Hello all,
I had the same error as this previous post, but after the suggested fix, I'm getting the following matlab output/error messages. Does anyone know what I'm doing wrong?
Thanks so much, Jenn
%------------------------------------------------- Parsing Arguments RescaleTarget = 1000 Checking Parameters AutoStimDur: 0 StimDur: Number of Runs: 3 Input Volume List 1 014/fmc 2 016/fmc 3 017/fmc Input Pardigm File List 1 014/parfile.par 2 016/parfile.par 3 017/parfile.par Output Volume funcanal/h F Omnibus Volume funcanal/omnibus/f Sig Omnibus Volume funcanal/omnibus/fsig TR 2.870000 TER 2.870000 Total Window 0 PreStim Window 0 Remove Baseline 1 Remove Trend 0 Remove QTrend 0 Rescale Target 1000 nSkip 0 InPlane Res 3.125 FWHM 0 Hanning Radius 0 Time Offset 0 GammaFit 0 GammaFit Alpha: 2 SPM HRF: -1 Seg Brain/Air 1 SynthSeed 0 firstslice 0 nslices 27 nyqreg 0 SynthSeed = 0 Conditions Found (6): 1 2 3 4 5 6 Run 1: 72 72 72 72 36 36 Run 2: 72 72 72 72 36 36 Run 3: 72 72 72 72 36 36 Slice 0, 0.000159 -------------- First Pass (Accumulation), 0.024409 Run 1/3, 0.024782 Excluding 0 Points: Run 2/3, 5.67758 Excluding 0 Points: Run 3/3, 11.2836 Excluding 0 Points: Second Pass (Residual Error Estimation), 16.6096 Paradigm Condition: 33.8741 Var Reduction Range: 65.7977 85.9199 97.4559 Computing hhat Run 1/3, 16.6695 Excluding 0 Points: Run 2/3, 17.4337 Excluding 0 Points: Run 3/3, 18.1927 Excluding 0 Points: Saving data to funcanal/h_000.bfloat Saving offset to funcanal/h-offset_000.bfloat ??? Error using ==> .* Matrix dimensions must agree.
Error in ==> /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m On line 657 ==> F = sign(qsum) .* Fnum ./ Fden;
??? Undefined function or variable 'r'.
quiting matlab
------------------------------------------ ERROR: fast_selxavg() failed\n ERROR (<subject_dir>/<subject>): selxavg failed
%----------------------------------------------------------
On 4/10/06, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Add the following lines to your startup.m file
FSH = getenv('FREESURFER_HOME'); fshmatlab = sprintf('%s/matlab',FSH); path(path,fshmatlab); clear fshmatlab;
Paymon Hosseini wrote:
hi
i am going over the fsfast tutorial. i have completed all steps up to "FsFastTutorial/905 Average session-level data by condition"
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial_2f905_20Average_20s...https://phsexchweb.partners.org/exchweb/bin/redir.asp?URL=https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial_2f905_20Average_20sessi on_2dlevel_20data_20by_20condition
when i run "selxavg-sess -sf sessid -df sesspar -analysis sem_assoc", i get the following error:
" ??? Undefined function or variable 'MRIread'.
Error in ==> /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m On line 160 ==> rstd = MRIread(instem,1);
??? Undefined function or variable 'r'.
quiting matlab
ERROR: fast_selxavg() failed\n ERROR (/autofs/space/engram_012/users/pman/bert-functional): selxavg failed "
can you please tell me why i am getting this error?
thanks paymon hosseini _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://phsexchweb.partners.org/exchweb/bin/redir.asp?URL=https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/freesurferhttps://phsexchweb.partners.org/exchweb/bin/redir.asp?URL=https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry, what's your command-line again?
Jenn Segawa wrote:
Hello all,
I had the same error as this previous post, but after the suggested fix, I'm getting the following matlab output/error messages. Does anyone know what I'm doing wrong?
