TR, and it
>> errors with "design is ill-conditioned". I searched the mailing list
>> archive, and the only past problem of this sort that I found was
>> associated with a faulty tpef file, which I am not using.
>>
>> The details: There is only one run. TR is 1.2s, and stimuli were
>> presented at intervals of 1/3 TR (0.4s) (the desired TER). The
>> paradigm file reflects this, it is of the form:
>>
>> 0 0
>> 0.4 1
>> 0.8 0
>> 1.2 2
>> 1.6 1
>> 2 0
>>
>> I loaded it into matlab and verified that the time points all have a
>> difference of 0.4s.
>>
>> The analysis is,
>> mkanalysis-sess -analysis analysis_name -TR 1.2 -TER 0.4 -paradigm
>> 03TR.par -designtype event-related -nconditions 2 -timewindow 19.2
>> -prestim 2.4 -mcextreg -funcstem fmcstcsm6 -polyfit 2 -runlistfile
>> runlist_03TR -noautostimdur -force
>>
>> I define two contrasts,
>>
>> mkcontrast_sess -analysis analysis_name -rmprestim -contrast AV-REST -a 1
>> -c 0
>> mkcontrast_sess -analysis analysis_name -rmprestim -contrast AVT-REST -a 2
>> -c 0
>>
>> And then selxavg3-sess,
>>
>> selxavg3-sess -analysis analysis_name -sf subjectname -df sessdir
>> -overwrite
>>
>> And this errors. Like I said, the only thing I found in the mailing
>> list was a problem with tpef, and so I left it out altogether (as
>> above), and the problem persists. If I change TER to equal TR (1.2),
>> then it works. So the problem has something to do with TER being less
>> than TR. Perhaps something in the par file then? I checked it in
>> matlab, and diff(par(:,1)) = 0.4 for all of the events.
>>
>> Any thoughts would be very appreciated!
>> Ben.
>> ___
>> 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
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] selxavg3-sess error "design is ill-conditioned"

[Douglas N Greve]

Did you optimize the stimulus schedule with the idea that you would do 
sub-TR FIR estimation? Eg, you would have had to have run optseq2 with 
this in mind. If not, then you probably cannot do an FIR analysis. 
Instead, assume a shape (eg, -gammafit 2.25 1.25)

doug

Ben Letham wrote:
> Hello,
>
> I'm trying to run selxavg3-sess for an analysis with TER < TR, and it
> errors with "design is ill-conditioned". I searched the mailing list
> archive, and the only past problem of this sort that I found was
> associated with a faulty tpef file, which I am not using.
>
> The details: There is only one run. TR is 1.2s, and stimuli were
> presented at intervals of 1/3 TR (0.4s) (the desired TER). The
> paradigm file reflects this, it is of the form:
>
> 0 0
> 0.4 1
> 0.8 0
> 1.2 2
> 1.6 1
> 2 0
>
> I loaded it into matlab and verified that the time points all have a
> difference of 0.4s.
>
> The analysis is,
> mkanalysis-sess -analysis analysis_name -TR 1.2 -TER 0.4 -paradigm
> 03TR.par -designtype event-related -nconditions 2 -timewindow 19.2
> -prestim 2.4 -mcextreg -funcstem fmcstcsm6 -polyfit 2 -runlistfile
> runlist_03TR -noautostimdur -force
>
> I define two contrasts,
>
> mkcontrast_sess -analysis analysis_name -rmprestim -contrast AV-REST -a 1 -c 0
> mkcontrast_sess -analysis analysis_name -rmprestim -contrast AVT-REST -a 2 -c > 0
>
> And then selxavg3-sess,
>
> selxavg3-sess -analysis analysis_name -sf subjectname -df sessdir -overwrite
>
> And this errors. Like I said, the only thing I found in the mailing
> list was a problem with tpef, and so I left it out altogether (as
> above), and the problem persists. If I change TER to equal TR (1.2),
> then it works. So the problem has something to do with TER being less
> than TR. Perhaps something in the par file then? I checked it in
> matlab, and diff(par(:,1)) = 0.4 for all of the events.
>
> Any thoughts would be very appreciated!
> Ben.
> ___
> 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
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] selxavg3-sess error "design is ill-conditioned"

[Ben Letham]

Hello,

I'm trying to run selxavg3-sess for an analysis with TER < TR, and it
errors with "design is ill-conditioned". I searched the mailing list
archive, and the only past problem of this sort that I found was
associated with a faulty tpef file, which I am not using.

The details: There is only one run. TR is 1.2s, and stimuli were
presented at intervals of 1/3 TR (0.4s) (the desired TER). The
paradigm file reflects this, it is of the form:

0 0
0.4 1
0.8 0
1.2 2
1.6 1
2 0

I loaded it into matlab and verified that the time points all have a
difference of 0.4s.

