Hello, I am a new freesurfer user. I have been trying to run recon-all on our data and have been unable to do so because recon-all crashes everytime at the same spot. Here is the error I get when I run recon-all with autorecon1 or when I run it with -nuintensitycor
*Iteration 1 Fri Dec 5 12:03:19 CST 2008 nu_correct -clobber ./tmp.mri_nu_correct.mni.8746/nu0.mnc ./tmp.mri_nu_correct.mni.8746/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8746/0/ nu_correct: couldn't find program "nu_estimate_np_and_em" nu_correct: couldn't find program "nu_evaluate" add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 486 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 521 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 530 add_default_args: warning: adding default arguments for unregistered program "nu_evaluate" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 530 spawn: error: program "nu_estimate_np_and_em" not registered at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 60 ERROR: nu_correct Linux chinook 2.6.18-53.1.21.el5 #1 SMP Wed May 7 08:42:13 EDT 2008 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Fri Dec 5 12:03:19 CST 2008*
I have made sure that the "nu_estimate_np_and_em" as well as "nu_evalutate" are both in the appropriate directory. I have also set the environment properly. Can anybody help me solve this? I appreciate any help or suggestions.
Thank you, Dev
Dev,
What happens when you type:
nu_estimate_np_and_em
you should see:
nu_estimate_np_and_em, version 1.10
Usage: nu_estimate_np_and_em [-help] [options] input_volume.mnc nu_field.imp Incorrect number of arguments
do you have perl installed at /usr/bin/perl ?
do you have another installation of the mni tools in your path, other than the one included with freesurfer?
Nick
On Fri, 2008-12-05 at 12:07 -0600, Devdutta W wrote:
Hello, I am a new freesurfer user. I have been trying to run recon-all on our data and have been unable to do so because recon-all crashes everytime at the same spot. Here is the error I get when I run recon-all with autorecon1 or when I run it with -nuintensitycor
Iteration 1 Fri Dec 5 12:03:19 CST 2008 nu_correct - clobber ./tmp.mri_nu_correct.mni.8746/nu0.mnc ./tmp.mri_nu_correct.mni.8746/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8746/0/ nu_correct: couldn't find program "nu_estimate_np_and_em" nu_correct: couldn't find program "nu_evaluate" add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 486 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 521 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 530 add_default_args: warning: adding default arguments for unregistered program "nu_evaluate" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 530 spawn: error: program "nu_estimate_np_and_em" not registered at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 60 ERROR: nu_correct Linux chinook 2.6.18-53.1.21.el5 #1 SMP Wed May 7 08:42:13 EDT 2008 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Fri Dec 5 12:03:19 CST 2008
I have made sure that the "nu_estimate_np_and_em" as well as "nu_evalutate" are both in the appropriate directory. I have also set the environment properly. Can anybody help me solve this? I appreciate any help or suggestions.
Thank you, Dev _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Nick, When I type nu_estimate_np_and_em, I did indeed see the message you mentioned. I also checked and found perl at /usr/bin/. I didn't find any other installations of the mni tools in my path. Are these the only things that usually cause recon-all to fail like this? Any other ideas why it is failing?
Thanks, Dev
On Fri, Dec 5, 2008 at 1:07 PM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
Dev,
What happens when you type:
nu_estimate_np_and_em
you should see:
nu_estimate_np_and_em, version 1.10
Usage: nu_estimate_np_and_em [-help] [options] input_volume.mnc nu_field.imp Incorrect number of arguments
do you have perl installed at /usr/bin/perl ?
do you have another installation of the mni tools in your path, other than the one included with freesurfer?
Nick
On Fri, 2008-12-05 at 12:07 -0600, Devdutta W wrote:
Hello, I am a new freesurfer user. I have been trying to run recon-all on our data and have been unable to do so because recon-all crashes everytime at the same spot. Here is the error I get when I run recon-all with autorecon1 or when I run it with -nuintensitycor
Iteration 1 Fri Dec 5 12:03:19 CST 2008 nu_correct - clobber ./tmp.mri_nu_correct.mni.8746/nu0.mnc
./tmp.mri_nu_correct.mni.8746/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8746/0/
nu_correct: couldn't find program "nu_estimate_np_and_em" nu_correct: couldn't find program "nu_evaluate" add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 486 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 521 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 530 add_default_args: warning: adding default arguments for unregistered program "nu_evaluate" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 530 spawn: error: program "nu_estimate_np_and_em" not registered at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 60 ERROR: nu_correct Linux chinook 2.6.18-53.1.21.el5 #1 SMP Wed May 7 08:42:13 EDT 2008 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Fri Dec 5 12:03:19 CST 2008
I have made sure that the "nu_estimate_np_and_em" as well as "nu_evalutate" are both in the appropriate directory. I have also set the environment properly. Can anybody help me solve this? I appreciate any help or suggestions.
Thank you, Dev _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
what OS are you using? what version of perl does it have? what is the output of:
env | grep MNI
On Fri, 2008-12-05 at 13:51 -0600, Devdutta W wrote:
Nick, When I type nu_estimate_np_and_em, I did indeed see the message you mentioned. I also checked and found perl at /usr/bin/. I didn't find any other installations of the mni tools in my path. Are these the only things that usually cause recon-all to fail like this? Any other ideas why it is failing?
Thanks, Dev
On Fri, Dec 5, 2008 at 1:07 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: Dev,
What happens when you type: nu_estimate_np_and_em you should see: nu_estimate_np_and_em, version 1.10 Usage: nu_estimate_np_and_em [-help] [options] input_volume.mnc nu_field.imp Incorrect number of arguments do you have perl installed at /usr/bin/perl ? do you have another installation of the mni tools in your path, other than the one included with freesurfer? Nick On Fri, 2008-12-05 at 12:07 -0600, Devdutta W wrote: > Hello, > I am a new freesurfer user. I have been trying to run recon-all on > our data and have been unable to do so because recon-all crashes > everytime at the same spot. > Here is the error I get when I run recon-all with autorecon1 or when I > run it with -nuintensitycor > > Iteration 1 Fri Dec 5 12:03:19 CST 2008 > nu_correct - > clobber ./tmp.mri_nu_correct.mni.8746/nu0.mnc ./tmp.mri_nu_correct.mni.8746/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8746/0/ > nu_correct: couldn't find program "nu_estimate_np_and_em" > nu_correct: couldn't find program "nu_evaluate" > add_default_args: warning: adding default arguments for unregistered > program "nu_estimate_np_and_em" > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 486 > add_default_args: warning: adding default arguments for unregistered > program "nu_estimate_np_and_em" > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 > add_default_args: warning: adding default arguments for unregistered > program "nu_estimate_np_and_em" > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 > add_default_args: warning: adding default arguments for unregistered > program "nu_estimate_np_and_em" > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 > add_default_args: warning: adding default arguments for unregistered > program "nu_estimate_np_and_em" > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 521 > add_default_args: warning: adding default arguments for unregistered > program "nu_estimate_np_and_em" > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 530 > add_default_args: warning: adding default arguments for unregistered > program "nu_evaluate" at /usr/local/imsw/freesurfer/mni/bin/nu_correct > line 530 > spawn: error: program "nu_estimate_np_and_em" not registered > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 60 > ERROR: nu_correct > Linux chinook 2.6.18-53.1.21.el5 #1 SMP Wed May 7 08:42:13 EDT 2008 > i686 i686 i386 GNU/Linux > > recon-all exited with ERRORS at Fri Dec 5 12:03:19 CST 2008 > > I have made sure that the "nu_estimate_np_and_em" as well as > "nu_evalutate" are both in the appropriate directory. I have also set > the environment properly. > Can anybody help me solve this? I appreciate any help or suggestions. > > Thank you, > Dev > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This is the output of env | grep MNI:
MNI_PERL5LIB=/usr/local/imsw/freesurfer/mni/lib/perl5/5.8.5 MNI_DIR=/usr/local/imsw/freesurfer/mni MNI_DATAPATH=/usr/local/imsw/freesurfer/mni/data
I am using Red Hat Enterprise Linux 5
Dev
On Fri, Dec 5, 2008 at 1:57 PM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
what OS are you using? what version of perl does it have? what is the output of:
env | grep MNI
On Fri, 2008-12-05 at 13:51 -0600, Devdutta W wrote:
Nick, When I type nu_estimate_np_and_em, I did indeed see the message you mentioned. I also checked and found perl at /usr/bin/. I didn't find any other installations of the mni tools in my path. Are these the only things that usually cause recon-all to fail like this? Any other ideas why it is failing?