Thanks so much, Jenn
%------------------------------------------------- Parsing Arguments RescaleTarget = 1000 Checking Parameters AutoStimDur: 0 StimDur: Number of Runs: 3 Input Volume List 1 014/fmc 2 016/fmc 3 017/fmc Input Pardigm File List 1 014/parfile.par 2 016/parfile.par 3 017/parfile.par Output Volume funcanal/h F Omnibus Volume funcanal/omnibus/f Sig Omnibus Volume funcanal/omnibus/fsig TR 2.870000 TER 2.870000 Total Window 0 PreStim Window 0 Remove Baseline 1 Remove Trend 0 Remove QTrend 0 Rescale Target 1000 nSkip 0 InPlane Res 3.125 FWHM 0 Hanning Radius 0 Time Offset 0 GammaFit 0 GammaFit Alpha: 2 SPM HRF: -1 Seg Brain/Air 1 SynthSeed 0 firstslice 0 nslices 27 nyqreg 0 SynthSeed = 0 Conditions Found (6): 1 2 3 4 5 6 Run 1: 72 72 72 72 36 36 Run 2: 72 72 72 72 36 36 Run 3: 72 72 72 72 36 36 Slice 0, 0.000159 -------------- First Pass (Accumulation), 0.024409 Run 1/3, 0.024782 Excluding 0 Points: Run 2/3, 5.67758 Excluding 0 Points: Run 3/3, 11.2836 Excluding 0 Points: Second Pass (Residual Error Estimation), 16.6096 Paradigm Condition: 33.8741 Var Reduction Range: 65.7977 85.9199 97.4559 Computing hhat Run 1/3, 16.6695 Excluding 0 Points: Run 2/3, 17.4337 Excluding 0 Points: Run 3/3, 18.1927 Excluding 0 Points: Saving data to funcanal/h_000.bfloat Saving offset to funcanal/h-offset_000.bfloat ??? Error using ==> .* Matrix dimensions must agree.
Error in ==> /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m On line 657 ==> F = sign(qsum) .* Fnum ./ Fden;
??? Undefined function or variable 'r'.
quiting matlab
ERROR: fast_selxavg() failed\n ERROR (<subject_dir>/<subject>): selxavg failed
%----------------------------------------------------------
On 4/10/06, Doug Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Add the following lines to your startup.m file
FSH = getenv('FREESURFER_HOME'); fshmatlab = sprintf('%s/matlab',FSH); path(path,fshmatlab); clear fshmatlab;
Paymon Hosseini wrote:
hi
i am going over the fsfast tutorial. i have completed all steps up to "FsFastTutorial/905 Average session-level data by condition"
MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial_2f905_20Average_20s... https://phsexchweb.partners.org/exchweb/bin/redir.asp?URL=https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial_2f905_20Average_20sessi on_2dlevel_20data_20by_20condition
when i run "selxavg-sess -sf sessid -df sesspar -analysis sem_assoc", i get the following error:
" ??? Undefined function or variable 'MRIread'.
Error in ==>
/usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m
On line 160 ==> rstd = MRIread(instem,1);
??? Undefined function or variable 'r'.
quiting matlab
ERROR: fast_selxavg() failed\n ERROR (/autofs/space/engram_012/users/pman/bert-functional): selxavg failed "
can you please tell me why i am getting this error?
thanks paymon hosseini _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from
"phsexchweb.partners.org" claiming to be MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://phsexchweb.partners.org/exchweb/bin/redir.asp?URL=https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@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
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from
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My command line is "selxavg-sess -sf sessid -df sesspar -analysis funcanal"
On 4/25/06, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Sorry, what's your command-line again?
Jenn Segawa wrote:
Hello all,
I had the same error as this previous post, but after the suggested fix, I'm getting the following matlab output/error messages. Does anyone know what I'm doing wrong?
