Re: [Freesurfer] ERROR running mkcontrast

2020-10-31 Thread Douglas N. Greve 

Do you have matlab installed? And is it in your path?

On 10/31/2020 5:30 AM, Nina Khatibi wrote:


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Hi,

I'm trying to use mkcontrast, but there's an error which I'll send 
below. I couldn't find any solution to solve it, I hope you help me 
fix this issue.
I'm using freesurfer-darwin-macOS-7.1.1-20200811-8b40551 , on my 
macbook pro 2018, macOS Mojave 10.14.6

I run

 "mkcontrast-sess -analysis mpk.fsaverage5Con.lh -contrast NorthSouth 
-a 4 -c 3"


and these appear:


INFO: Found 5 Non-Null Conditions

INFO: Found 1 Delays

Condition Weights: 0 0 -1. 1. 0

mkcontrast2 -config mpk.fsaverage5Con.lh/NorthSouth.config -anadir 
mpk.fsaverage5Con.lh -wcond 0 0 -1. 
1. 0 -sumconds -o 
mpk.fsaverage5Con.lh/NorthSouth.mat -prestim 0 -wdelay 1 -no-octave


mkcontrast2 7.1.1

cmtxfile mpk.fsaverage5Con.lh/NorthSouth.mat

nconds   5,  wcond  0 0 -1. 1. 0

ndelays   1, wdelay 1

ndelays   1, wpsa

sumconds 1

sumdelays 0

nircorr   0

TER       0.05

rdelta

rtau

cmtxfile  mpk.fsaverage5Con.lh/NorthSouth.mat

monly  0

NCond   5

WCond   0 0 -1. 1. 0

NDelay  1

WDelay  1

TER         0.05

sumconds   1

sumdelays  0

nircorr  0

TPreStim  0

RmPreStim  0

rdelta     0 0

rtau       0 0

ndelays    1

CNorm      1

setwdelay  0

setwcond   0

Matlab file is /tmp/mkcontrast2.2236.m

--- matlab output 

MATLAB: Undefined variable.

ERROR running mkcontrast

mkcontrast2 -config mpk.fsaverage5Con.lh/NorthSouth.config -anadir 
mpk.fsaverage5Con.lh -wcond 0 0 -1. 
1. 0 -sumconds -o 
mpk.fsaverage5Con.lh/NorthSouth.mat -prestim 0 -wdelay 1 -no-octave



Thanks,

Nina


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[Freesurfer] ERROR running mkcontrast

2020-10-31 Thread Nina Khatibi 
External Email - Use Caution

Hi,

I'm trying to use mkcontrast, but there's an error which I'll send below. I
couldn't find any solution to solve it, I hope you help me fix this issue.
I'm using freesurfer-darwin-macOS-7.1.1-20200811-8b40551 , on my macbook
pro 2018, macOS Mojave 10.14.6
I run

 "mkcontrast-sess -analysis mpk.fsaverage5Con.lh -contrast NorthSouth -a 4
-c 3"

and these appear:


INFO: Found 5 Non-Null Conditions

INFO: Found 1 Delays

Condition Weights: 0 0 -1. 1. 0

mkcontrast2 -config mpk.fsaverage5Con.lh/NorthSouth.config -anadir
mpk.fsaverage5Con.lh -wcond 0 0 -1.
1. 0 -sumconds -o mpk.fsaverage5Con.lh/NorthSouth.mat
-prestim 0 -wdelay 1 -no-octave

  mkcontrast2 7.1.1

cmtxfile  mpk.fsaverage5Con.lh/NorthSouth.mat

nconds5,  wcond  0 0 -1. 1. 0

ndelays   1, wdelay 1

ndelays   1, wpsa

sumconds  1

sumdelays 0

nircorr   0

TER   0.05

rdelta

rtau

  cmtxfile  mpk.fsaverage5Con.lh/NorthSouth.mat

  monly  0

  NCond   5

  WCond   0 0 -1. 1. 0

  NDelay  1

  WDelay  1

  TER 0.05

  sumconds   1

  sumdelays  0

  nircorr  0

  TPreStim  0

  RmPreStim  0

  rdelta 0 0

  rtau   0 0

  ndelays1

  CNorm  1

  setwdelay  0

  setwcond   0

Matlab file is /tmp/mkcontrast2.2236.m

--- matlab output 

MATLAB: Undefined variable.

ERROR running mkcontrast

mkcontrast2 -config mpk.fsaverage5Con.lh/NorthSouth.config -anadir
mpk.fsaverage5Con.lh -wcond 0 0 -1.
1. 0 -sumconds -o mpk.fsaverage5Con.lh/NorthSouth.mat
-prestim 0 -wdelay 1 -no-octave


Thanks,

Nina
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[Freesurfer] ERROR running mkcontrast, ERROR: cannot find matlab. Is it in your path?

2018-06-08 Thread 高 寒 
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Hello FreeSurfer Developers,

I am running FS-FAST on my mac. My freesurfer version is 
freesurfer-i386-apple-darwin11.4.2-stable6-20170119. My MAC version is macOS 
High Sierra 10.13.4 (17E202). I downloaded Matlbab Runtime on this site: 
http://www.freesurfer.net/fswiki/MatlabRuntime as constructed. When I run this 
command: { mkcontrast-sess -analysis my-language.sm05.lh -contrast 
language-v-base -a 1 }, I kept getting this error.

ERROR: cannot find matlab. Is it in your path?
ERROR running mkcontrast

Then I downloaded Matlab runtime R2014a (8.3). I still got the same error as 
above.