Thanks, Dev
On Fri, Dec 5, 2008 at 1:07 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: Dev,
What happens when you type: nu_estimate_np_and_em you should see: nu_estimate_np_and_em, version 1.10 Usage: nu_estimate_np_and_em [-help] [options] input_volume.mnc nu_field.imp Incorrect number of arguments do you have perl installed at /usr/bin/perl ? do you have another installation of the mni tools in your path, other than the one included with freesurfer? Nick On Fri, 2008-12-05 at 12:07 -0600, Devdutta W wrote: > Hello, > I am a new freesurfer user. I have been trying to run recon-all on > our data and have been unable to do so because recon-all crashes > everytime at the same spot. > Here is the error I get when I run recon-all with autorecon1 or when I > run it with -nuintensitycor > > Iteration 1 Fri Dec 5 12:03:19 CST 2008 > nu_correct - > clobber ./tmp.mri_nu_correct.mni.8746/nu0.mnc./tmp.mri_nu_correct.mni.8746/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8746/0/
> nu_correct: couldn't find program "nu_estimate_np_and_em" > nu_correct: couldn't find program "nu_evaluate" > add_default_args: warning: adding default arguments for unregistered > program "nu_estimate_np_and_em" > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 486 > add_default_args: warning: adding default arguments for unregistered > program "nu_estimate_np_and_em" > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 > add_default_args: warning: adding default arguments for unregistered > program "nu_estimate_np_and_em" > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 > add_default_args: warning: adding default arguments for unregistered > program "nu_estimate_np_and_em" > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 > add_default_args: warning: adding default arguments for unregistered > program "nu_estimate_np_and_em" > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 521 > add_default_args: warning: adding default arguments for unregistered > program "nu_estimate_np_and_em" > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 530 > add_default_args: warning: adding default arguments for unregistered > program "nu_evaluate" at /usr/local/imsw/freesurfer/mni/bin/nu_correct > line 530 > spawn: error: program "nu_estimate_np_and_em" not registered > at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 60 > ERROR: nu_correct > Linux chinook 2.6.18-53.1.21.el5 #1 SMP Wed May 7 08:42:13 EDT 2008 > i686 i686 i386 GNU/Linux > > recon-all exited with ERRORS at Fri Dec 5 12:03:19 CST 2008 > > I have made sure that the "nu_estimate_np_and_em" as well as > "nu_evalutate" are both in the appropriate directory. I have also set > the environment properly. > Can anybody help me solve this? I appreciate any help or suggestions. > > Thank you, > Dev > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
I'm trying to use the mri_volcluster command to make label files from a single volume of binary voxel clusters. Once I have split the volume into individual label files I want to convter the label files back into individual cluster volumes (I am trying to use mri_label2vol to do this). The commands I've been using are:
mri_volcluster --in microbleeds-reslice.mgz --allowdiag --thmin .5 --labelbase ../scripts/clusters/testing/cluster
mri_label2vol --label ../scripts/clusters/testing/cluster-0001.label --temp orig-flip-reslice.mgz --o cluster-0001.mgz
(NOTE: the -reslice is because these volumes have been resliced from 0.4492, 0.4492, 6.0000 sized voxels to conform to 1 mm^3 sized voxels; the dimensions of the image were altered as well, from 384 x 512 x 23 voxels to 173 x 230 x 138 voxels)
When I view cluster-0001.mgz with tkmedit the result is a 3D checkerboard like pattern with no two voxels having common edges (despite the original cluster in microbleeds-reslice.mgz being a solid cluster of 90 mm^3). What I wanted to see was that each cluster could be reconstructed in a single volume (i.e. cluster-0001.mgz, cluster-0002.mgz, etc with each volume containing only one cluster).
Also, when I use mri_cor2label and then mri_label2vol to switch between label files and volumes files, the clusters (despite not being split up like I want) are solid and do not display this checkerboard effect...leading me to think that its an issue with mri_volcluster.
Any help you can offer would be terrific. Thanks a ton.
Greg --
freesurfer@nmr.mgh.harvard.edu
-
Devdutta W -
Gregory Dierksen -
Nick Schmansky