Thanks so much, Jenn
%------------------------------------------------- Parsing Arguments RescaleTarget = 1000 Checking Parameters AutoStimDur: 0 StimDur: Number of Runs: 3 Input Volume List 1 014/fmc 2 016/fmc 3 017/fmc Input Pardigm File List 1 014/parfile.par 2 016/parfile.par 3 017/parfile.par Output Volume funcanal/h F Omnibus Volume funcanal/omnibus/f Sig Omnibus Volume funcanal/omnibus/fsig TR 2.870000 TER 2.870000 Total Window 0 PreStim Window 0 Remove Baseline 1 Remove Trend 0 Remove QTrend 0 Rescale Target 1000 nSkip 0 InPlane Res 3.125 FWHM 0 Hanning Radius 0 Time Offset 0 GammaFit 0 GammaFit Alpha: 2 SPM HRF: -1 Seg Brain/Air 1 SynthSeed 0 firstslice 0 nslices 27 nyqreg 0 SynthSeed = 0 Conditions Found (6): 1 2 3 4 5 6 Run 1: 72 72 72 72 36 36 Run 2: 72 72 72 72 36 36 Run 3: 72 72 72 72 36 36 Slice 0, 0.000159 -------------- First Pass (Accumulation), 0.024409 Run 1/3, 0.024782 Excluding 0 Points: Run 2/3, 5.67758 Excluding 0 Points: Run 3/3, 11.2836 Excluding 0 Points: Second Pass (Residual Error Estimation), 16.6096 Paradigm Condition: 33.8741 Var Reduction Range: 65.7977 85.9199 97.4559 Computing hhat Run 1/3, 16.6695 Excluding 0 Points: Run 2/3, 17.4337 Excluding 0 Points: Run 3/3, 18.1927 Excluding 0 Points: Saving data to funcanal/h_000.bfloat Saving offset to funcanal/h-offset_000.bfloat ??? Error using ==> .* Matrix dimensions must agree.
Error in ==> /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m On line 657 ==> F = sign(qsum) .* Fnum ./ Fden;
??? Undefined function or variable 'r'.
quiting matlab
ERROR: fast_selxavg() failed\n ERROR (<subject_dir>/<subject>): selxavg failed
%----------------------------------------------------------
On 4/10/06, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Add the following lines to your startup.m file
FSH = getenv('FREESURFER_HOME'); fshmatlab = sprintf('%s/matlab',FSH); path(path,fshmatlab); clear fshmatlab;
Paymon Hosseini wrote:
hi
i am going over the fsfast tutorial. i have completed all steps up to "FsFastTutorial/905 Average session-level data by condition"
*MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be* *MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial_2f905_20Average_20s... *https://phsexchweb.partners.org/exchweb/bin/redir.asp?URL=https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial_2f905_20Average_20sessi
on_2dlevel_20data_20by_20condition
when i run "selxavg-sess -sf sessid -df sesspar -analysis sem_assoc", i get the following error:
" ??? Undefined function or variable 'MRIread'.
Error in ==>
/usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m
On line 160 ==> rstd = MRIread(instem,1);
??? Undefined function or variable 'r'.
quiting matlab
ERROR: fast_selxavg() failed\n ERROR (/autofs/space/engram_012/users/pman/bert-functional): selxavg failed "
can you please tell me why i am getting this error?
thanks paymon hosseini _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu **MailScanner has detected a possible fraud attempt from
"phsexchweb.partners.org" claiming to be* *MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer *https://phsexchweb.partners.org/exchweb/bin/redir.asp?URL=https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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 **MailScanner has detected a possible fraud attempt from
"phsexchweb.partners.org" claiming to be* *MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer *https://phsexchweb.partners.org/exchweb/bin/redir.asp?URL=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 Centergreve@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
Can you send your analysis.dat and analysis.info?
