Hi Bruce,<br>    After exhausting all of our options, Tali Swisher 
informed me that I should contact you. I have been trying to run 
freesurfer on a brain and have been running into a lot of problems. 
After first running:<br>
<span style="background-color:rgb(255,153,0)">recon-all -i nifti-files/002-t1w-realign-masked.nii.gz
 -autorecon1 -noskullstrip -subjid 002 &amp;&amp; cp 
subjects/002/mri/T1.mgz subjects/002/mri/brainmask.mgz &amp;&amp; 
recon-all -autorecon2 -subjid 002 &amp;&amp; recon-all -autorecon3 
-subjid 002</span><br>
the process stopped within 10 minutes with a talairach_afd error.<br><br>I followed our instructions (<a href="https://intweb.spl.harvard.edu/Freesurfer_Notes#Stopping_after_talairach_afd" target="_blank">https://intweb.spl.harvard.edu/Freesurfer_Notes#Stopping_after_talairach_afd</a>)
 to create the xformed-t1w.xfm file, and compared it with the 
talairach.xfm file in the subjects/002/mri/transforms folder. Since they
 were different, I replaced the values in the talairach.xfm file with 
the ones from the xformed-t1w.xfm file (side note: the xformed-t1w is 
4x4 and talairach.xfm is 3x4-- i attempted both including the last line 
and excluding it; to no avail).<br>
<br>Afterwards, I ran the script: <span style="background-color:rgb(255,153,0)">recon-all
 -autorecon1 -notal-check -noskullstrip -subjid 002 &amp;&amp; cp 
subjects/002/mri/T1.mgz subjects/002/mri/brainmask.mgz &amp;&amp; 
recon-all -autorecon2 -subjid 002 &amp;&amp; recon-all -autorecon3 
-subjid 002</span><br>
<br>and while I got past the initial 20 minutes, I ended up exiting with
 errors. I have included the entire process below, but highlighted areas
 I believe to be problems: <br><br><br>&lt;121&gt; pnl-d6-4 /projects/schiz/ra/eli/<div id=":17m">freesurfer5.1 % source SetUpFreeSurfer.csh <br>
-------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 --------<br>Setting up environment for FreeSurfer/FS-FAST (and FSL)<br>FREESURFER_HOME   /projects/schiz/ra/eli/freesurfer5.1<br>FSFAST_HOME       /projects/schiz/ra/eli/freesurfer5.1/fsfast<br>

FSF_OUTPUT_FORMAT nii.gz<br>SUBJECTS_DIR      /projects/schiz/ra/eli/freesurfer5.1/subjects<br>MNI_DIR           /projects/schiz/ra/eli/freesurfer5.1/mni<br>FSL_DIR           /projects/schiz/software/fsl-4.1-64bit<br>&lt;122&gt; pnl-d6-4 /projects/schiz/ra/eli/freesurfer5.1
 % recon-all -autorecon1 -notal-check -noskullstrip -subjid 002 
&amp;&amp; cp subjects/002/mri/T1.mgz subjects/002/mri/brainmask.mgz 
&amp;&amp; recon-all -autorecon2 -subjid 002 &amp;&amp; recon-all 
-autorecon3 -subjid 002<br>
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0<br>Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0<br>INFO: SUBJECTS_DIR is /projects/schiz/ra/eli/freesurfer5.1/subjects<br>Actual FREESURFER_HOME /projects/schiz/ra/eli/freesurfer5.1<br>

-rw-rw-r-- 1 eli schiz 22143 Feb 19 19:37 /projects/schiz/ra/eli/freesurfer5.1/subjects/002/scripts/recon-all.log<br>Linux <a href="http://pnl-d6-4.bwh.harvard.edu" target="_blank">pnl-d6-4.bwh.harvard.edu</a> 2.6.34.9-69.fc13.x86_64 #1 SMP Tue May 3 09:23:03 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux<br>

#--------------------------------------------<br>#@# MotionCor Wed Feb 20 13:31:51 EST 2013<br>Found 1 runs<br>/projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/orig/001.mgz<br>Checking for (invalid) multi-frame inputs...<br>

WARNING: only one run found. This is OK, but motion<br>correction cannot be performed on one run, so I&#39;ll<br>copy the run to rawavg and continue.<br><br> cp /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/orig/001.mgz /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/rawavg.mgz <br>