The analysis is,
mkanalysis-sess -analysis analysis_name -TR 1.2 -TER 0.4 -paradigm
03TR.par -designtype event-related -nconditions 2 -timewindow 19.2
-prestim 2.4 -mcextreg -funcstem fmcstcsm6 -polyfit 2 -runlistfile
runlist_03TR -noautostimdur -force

I define two contrasts,

mkcontrast_sess -analysis analysis_name -rmprestim -contrast AV-REST -a 1 -c 0
mkcontrast_sess -analysis analysis_name -rmprestim -contrast AVT-REST -a 2 -c 0

And then selxavg3-sess,

selxavg3-sess -analysis analysis_name -sf subjectname -df sessdir -overwrite

And this errors. Like I said, the only thing I found in the mailing
list was a problem with tpef, and so I left it out altogether (as
above), and the problem persists. If I change TER to equal TR (1.2),
then it works. So the problem has something to do with TER being less
than TR. Perhaps something in the par file then? I checked it in
matlab, and diff(par(:,1)) = 0.4 for all of the events.

Any thoughts would be very appreciated!
Ben.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] selxavg3-sess error: matrix is singular to working precision

[Douglas N Greve]

Hmmm, not sure. Can you send your par file?

Jeremy Elman wrote:

Hello all,

I am trying to run a first level analysis on a subject with 
selxavg3-sess but keep running into the same error. The dof file is 
created, but that is it. Any ideas what might be causing this? Below 
is the error given.


Thank you very much for your help,
Jeremy


[jel...@psych118 functional]$ selxavg3-sess -s LDR001-1 -analysis 
LDR-fmcsm4-rec

--
selxavg3-sess logfile is 
/mtl/LDR/functional/log/selxavg3-sess-bold-LDR-fmcsm4-rec-090326144433.log 


--
---
/mtl/LDR/functional/LDR001-1
Thu Mar 26 14:44:35 PDT 2009
anadir = /mtl/LDR/functional/LDR001-1/bold/LDR-fmcsm4-rec
--
--- matlab output 
Warning: Unable to open display 'iconic'.  You will not be able to 
display graphics on the screen.


  < M A T L A B (R) >
Copyright 1984-2008 The MathWorks, Inc.
   Version 7.6.0.324 (R2008a)
   February 10, 2008


To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.

>> >> >> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: 
fast_selxavg3.m,v 1.55.2.6 2008/05/14 20:01:35 greve Exp $

outtop = /mtl/LDR/functional
Extension format = nii
UseFloat = 0
INFO: acfbins is not set, setting to 10
INFO: mask is not set, setting to brain
1 old-v-new.mat
Loaded /mtl/LDR/functional/LDR001-1/bold/007/ldr_paradigm.par as a 
par4 file.

nruns = 2
autostimdur = 1


outanadir = /mtl/LDR/functional/LDR001-1/bold/LDR-fmcsm4-rec
Found 155793/475136 (32.8) voxels in mask
Creating Design Matrix
Loaded /mtl/LDR/functional/LDR001-1/bold/007/ldr_paradigm.par as a 
par4 file.

Warning: Matrix is singular to working precision.
> In fast_selxavg3 at 208
Loaded /mtl/LDR/functional/LDR001-1/bold/011/ldr_paradigm.par as a 
par4 file.

Warning: Matrix is singular to working precision.
> In fast_selxavg3 at 208
ntptot = 364, nX = 14, DOF = 350
??? Error using ==> svd
Input to SVD must not contain NaN or Inf.

Error in ==> cond at 40
 s = svd(A);

Error in ==> fast_selxavg3 at 239
XCond = cond(XtX);

>> --
ERROR: fast_selxavg3() failed\n

___
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
gr...@nmr.mgh.harvard.edu
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


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] selxavg3-sess error: matrix is singular to working precision

[Jeremy Elman]

Hello all,

I am trying to run a first level analysis on a subject with 
selxavg3-sess but keep running into the same error. The dof file is 
created, but that is it. Any ideas what might be causing this? Below is 
the error given.


Thank you very much for your help,
Jeremy


[jel...@psych118 functional]$ selxavg3-sess -s LDR001-1 -analysis 
LDR-fmcsm4-rec

--
selxavg3-sess logfile is 
/mtl/LDR/functional/log/selxavg3-sess-bold-LDR-fmcsm4-rec-090326144433.log

--
---
/mtl/LDR/functional/LDR001-1
Thu Mar 26 14:44:35 PDT 2009
anadir = /mtl/LDR/functional/LDR001-1/bold/LDR-fmcsm4-rec
--
--- matlab output 
Warning: Unable to open display 'iconic'.  You will not be able to 
display graphics on the screen.


  < M A T L A B (R) >
Copyright 1984-2008 The MathWorks, Inc.
   Version 7.6.0.324 (R2008a)
   February 10, 2008


To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.

