Hi Siddharth
can you cc the list so others can answer? Did you check the norm to make sure it's ok?
You can definitely take the mri_cc from 5.3 and use the rest of 5.1. If you let us know your hardware/software environment we'll send you an updated binary, but as I said it's usually a symptom of something else going wrong Bruce
On Thu, 16 May 2013, Ray, Siddharth wrote:
Hi Bruce,
Thanks for the prompt reply. I am using 5.1 version and I don’t think I can switch to a new version because I already have subjects processed using this one.
So do we have any fix for this version?
Please let me know.
-Siddharth
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, May 16, 2013 2:08 PM To: Ray, Siddharth Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] F Problem running : mri_cc -aseg.auto_
Hi Siddharth
what FS version are you running? I did fix this recently, and the fix is certainly in 5.3. It only happened if there was something badly wrong, like the norm.mgz being empty for example, so it was more a symptom of an earlier failure then a problem of it's own (although I did have it print out an error message instead of running forever)
cheers Bruce
On Thu, 16 May 2013, Ray, Siddharth wrote:
Hi,
I am new to freesurfer and was trying to run it on couple of my subjects but I am stuck (for last 40 hrs) at stage
“mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/sray2/Desktop/combirx/cr052_ip_output/mri/transforms/cc_up.lta cr052_ip_output”
it seems. The last few lines of the log file were:
searching scale 1 Z rot 9.9
searching scale 1 Z rot 10.1 global minimum found at slice 122.0, rotations (-3.99, 3.36)
final transformation (x=122.0, yr=-3.992, zr=3.355):
0.996 -0.059 -0.069 25.704;
0.058 0.998 -0.004 -3.212;
0.070 0.000 0.998 -51.078;
0.000 0.000 0.000 1.000;
Have anyone came across this error before ? and know how to fix this. Please let me know.
Thanks in advance.
~Siddharth Ray
P.S. I have attached the log file here.
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/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.
Hi Bruce,
Sorry to get back late on this. The norm file was blank.
Can you send me the updated binary??, My system specification is following:
Red Hat Enterprise LINUX Workstation Release 6.0 (Santiago) Kernel Linux 2.6.37-71.el6.x86_64 GNOME 2.28.2
Also, just for information this is not going to affect any output (I was looking for cortical thickness), right?
And if I use version 5.3, Will that going to affect any of the output (if you already know them..) that I get from FS 5.1.0?
Please let me know.
Thanks!
~Siddharth
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, May 16, 2013 2:26 PM To: Ray, Siddharth Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] F Problem running : mri_cc -aseg.auto_
Hi Siddharth
can you cc the list so others can answer? Did you check the norm to make sure it's ok?
You can definitely take the mri_cc from 5.3 and use the rest of 5.1. If you let us know your hardware/software environment we'll send you an updated binary, but as I said it's usually a symptom of something else going wrong Bruce
On Thu, 16 May 2013, Ray, Siddharth wrote:
Hi Bruce,
Thanks for the prompt reply. I am using 5.1 version and I don’t think I can switch to a new version because I already have subjects processed using this one.
So do we have any fix for this version?
Please let me know.
-Siddharth
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, May 16, 2013 2:08 PM To: Ray, Siddharth Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] F Problem running : mri_cc -aseg.auto_
Hi Siddharth
what FS version are you running? I did fix this recently, and the fix is certainly in 5.3. It only happened if there was something badly wrong, like the norm.mgz being empty for example, so it was more a symptom of an earlier failure then a problem of it's own (although I did have it print out an error message instead of running forever)
cheers Bruce
On Thu, 16 May 2013, Ray, Siddharth wrote:
Hi,
I am new to freesurfer and was trying to run it on couple of my subjects but I am stuck (for last 40 hrs) at stage
“mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/sray2/Desktop/combirx/cr052_ip_output/mri/transforms/cc_up.lta cr052_ip_output”
it seems. The last few lines of the log file were:
searching scale 1 Z rot 9.9
searching scale 1 Z rot 10.1 global minimum found at slice 122.0, rotations (-3.99, 3.36)
final transformation (x=122.0, yr=-3.992, zr=3.355):
0.996 -0.059 -0.069 25.704;
0.058 0.998 -0.004 -3.212;
0.070 0.000 0.998 -51.078;
0.000 0.000 0.000 1.000;
Have anyone came across this error before ? and know how to fix this. Please let me know.
Thanks in advance.
~Siddharth Ray
P.S. I have attached the log file here.
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/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.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Ray, Siddharth