# recon-all -i /root/Desktop/F200.mnc -subjid F200 -sd /usr/local/freesurfer/subjects -all
I've attached the output to a text file. Any help is greatly appreciated.
Thanks - Anil Roy.
On 6/23/06, Bruce Fischl <[EMAIL PROTECTED]> wrote:
well, you specified -autorecon3, which assumes some stuff has been run
before. If you want to do everything from beginning to end run -all instead
Bruce
On Fri, 23 Jun 2006, Anil Roy wrote:
> This is the first step. I assumed that recon-all should do all the
> processing by itself without the need to run anything previously. Please
> mention if any extra steps have to be taken before the parcellation stats
> (or the entire recon-all process) can be obtained from the minc file.
>
> Thanks - Anil.
>
> On 6/23/06, Bruce Fischl <[EMAIL PROTECTED]> wrote:
>>
>> what steps have you run previously? You don't need to specify -i on later
>> stages, just the subjid and sd.
>>
>> On Fri, 23 Jun 2006, Anil Roy wrote:
>>
>> > Hello All,
>> >
>> > So I tried using recon-all to get a few parcellations stats from a minc
>> file
>> > it but I'm getting the following error. Please could someone say how
>> this
>> > can be rectified. Thanks. - Anil Roy.
>> >
>> > This is the command I'm giving:
>> >
>> > # recon-all -force -i /root/Desktop/F100.mnc -subjid F100 -sd
>> > /usr/local/freesurfer/subjects -autorecon3
>> >
>> > This is the output.
>> >
>> > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
>> > INFO: /usr/local/freesurfer/subjects/F100 exists with -i, but -force
>> > specified.
>> > Deleting any previous source volumes
>> > Actual FREESURFER_HOME /usr/local/freesurfer
>> > -rw-rw-r-- 1 root root 30123 Jun 23 15:50
>> > /usr/local/freesurfer/subjects/F100/scripts/recon-all.log
>> > Linux dhcp-129-105-146-155.speech.northwestern.edu 2.6.11-1.1369_FC4smp#1
>> > SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux
>> > WM removal version
>> > /usr/local/freesurfer/subjects/F100
>> >
>> > mri_convert /root/Desktop/F100.mnc
>> > /usr/local/freesurfer/subjects/F100/mri/orig/001.mgz
>> >
>> > mri_convert /root/Desktop/F100.mnc
>> > /usr/local/freesurfer/subjects/F100/mri/orig/001.mgz
>> > reading from /root/Desktop/F100.mnc...
>> > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>> > i_ras = (1, 0, 0)
>> > j_ras = (0, 1, 0)
>> > k_ras = (0, 0, 1)
>> > writing to /usr/local/freesurfer/subjects/F100/mri/orig/001.mgz...
>> > #--------------------------------------------
>> > [EMAIL PROTECTED] Sphere lh Fri Jun 23 15:56:29 CDT 2006
>> > /usr/local/freesurfer/subjects/F100/scripts
>> >
>> > mris_sphere ../surf/lh.inflated ../surf/lh.sphere
>> >
>> > $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $
>> > $Id: mrisurf.c,v 1.441.2.3 2006/04/12 02:03:02 nicks Exp $
>> > MRISread(../surf/lh.inflated): could not open file
>> > No such file or directory
>> > mris_sphere: could not read surface file ../surf/lh.inflated
>> > No such file or directory
>> > Linux speech.northwestern.edu 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2
>> 23:08:39
>> > EDT 2005 i686 i686 i386 GNU/Linux
>> >
>> > recon-all exited with ERRORS at Fri Jun 23 15:56:29 CDT 2006
>> >
>>
>
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects ERROR: /usr/local/freesurfer/subjects/F200 exists, delete or re-run with -force [EMAIL PROTECTED] freesurfer]# recon-all -force -i /root/Desktop/F200.mnc -subjid F200 -sd /usr/local/freesurfer/subjects -all INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects INFO: /usr/local/freesurfer/subjects/F200 exists with -i, but -force specified. Deleting any previous source volumes Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 9126 Jun 25 15:42 /usr/local/freesurfer/subjects/F200/scripts/recon-all.log Linux dhcp-129-105-146-220.speech.northwestern.edu 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux WM removal version /usr/local/freesurfer/subjects/F200
mri_convert /root/Desktop/F200.mnc /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz mri_convert /root/Desktop/F200.mnc /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz reading from /root/Desktop/F200.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz... #-------------------------------------------- [EMAIL PROTECTED] MotionCor Sun Jun 25 15:42:47 CDT 2006 Found 1 runs /usr/local/freesurfer/subjects/F200/mri/orig/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/F200/mri/orig/001.mgz /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz /usr/local/freesurfer/subjects/F200 mri_convert /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz /usr/local/freesurfer/subjects/F200/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz /usr/local/freesurfer/subjects/F200/mri/orig.mgz --conform reading from /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (1, 1, 1) mm size and (181, 217, 181) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 4 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/F200/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/F200/mri/orig.mgz /usr/local/freesurfer/subjects/F200/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- [EMAIL PROTECTED] Nu Intensity Correction Sun Jun 25 15:43:04 CDT 2006 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /usr/local/freesurfer/subjects/F200/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 1.3 2005/12/08 01:27:21 greve Exp $ Linux dhcp-129-105-146-220.speech.northwestern.edu 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux Sun Jun 25 15:43:04 CDT 2006 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by [EMAIL PROTECTED] (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 tmpdir is ./tmp.mri_nu_correct.mni.3620 /usr/local/freesurfer/subjects/F200/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3620/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3620/nu0.mnc Can't find the talairach xform '/usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.3620/nu0.mnc... -------------------------------------------------------- Iteration 1 Sun Jun 25 15:43:10 CDT 2006 nu_correct -clobber ./tmp.mri_nu_correct.mni.3620/nu0.mnc ./tmp.mri_nu_correct.mni.3620/nu1.mnc [EMAIL PROTECTED]:/usr/local/freesurfer/subjects/F200/mri/] [2006-06-25 15:43:11] running: /usr/local/freesurfer/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 /usr/tmp/nu_correct_3670/ ./tmp.mri_nu_correct.mni.3620/nu0.mnc ./tmp.mri_nu_correct.mni.3620/nu1.imp /usr/local/freesurfer/mni/bin/volume_stats: error while loading shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directory nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) ERROR: nu_correct Linux dhcp-129-105-146-220.speech.northwestern.edu 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Sun Jun 25 15:43:11 CDT 2006
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