>> >> >> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: 
fast_selxavg3.m,v 1.55.2.6 2008/05/14 20:01:35 greve Exp $

outtop = /mtl/LDR/functional
Extension format = nii
UseFloat = 0
INFO: acfbins is not set, setting to 10
INFO: mask is not set, setting to brain
1 old-v-new.mat
Loaded /mtl/LDR/functional/LDR001-1/bold/007/ldr_paradigm.par as a par4 
file.

nruns = 2
autostimdur = 1


outanadir = /mtl/LDR/functional/LDR001-1/bold/LDR-fmcsm4-rec
Found 155793/475136 (32.8) voxels in mask
Creating Design Matrix
Loaded /mtl/LDR/functional/LDR001-1/bold/007/ldr_paradigm.par as a par4 
file.

Warning: Matrix is singular to working precision.
> In fast_selxavg3 at 208
Loaded /mtl/LDR/functional/LDR001-1/bold/011/ldr_paradigm.par as a par4 
file.

Warning: Matrix is singular to working precision.
> In fast_selxavg3 at 208
ntptot = 364, nX = 14, DOF = 350
??? Error using ==> svd
Input to SVD must not contain NaN or Inf.

Error in ==> cond at 40
 s = svd(A);

Error in ==> fast_selxavg3 at 239
XCond = cond(XtX);

>> --
ERROR: fast_selxavg3() failed\n

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] selxavg3-sess error (??? Error using ==> fclose)

[Avram Holmes]

All,

Nevermind. It looks like the error was being caused by a space issue.

Sorry for eating up your time,
Avram

On 2/16/2009 1:34 PM, Avram Holmes wrote:

All,

I'm encountering an error when I run selxavg3-sess and I am not sure 
how to get around the problem, or what it means.


I am running the following command, which has worked with the data for 
the other participants in my study.


selxavg3-sess -s c43 -d . -analysis Flanker_nResp -overwrite

Several minutes in I am getting the following error...

GLS Beta Pass
 run 1t= 0.0
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/006/flanker_nResp.par 
as a par3 file.

 run 2t= 5.7
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/007/flanker_nResp.par 
as a par3 file.

 run 3t=11.3
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/008/flanker_nResp.par 
as a par3 file.

 run 4t=17.1
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/009/flanker_nResp.par 
as a par3 file.

 run 5t=22.7
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/010/flanker_nResp.par 
as a par3 file.

GLS Residual Pass
/users/aholmes/.bashrc: line 229: SetUpFreeSurfer.sh: No such file or 
directory

 run 1t= 0.0
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/006/flanker_nResp.par 
as a par3 file.

??? Error using ==> fclose
Invalid file identifier.  Use fopen to generate a valid file identifier.

Error in ==> save_nifti at 162
fclose(fp);

Error in ==> MRIwrite at 145
 err = save_nifti(hdr,fspec);

Error in ==> fast_selxavg3 at 634
 MRIwrite(rrunmri,fname);

>> --
ERROR: fast_selxavg3() failed\n


Does anyone know what might be going on and/or how I can correct the 
problem?


Thanks,
Avram



--

Avram Holmes
Department of Psychology
Harvard University
1210 William James Hall  Phone:(617) 495-0790
33 Kirkland Street   Fax:(617) 495-3728
Cambridge, MA 02138, USA Email: hol...@fas.harvard.edu


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] selxavg3-sess error (??? Error using ==> fclose)

[Avram Holmes]

All,

I'm encountering an error when I run selxavg3-sess and I am not sure how 
to get around the problem, or what it means.


I am running the following command, which has worked with the data for 
the other participants in my study.


selxavg3-sess -s c43 -d . -analysis Flanker_nResp -overwrite

Several minutes in I am getting the following error...

GLS Beta Pass
 run 1t= 0.0
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/006/flanker_nResp.par 
as a par3 file.

 run 2t= 5.7
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/007/flanker_nResp.par 
as a par3 file.

 run 3t=11.3
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/008/flanker_nResp.par 
as a par3 file.

 run 4t=17.1
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/009/flanker_nResp.par 
as a par3 file.

 run 5t=22.7
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/010/flanker_nResp.par 
as a par3 file.

GLS Residual Pass
/users/aholmes/.bashrc: line 229: SetUpFreeSurfer.sh: No such file or 
directory

 run 1t= 0.0
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/006/flanker_nResp.par 
as a par3 file.

??? Error using ==> fclose
Invalid file identifier.  Use fopen to generate a valid file identifier.

Error in ==> save_nifti at 162
fclose(fp);

Error in ==> MRIwrite at 145
 err = save_nifti(hdr,fspec);

Error in ==> fast_selxavg3 at 634
 MRIwrite(rrunmri,fname);

>> --
ERROR: fast_selxavg3() failed\n


Does anyone know what might be going on and/or how I can correct the 
problem?


Thanks,
Avram

--

Avram Holmes
Department of Psychology
Harvard University
1210 William James Hall  Phone:(617) 495-0790
33 Kirkland Street   Fax:(617) 495-3728
Cambridge, MA 02138, USA Email: hol...@fas.harvard.edu


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer