this is on miracle. I opened a new terminal window and here is the output from nu_correct

[miracle:STRUCS] (nmr-std-env) nu_correct Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/5.8.5/i386-li nux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i386-linux- thread-multi /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/per l5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386-l inux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/li b/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5 / usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site _perl/5.8.2 /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/l ib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr /lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/ 5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread -multi /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/v endor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5 /usr/l ib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendo r_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 / usr/lib/perl5/vendor_perl .) at /usr/pubsw/packages/mni/current/bin/nu_correct l ine 37. BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/current/bin/nu_corr ect line 37.

Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139

On Wed, 24 Aug 2005, Nick Schmansky wrote:

Keyma,

Hi, on which machine does this occur? If you start a new shell, and type:

nu_correct

What does it display?

Nick

On Wed, 2005-08-24 at 11:34 -0400, Keyma Prince wrote:

...

I just tried to run the following command and I got an error which has appeared before on the freesurfer list after the MINC toolkit was rebuilt. Can you let me know if this has happened again and what I can do about it?

thanks,

-Keyma

Command: recon-all -stage1 -subjid Y24_031905a_STRUC

Error output:

i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (-0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to .... Started at: Wed Aug 24 11:21:42 EDT 2005 Ended at: Wed Aug 24 11:23:46 EDT 2005 mri_motion_correct2: done

---

Nu Intensity Correction Wed Aug 24 11:23:46 EDT 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=2530.00, TE=3.30, TI=1100.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (-0, 1, 0) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. ERROR: nu_correct

---

Filesystem 1K-blocks Used Available Use% Mounted on engram:/local_mount/space/engram/11 68682136 44104560 24577576 65% /autofs/space/engram_011

---

recon-all exited with errors at Wed Aug 24 11:24:01 EDT 2005

Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

I get the same error.

Here is output you asked for:

[miracle:STRUCS] (nmr-std-env) cat /etc/redhat-release CentOS release 4.1 (Final) [miracle:STRUCS] (nmr-std-env) uname -a Linux miracle 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686 athlon i386 GNU/Linux [miracle:STRUCS] (nmr-std-env)

Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139

On Wed, 24 Aug 2005, Nick Schmansky wrote:

Kayma,

Can you give it a try now?

Also, can you type the following for me?

cat /etc/redhat-release uname -a

This will tell me the machine OS and type. Unfortunately, I can't login to miracle.

Nick

On Wed, 2005-08-24 at 11:40 -0400, Keyma Prince wrote:

...

this is on miracle. I opened a new terminal window and here is the output from nu_correct

[miracle:STRUCS] (nmr-std-env) nu_correct Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/5.8.5/i386-li nux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i386-linux- thread-multi /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/per l5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386-l inux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/li b/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5 / usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site _perl/5.8.2 /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/l ib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr /lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/ 5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread -multi /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/v endor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5 /usr/l ib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendo r_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 / usr/lib/perl5/vendor_perl .) at /usr/pubsw/packages/mni/current/bin/nu_correct l ine 37. BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/current/bin/nu_corr ect line 37.

Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139

On Wed, 24 Aug 2005, Nick Schmansky wrote:

...

Keyma,

Hi, on which machine does this occur? If you start a new shell, and type:

nu_correct

What does it display?

Nick

On Wed, 2005-08-24 at 11:34 -0400, Keyma Prince wrote:

...

I just tried to run the following command and I got an error which has appeared before on the freesurfer list after the MINC toolkit was rebuilt. Can you let me know if this has happened again and what I can do about it?

thanks,

-Keyma

Command: recon-all -stage1 -subjid Y24_031905a_STRUC

Error output:

i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (-0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to .... Started at: Wed Aug 24 11:21:42 EDT 2005 Ended at: Wed Aug 24 11:23:46 EDT 2005 mri_motion_correct2: done

---

Nu Intensity Correction Wed Aug 24 11:23:46 EDT 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=2530.00, TE=3.30, TI=1100.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (-0, 1, 0) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. ERROR: nu_correct

---

Filesystem 1K-blocks Used Available Use% Mounted on engram:/local_mount/space/engram/11 68682136 44104560 24577576 65% /autofs/space/engram_011

---

recon-all exited with errors at Wed Aug 24 11:24:01 EDT 2005

Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer