Re: [Freesurfer] mri_cvs_register error in step 2

hi Lilla,

I ended up with the same error... so I'm not sure what else to try. Do you have an ideas for troubleshooting?

I've also attached the latest log file, although it's probably very similar to the first one.

thanks, jackie

On Fri, Apr 20, 2012 at 6:10 PM, Jackie Leung < jackie.leung@alumni.utoronto.ca> wrote:

The files in the folder are around 4.7MB... and 2 .annot files that are around 1Mb. I am able to open these surface files using Freeview.

Like I said before, I tried copying and surf2vol command line and running it separately, and this error won't appear. In contrast, if i run mri_cvs_register --mov sub26 --template sub47 --outdir CVS_test_26to47_1 --step2 --nocleanup The same error pops up.

very puzzling.

i will rerun everything overnight to see if i get the same problem.

thanks, jackie

On Fri, Apr 20, 2012 at 3:56 PM, Lilla Zollei <lzollei@nmr.mgh.harvard.edu

...

wrote:

...

Hi Jackie,

What is the size of the *resample* files? The only thing I can think about is that the files are corrupted and the code cannot read those files in. You could try to read the resampled files into Freeview, to test whether they can be opened or you could delete the files and then they will be regenerated.

--Lilla

On Thu, 19 Apr 2012, Jackie Leung wrote:

ok... please see attached.

...

note: The directory name is different in this log file, but the error is the same. I've been testing this problem with many different directories.

thanks, jackie

On Thu, Apr 19, 2012 at 5:37 PM, Lilla Zollei < lzollei@nmr.mgh.harvard.edu> wrote:

 Hi Jackie,

 Could you attach the log file?

 Thanks, Lilla

 On Thu, 19 Apr 2012, Jackie Leung wrote:

       hi,

       I'm trying to run mri_cvs_register and I'm getting a strange

error message.

       MRISread(CVS_test_26to47_1/lh.**resample.white): could not

open file No such file or directory Error reading surface CVS_test_26to47_1/lh.resample.**white

       I've checked the directory and the file definitely exists.

       It seems to be popping up in step 2 of the script, where it

calls the surf2vol function. I've tried running this function on its own and didn't get this error, so I'm really confused as to what the problem may be.

       Any help will be greatly appreciated!

       thanks,
       jackie

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

-- Jackie Leung Lab Research Project Coordinator Dept of Physiology & Experimental Medicine Hospital for Sick Children Tel: (416) 813-7654 x2396

-- Jackie Leung Lab Research Project Coordinator Dept of Physiology & Experimental Medicine Hospital for Sick Children Tel: (416) 813-7654 x2396