Forum Replies Created
-
AuthorPosts
-
LDO
ParticipantThank you for this. Unfortunately that was from 4 or 5 months ago and I no longer remember which image that was.
LDO
ParticipantOf 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 =
-1Note 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 –UHad to use the –U flag because this machine is only a dual core i5
LDO
Participant“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, 9.6Not sure how to check environment variables…
LDO
ParticipantNo, 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
ParticipantSee 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
ParticipantYes! 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:invalidMEXFileBut, 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
ParticipantYes, 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
ParticipantJoshi,
———————————————————————————————
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?
ThanksLDO
ParticipantSame issue with files saved by version 18a
-
AuthorPosts