Then I downloaded Matlab runtime R2018a (9.4). Still the same error.

I assume I should download a certain version of Matlab Runtime in order to run 
FS-FAST on freesurfer-i386-apple-darwin11.4.2-stable6-20170119 on my macOS High 
Sierra 10.13.4 (17E202).

Could you help me? Thank you.

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[Freesurfer] ERROR running mkcontrast

2016-03-31 Thread Joseph Dien 
Hi, I ran into an odd problem which I was able to fix but wanted to let others 
know about.
This is OS X 10.11.4 with Matlab 2016a and FreeSurfer 5.3.

I got the following error when I ran mkcontrast using batch files that 
previously worked fine:

/private/var/folders/wt/vj5q34fs20x50sh_6rcrtkn8gn/T/Cleanup At 
Startup/sh.h4SI0w: No such file or directory.
ERROR running mkcontrast

Looking into the directories in question, I found that while there was no 
directory named 'Cleanup At Startup’ inside the T directory, there was such a 
directory inside ‘vj5q34fs20x50sh_6rcrtkn8gn’.  I’m guessing some version 
update changed the location of this directory.  I went into T and performed the 
following command:

mkdir 'Cleanup At Startup'

after doing so, everything worked again.

Cheers!

Joe



Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com
Cell Phone: 202-297-8117
http://joedien.com

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[Freesurfer] ERROR running mkcontrast - in FsFastTutorialV5.1

2011-09-27 Thread Carl Anderson 
Dear Free Surfer,

I have gotten to 3. Configure Contrasts in
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastFirstLevel

When I run  *mkcontrast-sess -analysis my-workmem.sm05.lh -contrast
encode-v-base -a 1*
I get the following result and error:

vermisii:fsfast-functional carlanderson$ mkcontrast-sess -analysis
my-workmem.sm05.lh -contrast encode-v-base -a 1
INFO: Found 5 Non-Null Conditions
INFO: Found 1 Delays
Condition Weights: 1. 0 0 0 0
mkcontrast -anadir my-workmem.sm05.lh -wcond 1. 0 0 0 0
-sumconds -o my-workmem.sm05.lh/encode-v-base.mat -wdelay 1 -no-octave
  $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $
cmtxfile  my-workmem.sm05.lh/encode-v-base.mat
nconds5,  wcond  1. 0 0 0 0
ndelays   1, wdelay 1
ndelays   1, wpsa
sumconds  1
sumdelays 0
nircorr   0
TER   0.05
rdelta
rtau
ERROR running mkcontrast
mkcontrast -anadir my-workmem.sm05.lh -wcond 1. 0 0 0 0
-sumconds -o my-workmem.sm05.lh/encode-v-base.mat -wdelay 1 -no-octave
Tue Sep 27 10:58:43 EDT 2011

Any suggestions?

Thanks!

•~~•~~•~~•~~•~~•~~•~~•
Carl M. Anderson, Ph.D. (mail stop 204)
Assistant Professor of Psychiatry,
Harvard Medical School 
The Neuroimaging Center,
McLean Hospital 115 Mill St.  Belmont, MA 02478
Ph: 617-855-2972;  Fax: 617-855-2770
e-mail: remfr...@gmail.com; carl_ander...@hms.harvard.edu
•~~•~~•~~•~~•~~•~~•~~•
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Re: [Freesurfer] ERROR running mkcontrast - in FsFastTutorialV5.1

2011-09-27 Thread Douglas N Greve 
Try giving it a -c 0
doug

Carl Anderson wrote:
 Dear Free Surfer,

 I have gotten to 3. Configure Contrasts 
 in 
 http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastFirstLevel 


 When I run  *mkcontrast-sess -analysis my-workmem.sm05.lh -contrast 
 encode-v-base -a 1*
 I get the following result and error:

 vermisii:fsfast-functional carlanderson$ mkcontrast-sess -analysis 
 my-workmem.sm05.lh -contrast encode-v-base -a 1
 INFO: Found 5 Non-Null Conditions
 INFO: Found 1 Delays
 Condition Weights: 1. 0 0 0 0
 mkcontrast -anadir my-workmem.sm05.lh -wcond 1. 0 
 0 0 0 -sumconds -o my-workmem.sm05.lh/encode-v-base.mat -wdelay 1 
 -no-octave
   $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $
 cmtxfile  my-workmem.sm05.lh/encode-v-base.mat
 nconds5,  wcond  1. 0 0 0 0
 ndelays   1, wdelay 1
 ndelays   1, wpsa   
 sumconds  1
 sumdelays 0
 nircorr   0
 TER   0.05
 rdelta
 rtau  
 ERROR running mkcontrast
 mkcontrast -anadir my-workmem.sm05.lh -wcond 1. 0 
 0 0 0 -sumconds -o my-workmem.sm05.lh/encode-v-base.mat -wdelay 1 
 -no-octave
 Tue Sep 27 10:58:43 EDT 2011

 Any suggestions?

 Thanks!

 •~~•~~•~~•~~•~~•~~•~~•
 Carl M. Anderson, Ph.D. (mail stop 204)
 Assistant Professor of Psychiatry,
 Harvard Medical School 
 The Neuroimaging Center,
 McLean Hospital 115 Mill St.  Belmont, MA 02478
 Ph: 617-855-2972;  Fax: 617-855-2770
 e-mail: remfr...@gmail.com mailto:remfr...@gmail.com; 
 carl_ander...@hms.harvard.edu mailto:carl_ander...@hms.harvard.edu
 •~~•~~•~~•~~•~~•~~•~~•

 

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