[LDO]

Thank you for this. Unfortunately that was from 4 or 5 months ago and I no longer remember which image that was.

[LDO]

Of course this is done after having run the Cortical Extraction Sequence first.
Then, here is a bit of the Matlab code used to call svreg:

Name = ’xnrT1.nii.gz’ %(skull stripped T1)
basename = string(name(1:(length(name)-7))) %(.nii.gz extension)
st=’svreg.exe ‘+ basename + ‘ -U’
dos(st)

This results in:
basename= ‘xnrT1’
st=svreg.exe “C:\Users\Larry Olson\Desktop\jtTestCase\BS”\xnrT1 -U
these are the errors (from running the script OR from pasting into matlab command window):
…curvature resolution 8/10
curvature resolution 9/10
curvature resolution 10/10
Multiresolution curvature maps are calculated
Computing additive curvature
Performing curvature registration
Curvature registration at resolution 1/4
Error using imhist (line 76)
Invalid MEX-file ‘C:\Users\LARRYO~1\AppData\Local\Temp\Larry Olson\mcrCache9.0\svreg_1\toolbox\images\images\private\imhistc.mexw64’: The specified procedure could not be found.
Error in histeq>computeCumulativeHistogram (line 181)
Error in histeq (line 138)
Error in register_images_elastic_anand_landmarks_cg (line 26)
Error in curvature_registration512g_wt_multi_bs_elastic_xyz_cg (line 129)
Error in curvature_registration_newbs_elastic_xyz (line 73)
Error in svreg_label_surf_hemi (line 191)
Error in svreg (line 180)
MATLAB:invalidMEXFile
ans =
-1

Note I pasted the exact same call into a DOS Command Prompt, and it ran all the way through:
svreg.exe “C:\Users\Larry Olson\Desktop\jtTestCase\BS”\xnrT1 –U

Had to use the –U flag because this machine is only a dual core i5

[LDO]

“check environment variables in matlab by typing env”
>’env’ is not recognized as an internal or external command, operable program or batch file.
(On Windows here)

Actually I have only one Matlab Compiler Runtime: 7.13
But 3 Matlab Runtimes: 9.0, 9.5, 9.6

Not sure how to check environment variables…

[LDO]

No, it is 64 bit MCR
It works from the GUI
It works (with the same DOS command) from the Windows command prompt
*It just aborts part way through (with the same DOS command) when started within Matlab

(MCR_R2015b_win64_installer.exe)
(but I also have other versions installed for creating Matlab standalone programs)

That is so puzzling

[LDO]

See above. The svreg.exe with -U failed when I called it from Matlab 2019a. I just ran exactly the same call from the command prompt in Windows and it worked perfectly. I am puzzled…

[LDO]

Yes! That did start the process.
But it stops after a few minutes:

…curvature resolution 10/10
Multiresolution curvature maps are calculated
Computing additive curvature
Performing curvature registration
Curvature registration at resolution 1/4
Error using imhist (line 76)
Invalid MEX-file ‘C:\Users\LARRYO~1\AppData\Local\Temp\Larry Olson\mcrCache9.0\svreg_0\toolbox\images\images\private\imhistc.mexw64’: The specified procedure could not be found.

Error in histeq>computeCumulativeHistogram (line 181)
Error in histeq (line 138)
Error in register_images_elastic_anand_landmarks_cg (line 26)
Error in curvature_registration512g_wt_multi_bs_elastic_xyz_cg (line 129)
Error in curvature_registration_newbs_elastic_xyz (line 73)
Error in svreg_label_surf_hemi (line 165)
Error in svreg (line 180)
MATLAB:invalidMEXFile

But, oddly, if I look in ‘C:\Users\LARRYO~1\AppData\Local\Temp\Larry Olson\mcrCache9.0\svreg_0\toolbox\images\images\private\imhistc.mexw64’, imhistc.mexw64 is there

[LDO]

Yes, this file exists: C:\Users\lolson\Desktop\JJnew\IA\bfc\nrT.svreg.init.label.nii.gz as C:\Users\lolson\Desktop\JJnew\IA\bfc\nrT1.svreg.init.label.nii but has been converted to uncompressed nifty for compatibility with Matlab SPM tools.

Is that really a problem?

[LDO]

Joshi,

———————————————————————————————
FYI, I sent email to your response but got this:
” —– The following addresses had permanent fatal errors —– <cbhushan@usc.edu>
(reason: 550-5.2.1 The email account that you tried to reach is disabled. Learn more at)”
———————————————————————————————

Thank you for your prompt response! Difficult to troubleshoot, but I get this error:

C:\Program Files\BrainSuite18a\svreg\bin>svreg_labelwith_atlas.exe C:\Users\lolson\Desktop\JJnew\IA\bfc\nrT1 C:\Users\lolson\Desktop\BrainSuiteAtlas1\mri mod
Error using copyfile
No matching files were found.

Error in svreg_labelwith_atlas (line 77)

MATLAB:COPYFILE:FileDoesNotExist

Not sure which files are missing?
Thanks

[LDO]

Same issue with files saved by version 18a

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