Jenn Segawa wrote:
My command line is "selxavg-sess -sf sessid -df sesspar -analysis funcanal"
On 4/25/06, Doug Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, what's your command-line again? Jenn Segawa wrote: Hello all, I had the same error as this previous post, but after the suggested fix, I'm getting the following matlab output/error messages. Does anyone know what I'm doing wrong? Thanks so much, Jenn %------------------------------------------------- Parsing Arguments RescaleTarget = 1000 Checking Parameters AutoStimDur: 0 StimDur: Number of Runs: 3 Input Volume List 1 014/fmc 2 016/fmc 3 017/fmc Input Pardigm File List 1 014/parfile.par 2 016/parfile.par 3 017/parfile.par Output Volume funcanal/h F Omnibus Volume funcanal/omnibus/f Sig Omnibus Volume funcanal/omnibus/fsig TR 2.870000 TER 2.870000 Total Window 0 PreStim Window 0 Remove Baseline 1 Remove Trend 0 Remove QTrend 0 Rescale Target 1000 nSkip 0 InPlane Res 3.125 FWHM 0 Hanning Radius 0 Time Offset 0 GammaFit 0 GammaFit Alpha: 2 SPM HRF: -1 Seg Brain/Air 1 SynthSeed 0 firstslice 0 nslices 27 nyqreg 0 SynthSeed = 0 Conditions Found (6): 1 2 3 4 5 6 Run 1: 72 72 72 72 36 36 Run 2: 72 72 72 72 36 36 Run 3: 72 72 72 72 36 36 Slice 0, 0.000159 -------------- First Pass (Accumulation), 0.024409 Run 1/3, 0.024782 Excluding 0 Points: Run 2/3, 5.67758 Excluding 0 Points: Run 3/3, 11.2836 Excluding 0 Points: Second Pass (Residual Error Estimation), 16.6096 Paradigm Condition: 33.8741 Var Reduction Range: 65.7977 85.9199 97.4559 Computing hhat Run 1/3, 16.6695 Excluding 0 Points: Run 2/3, 17.4337 Excluding 0 Points: Run 3/3, 18.1927 Excluding 0 Points: Saving data to funcanal/h_000.bfloat Saving offset to funcanal/h-offset_000.bfloat ??? Error using ==> .* Matrix dimensions must agree. Error in ==> /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m On line 657 ==> F = sign(qsum) .* Fnum ./ Fden;??? Undefined function or variable 'r'.
quiting matlab
------------------------------------------ ERROR: fast_selxavg() failed\n ERROR (<subject_dir>/<subject>): selxavg failed %---------------------------------------------------------- On 4/10/06, Doug Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:Add the following lines to your startup.m file
FSH = getenv('FREESURFER_HOME'); fshmatlab = sprintf('%s/matlab',FSH); path(path,fshmatlab); clear fshmatlab;
Paymon Hosseini wrote:
hi
i am going over the fsfast tutorial. i have completed all steps
up to"FsFastTutorial/905 Average session-level data by condition"
MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial_2f905_20Average_20sessi <https://phsexchweb.partners.org/exchweb/bin/redir.asp?URL=https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial_2f905_20Average_20sessi> on_2dlevel_20data_20by_20conditionwhen i run "selxavg-sess -sf sessid -df sesspar -analysis
sem_assoc",i get the following error:
" ??? Undefined function or variable 'MRIread'.
Error in ==>
/usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.mOn line 160 ==> rstd = MRIread(instem,1);
??? Undefined function or variable 'r'.
quiting matlab
ERROR: fast_selxavg() failed\n ERROR (/autofs/space/engram_012/users/pman/bert-functional):
selxavgfailed "
can you please tell me why i am getting this error?
thanks paymon hosseini _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu> > > MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://phsexchweb.partners.org/exchweb/bin/redir.asp?URL=https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@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
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu> > MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be MailScanner has detected a possible fraud attempt from "phsexchweb.partners.org" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://phsexchweb.partners.org/exchweb/bin/redir.asp?URL=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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Jenn Segawa