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 dgreve@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 -------------------- 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.strappini@weizmann.ac.il

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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 <francescastrappini@gmail.com mailto:francescastrappini@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
<http://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 <dgreve@mgh.harvard.edu
<mailto:dgreve@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 --------------------
    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
    <http://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.strappini@weizmann.ac.il
    <mailto:francesca.strappini@weizmann.ac.il>


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

    _______________________________________________
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    Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
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    The information in this e-mail is intended only for the person
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    addressed. If you believe this e-mail was sent to you in error
    and the e-mail
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-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>

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

---

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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 <dgreve@mgh.harvard.edu mailto:dgreve@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
> <francescastrappini@gmail.com
<mailto:francescastrappini@gmail.com>
<mailto:francescastrappini@gmail.com
<mailto:francescastrappini@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
<http://www.mathworks.com>
>     <http://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
<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>
>     <mailto:dgreve@mgh.harvard.edu
<mailto:dgreve@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 --------------------
>>         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
<http://www.mathworks.com>
>>         <http://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.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>
>>         <mailto:francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>>
>>
>>
>>  _______________________________________________
>>         Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>         <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>       
 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>
>
>         _______________________________________________
>         Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>         <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>       
 <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
>         <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.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>
>     <mailto:francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>>
>
>
>
>
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>
> <mailto:francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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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

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