<br>/projects/schiz/ra/eli/freesurfer5.1/subjects/002<br><br> mri_convert /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/rawavg.mgz /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/orig.mgz --conform <br><br>
mri_convert /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/rawavg.mgz /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/orig.mgz --conform <br>
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $<br>reading from /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/rawavg.mgz...<br>TR=0.00, TE=0.00, TI=0.00, flip angle=0.00<br>i_ras = (0, -0.989776, -0.142629)<br>

j_ras = (0, 0.142629, -0.989776)<br>k_ras = (1, 0, 0)<br>Original Data has (1, 1, 1) mm size and (216, 220, 176) voxels.<br>Data is conformed to 1 mm size and 256 voxels for all directions<br>changing data type from float to uchar (noscale = 0)...<br>

MRIchangeType: Building histogram <br>Reslicing using trilinear interpolation <br>writing to /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/orig.mgz...<br><br> mri_add_xform_to_header -c /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/transforms/talairach.xfm /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/orig.mgz /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/orig.mgz <br>

<br>INFO: extension is mgz<br>#--------------------------------------------<br>#@# Talairach Wed Feb 20 13:32:06 EST 2013<br>/projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri<br><br> talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm <br>

<br><br>INFO: transforms/talairach.xfm already exists!<br>The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm<br>This is done to retain any edits made to transforms/talairach.xfm<br>Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm<br>

<br>#--------------------------------------------<br>#@# Nu Intensity Correction Wed Feb 20 13:33:08 EST 2013<br><br> mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 <br><br>/projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri<br>

/projects/schiz/ra/eli/freesurfer5.1/bin/mri_nu_correct.mni<br>--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2<br>nIters 2<br>$Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $<br>Linux <a href="http://pnl-d6-4.bwh.harvard.edu" target="_blank">pnl-d6-4.bwh.harvard.edu</a> 2.6.34.9-69.fc13.x86_64 #1 SMP Tue May 3 09:23:03 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux<br>

Wed Feb 20 13:33:08 EST 2013<br>Program nu_correct, built from:<br>Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37<br>tmpdir is ./tmp.mri_nu_correct.mni.24409<br>

/projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri<br>mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24409/nu0.mnc -odt float<br>mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24409/nu0.mnc -odt float <br>$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $<br>

reading from orig.mgz...<br>TR=0.00, TE=0.00, TI=0.00, flip angle=0.00<br>i_ras = (-1, 0, 0)<br>j_ras = (2.38419e-07, 0, -1)<br>k_ras = (-1.93715e-07, 1, 0)<br>changing data type from uchar to float (noscale = 0)...<br>writing to ./tmp.mri_nu_correct.mni.24409/nu0.mnc...<br>

 <br>--------------------------------------------------------<br>Iteration 1 Wed Feb 20 13:33:15 EST 2013<br>nu_correct -clobber ./tmp.mri_nu_correct.mni.24409/nu0.mnc ./tmp.mri_nu_correct.mni.24409/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24409/0/<br>

[eli@pnl-d6-4.bwh.harvard.edu:/projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/] [2013-02-20 13:33:15] running:<br>  /projects/schiz/ra/eli/freesurfer5.1/mni/bin/nu_estimate_np_and_em
 -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 
-auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber 
-nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.24409/0/ ./tmp.mri_nu_correct.mni.24409/nu0.mnc ./tmp.mri_nu_correct.mni.24409/nu1.imp<br>
<br>Processing:.................................................................Done<br>Processing:.................................................................Done<br>Processing:.................................................................Done<br>

Number of iterations: 3 <br>CV of field change: 0.000383553<br>[eli@pnl-d6-4.bwh.harvard.edu:/projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/] [2013-02-20 13:33:21] running:<br>  /projects/schiz/ra/eli/freesurfer5.1/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24409/nu0.mnc ./tmp.mri_nu_correct.mni.24409/0//template.mnc<br>

<br>Transforming slices:......................................................................................Done<br>Transforming slices:................................................................................................................................................................................................................................................................Done<br>

 <br> <br>--------------------------------------------------------<br>Iteration 2 Wed Feb 20 13:33:31 EST 2013<br>nu_correct -clobber ./tmp.mri_nu_correct.mni.24409/nu1.mnc ./tmp.mri_nu_correct.mni.24409/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.24409/1/<br>

[eli@pnl-d6-4.bwh.harvard.edu:/projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/] [2013-02-20 13:33:31] running:<br>  /projects/schiz/ra/eli/freesurfer5.1/mni/bin/nu_estimate_np_and_em
 -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 
-auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber 
-nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.24409/1/ ./tmp.mri_nu_correct.mni.24409/nu1.mnc ./tmp.mri_nu_correct.mni.24409/nu2.imp<br>
<br>Processing:.................................................................Done<br>Processing:.................................................................Done<br>Number of iterations: 2 <br>CV of field change: 0.000575678<br>

[eli@pnl-d6-4.bwh.harvard.edu:/projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri/] [2013-02-20 13:33:36] running:<br>  /projects/schiz/ra/eli/freesurfer5.1/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24409/nu1.mnc ./tmp.mri_nu_correct.mni.24409/1//template.mnc<br>

<br>Transforming slices:......................................................................................Done<br>Transforming slices:................................................................................................................................................................................................................................................................Done<br>

 <br> <br> <br>mri_binarize --i ./tmp.mri_nu_correct.mni.24409/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24409/ones.mgz<br><br>$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $<br>cwd /projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri<br>

cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.24409/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24409/ones.mgz <br>sysname  Linux<br>hostname <a href="http://pnl-d6-4.bwh.harvard.edu" target="_blank">pnl-d6-4.bwh.harvard.edu</a><br>

machine  x86_64<br>user     eli<br><br>input      ./tmp.mri_nu_correct.mni.24409/nu2.mnc<br>frame      0<br>nErode3d   0<br>nErode2d   0<br>output     ./tmp.mri_nu_correct.mni.24409/ones.mgz<br>Binarizing based on threshold<br>

min        -1<br>max        +infinity<br>binval        1<br>binvalnot     0<br>Found 16777216 values in range<br>Counting number of voxels<br>Found 16777216 voxels in final mask<br>mri_binarize done<br>mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24409/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24409/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24409/input.mean.dat<br>

<br>$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $<br>cwd <br>cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24409/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24409/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24409/input.mean.dat <br>

sysname  Linux<br>hostname <a href="http://pnl-d6-4.bwh.harvard.edu" target="_blank">pnl-d6-4.bwh.harvard.edu</a><br>machine  x86_64<br>user     eli<br>Loading ./tmp.mri_nu_correct.mni.24409/ones.mgz<br>Loading orig.mgz<br>
Voxel Volume is 1 mm^3<br>
Generating list of segmentation ids<br>Found   1 segmentations<br>Computing statistics for each segmentation<br>  0     1   16777216  1.67772e+07<br><br>Reporting on   1 segmentations<br>Computing spatial average of each frame<br>

  0<br>Writing to ./tmp.mri_nu_correct.mni.24409/input.mean.dat<br>mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24409/ones.mgz --i ./tmp.mri_nu_correct.mni.24409/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24409/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24409/output.mean.dat<br>

<br>$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $<br>cwd <br>cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24409/ones.mgz --i ./tmp.mri_nu_correct.mni.24409/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24409/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24409/output.mean.dat <br>

sysname  Linux<br>hostname <a href="http://pnl-d6-4.bwh.harvard.edu" target="_blank">pnl-d6-4.bwh.harvard.edu</a><br>machine  x86_64<br>user     eli<br>Loading ./tmp.mri_nu_correct.mni.24409/ones.mgz<br>Loading ./tmp.mri_nu_correct.mni.24409/nu2.mnc<br>

Voxel Volume is 1 mm^3<br>Generating list of segmentation ids<br>Found   1 segmentations<br>Computing statistics for each segmentation<br>  0     1   16777216  1.67772e+07<br><br>Reporting on   1 segmentations<br>Computing spatial average of each frame<br>

  0<br>Writing to ./tmp.mri_nu_correct.mni.24409/output.mean.dat<br>mris_calc -o ./tmp.mri_nu_correct.mni.24409/nu2.mnc ./tmp.mri_nu_correct.mni.24409/nu2.mnc mul .98003231285471643398<br>Saving result to &#39;./tmp.mri_nu_correct.mni.24409/nu2.mnc&#39; (type = MINC )                       [ ok ]<br>

mri_convert ./tmp.mri_nu_correct.mni.24409/nu2.mnc nu.mgz --like orig.mgz<br>mri_convert ./tmp.mri_nu_correct.mni.24409/nu2.mnc nu.mgz --like orig.mgz <br>$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $<br>

reading from ./tmp.mri_nu_correct.mni.24409/nu2.mnc...<br>TR=0.00, TE=0.00, TI=0.00, flip angle=0.00<br>i_ras = (-1, 0, 0)<br>j_ras = (2.38419e-07, 0, -1)<br>k_ras = (-1.93715e-07, 1, 0)<br>INFO: transform src into the like-volume: orig.mgz<br>

