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

2018-06-08 Thread
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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] FS-FAST error:

2018-05-29 Thread
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FS-FAST error: analysis language.sm05.lh does not exist, see mkanalysis-sess

Hello FreeSurfer Developers,

I'm attempting to run FS-FAST on my own data, as described on the FS-FAST 
tutorial 
(http://www.freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastFirstLevel), but I 
get the following error when I run the selxavg3-sess command:

ERROR: analysis language.sm05.lh does not exist, see mkanalysis-sess

I assume there is something wrong with my mkanalysis-sess command because I can 
finish the whole process with the fsfast-functional data without an error.

My research paradigm is like this:

Task-fMRI*, ﰕﰗPicture Namingﰞ, Block-design with 30s On - 30s Off. 3 Trials.
TR = 3000 ms; TE = 30 ms; flip angle = 90 degrees; matrix size = 96 ﰝ 96; FOV = 
240 ﰝ 240 mm; 46 contiguous transversal slices; voxel size = 2.5 ﰝ 2.5 ﰝ 3 mm3; 
3 dummy scansﰘScanning time = 3 min 09s.


The first 3 TR have already been removed before I got the data. So I got 60 TR.

And this the paradigm 
file I set 
up:

  0.000   1 30.000 1.000 recited

 30.000   2 30.000 1.000 null

 60.000   1 30.000 1.000 recited

 90.000   2 30.000 1.000 null

120.000   1 30.000 1.000 recited

150.000   2 30.000 1.000 null


This is the mkanalysis-sess command I set up:

mkanalysis-sess \

  -fsd bold -stc up  -surface fsaverage lh -fwhm 5  \

  -event-related  -paradigm language.par -nconditions 2 \

  -spmhrf 0 -TR 3 -refeventdur 30 -nskip 0 -polyfit 2 \

  -analysis my-language.sm05.lh  -per-run -force \



Thank you for help.

Sincerely yours.

Gao Han
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