Do you have the MNI software installed? See our installation page on the wiki.
doug
Pom Sailasuta wrote:
Hi Bruce,
Thank you so much.
I got new error as follow
////////////////////////////// Pom@pom-PC subjects]$ recon-all -s 211-1029-MKA_elan -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux pom-PC.SME 2.6.35.6-45.fc14.i686 #1 SMP Mon Oct 18 23:56:17 UTC 2010 i686 i686 i386 GNU/Linux nu_correct: Command not found. #-------------------------------------------- #@# MotionCor Fri Feb 25 09:46:49 PST 2011 Found 1 runs /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri//001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue.
cp /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri//001.mgz /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/rawavg.mgz
/usr/local/freesurfer/subjects/211-1029-MKA_elan
mri_convert /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/rawavg.mgz /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz --conform
mri_convert /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/rawavg.mgz /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz --conform $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/rawavg.mgz... TR=4083.33, TE=14.00, TI=0.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) Original Data has (1.0156, 1.0156, 3) mm size and (256, 256, 60) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz...
mri_add_xform_to_header -c /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Fri Feb 25 09:47:00 PST 2011
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2
/usr/local/freesurfer/subjects/211-1029-MKA_elan/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.12 2009/12/16 20:15:41 greve Exp $ Linux pom-PC.SME 2.6.35.6-45.fc14.i686 #1 SMP Mon Oct 18 23:56:17 UTC 2010 i686 i686 i386 GNU/Linux Fri Feb 25 09:47:00 PST 2011 nu_correct: Command not found. tmpdir is ./tmp.mri_nu_correct.mni.17383 /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17383/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17383/nu0.mnc -odt float $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from orig.mgz... TR=4083.33, TE=14.00, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.17383/nu0.mnc...
Iteration 1 Fri Feb 25 09:47:03 PST 2011 nu_correct -clobber ./tmp.mri_nu_correct.mni.17383/nu0.mnc ./tmp.mri_nu_correct.mni.17383/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17383/0/ nu_correct: Command not found. ERROR: nu_correct Linux pom-PC.SME 2.6.35.6-45.fc14.i686 #1 SMP Mon Oct 18 23:56:17 UTC 2010 i686 i686 i386 GNU/Linux
recon-all -s 211-1029-MKA_elan exited with ERRORS at Fri Feb 25 09:47:03 PST 2011 ////////////////////////////////////////////
There is nu_correct in /usr/local/freesurfer/mni/bin as follows:
[Pom@pom-PC subjects]$ which nu_correct /usr/local/freesurfer/mni/bin/nu_correct
thanks again.
-- Pom
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