Reslicing using trilinear interpolation <br>writing to nu.mgz...<br>mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz<br>type change took 0 minutes and 11 seconds.<br>mapping ( 0,  0) to ( 3, 110)<br> <br> <br>Wed Feb 20 13:35:04 EST 2013<br>

mri_nu_correct.mni done<br>#--------------------------------------------<br><span style="background-color:rgb(255,102,102)">#@# Intensity Normalization Wed Feb 20 13:35:04 EST 2013</span><br style="background-color:rgb(255,102,102)">

<span style="background-color:rgb(255,102,102)">/projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri</span><br style="background-color:rgb(255,102,102)"><br style="background-color:rgb(255,102,102)"><span style="background-color:rgb(255,102,102)"> mri_normalize -g 1 nu.mgz T1.mgz </span><br style="background-color:rgb(255,102,102)">

<br style="background-color:rgb(255,102,102)"><span style="background-color:rgb(255,102,102)">using max gradient = 1.000</span><br style="background-color:rgb(255,102,102)"><span style="background-color:rgb(255,102,102)">reading from nu.mgz...</span><br style="background-color:rgb(255,102,102)">

<span style="background-color:rgb(255,102,102)">normalizing image...</span><br style="background-color:rgb(255,102,102)"><span style="background-color:rgb(255,102,102)">MRInormalize: could not find any valid peaks.</span><br style="background-color:rgb(255,102,102)">

<br style="background-color:rgb(255,102,102)"><span style="background-color:rgb(255,102,102)">Make sure the Talairach alignment is correct!</span><br><br>building Voronoi diagram...<br>performing soap bubble smoothing...<br>

3d normalization pass 1 of 2<br>building Voronoi diagram...<br>performing soap bubble smoothing...<br>3d normalization pass 2 of 2<br>building Voronoi diagram...<br>performing soap bubble smoothing...<br>writing output to T1.mgz<br>

3D bias adjustment took 6 minutes and 5 seconds.<br>1d normalization failed - trying no1d...<br>white matter peak found at -nan<br>white matter peak found at  0<br>gm peak at  0 (0), valley at  0 (-10)<br>csf peak at  0, setting threshold to  0<br>

white matter peak found at -nan<br>white matter peak found at  0<br>gm peak at  0 (0), valley at  0 (-10)<br>csf peak at  0, setting threshold to  0<br><br>#------------------------------------------<br><br>recon-all -s 002 finished without error at Wed Feb 20 13:41:11 EST 2013<br>

done<br>Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0<br>Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0<br>INFO: SUBJECTS_DIR is /projects/schiz/ra/eli/freesurfer5.1/subjects<br>Actual FREESURFER_HOME /projects/schiz/ra/eli/freesurfer5.1<br>

-rw-rw-r-- 1 eli schiz 50049 Feb 20 13:41 /projects/schiz/ra/eli/freesurfer5.1/subjects/002/scripts/recon-all.log<br>Linux <a href="http://pnl-d6-4.bwh.harvard.edu" target="_blank">pnl-d6-4.bwh.harvard.edu</a> 2.6.34.9-69.fc13.x86_64 #1 SMP Tue May 3 09:23:03 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux<br>

#-------------------------------------<br>#@# EM Registration Wed Feb 20 13:41:16 EST 2013<br>/projects/schiz/ra/eli/freesurfer5.1/subjects/002/mri<br><br> mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /projects/schiz/ra/eli/freesurfer5.1/average/RB_all_2008-03-26.gca transforms/talairach.lta <br>

<br>aligning to atlas containing skull, setting unknown_nbr_spacing = 3<br>using MR volume brainmask.mgz to mask input volume...<br>reading 1 input volumes...<br>logging results to talairach.log<br>reading &#39;/projects/schiz/ra/eli/freesurfer5.1/average/RB_all_2008-03-26.gca&#39;...<br>

gcaAllocMax: node dims 64 64 64<br>gcaAllocMax: prior dims 128 128 128<br>gcaAllocMax: max_labels 0<br>average std = 6.9   using min determinant for regularization = 4.7<br>0 singular and 1812 ill-conditioned covariance matrices regularized<br>

reading &#39;nu.mgz&#39;...<br>freeing gibbs priors...done.<br>bounding unknown intensity as &lt; 14.9 or &gt; 790.2 <br>total sample mean = 84.4 (994 zeros)<br>************************************************<br>spacing=8, using 2772 sample points, tol=1.00e-05...<br>

************************************************<br><span style="background-color:rgb(255,102,102)">register_mri: find_optimal_transform</span><br style="background-color:rgb(255,102,102)"><span style="background-color:rgb(255,102,102)">find_optimal_transform: nsamples 2772, passno 0, spacing 8</span><br style="background-color:rgb(255,102,102)">

<span style="background-color:rgb(255,102,102)">GCAhistoScaleImageIntensities: could not find wm peak</span><br style="background-color:rgb(255,102,102)"><span style="background-color:rgb(255,102,102)">resetting wm mean[0]: 102 --&gt; 107</span><br style="background-color:rgb(255,102,102)">

<span style="background-color:rgb(255,102,102)">resetting gm mean[0]: 64 --&gt; 64</span><br style="background-color:rgb(255,102,102)"><span style="background-color:rgb(255,102,102)">input volume #1 is the most T1-like</span><br style="background-color:rgb(255,102,102)">

<span style="background-color:rgb(255,102,102)">using real data threshold=0.0</span><br style="background-color:rgb(255,102,102)"><span style="background-color:rgb(255,102,102)">skull bounding box = (0, 0, 0) --&gt; (255, 255, 255)</span><br style="background-color:rgb(255,102,102)">

<span style="background-color:rgb(255,102,102)">using (85, 85, 128) as brain centroid...</span><br style="background-color:rgb(255,102,102)"><span style="background-color:rgb(255,102,102)">mean wm in atlas = 107, using box (53,53,96) --&gt; (116, 116,159) to find MRI wm</span><br style="background-color:rgb(255,102,102)">

<span style="background-color:rgb(255,102,102)">WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri-&gt;nbins=1, mri_peak=-1</span><br style="background-color:rgb(255,102,102)"><span style="background-color:rgb(255,102,102)">before smoothing, mri peak at 0</span><br style="background-color:rgb(255,102,102)">

<span style="background-color:rgb(255,102,102)">WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri-&gt;nbins=1, mri_peak=-1</span><br style="background-color:rgb(255,102,102)"><span style="background-color:rgb(255,102,102)">after smoothing, mri peak at 0, scaling input intensities by inf</span><br style="background-color:rgb(255,102,102)">

<span style="background-color:rgb(255,102,102)">Linux <a href="http://pnl-d6-4.bwh.harvard.edu" target="_blank">pnl-d6-4.bwh.harvard.edu</a> 2.6.34.9-69.fc13.x86_64 #1 SMP Tue May 3 09:23:03 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux</span><br style="background-color:rgb(255,102,102)">

<br style="background-color:rgb(255,102,102)"><span style="background-color:rgb(255,102,102)">recon-all -s 002 exited with ERRORS at Wed Feb 20 13:41:52 EST 2013</span><br><br>For more details, see the log file /projects/schiz/ra/eli/freesurfer5.1/subjects/002/scripts/recon-all.log<br>

To report a problem, see <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting" target="_blank">http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting</a><br><br clear="all"><b>The
 only thing I am not sure about, is maybe I needed to edit the 
talairach.auto.xfm file as well? I haven&#39;t tried that because I am not 
sure if there would be unintended consequences.<br>
<br><br><br>Thanks,<br>Eli<span class="HOEnZb"><font color="#888888"><br></font></span></b></div><br clear="all"><br>-- <br><span><font color="#888888">Eli Fredman, BA<br>Research Assistant<br>Psychiatry Neuroimaging Laboratory<br>
Harvard Medical School, Brigham and Women&#39;s Hospital<br>1249 Boylston St, 3rd Floor<br>



Boston, MA 02215<br>Office: <a value="+16175256119">(617) 525-6118</a><br>Cell: <a value="+13365775071">(314) 952-8098</a><br>


Fax: <a value="+16175256150">(617) 525-6150</a></font></span>