Hi Freesurfer experts,

I am successfully running recon-all on my cluster. However I find that the subject folders have sizes ranging from 300mb to 900mb.

I grepped all recon-all.log files for "finished without error" and that seemed fine for all subjects. 

But I would like to know what is the expected subject folder size when you run recon-all (with -all option) starting from a standard MPRAGE T1 image. This might be useful since I have limited control over the cluster nodes where the processing takes place.

Thank you

Durai

On Mon, Feb 17, 2014 at 2:55 AM, Durai Arasan <durai23@gmail.com> wrote:

Hi Freesurfer experts, 

so I got this error when I ran recon-all on my cluster. I am really hoping this is just a case of missing GCC libraries and nothing is wrong with the Freesurfer installation on the nodes. Kindly confirm this. 

Thank you

**********************************************************************************************************************************

Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /******************

Actual FREESURFER_HOME /**************************************

Linux *****************************  SMP Fri Mar 22 05:41:51 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux

mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert)

mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert)

mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_convert)

mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert)

mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert)

mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_convert)

tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by tkregister2_cmdl)

tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by tkregister2_cmdl)

tkregister2_cmdl: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by tkregister2_cmdl)

mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_make_uchar)

mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_make_uchar)

mri_make_uchar: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_make_uchar)

mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_normalize)

mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_normalize)

mri_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_normalize)

mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_watershed)

mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_watershed)

mri_watershed: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_watershed)

mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_gcut)

mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_gcut)

mri_gcut: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_gcut)

mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_segment)

mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_segment)

mri_segment: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_segment)

mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_label2label)

mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_label2label)

mri_label2label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_label2label)

mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_em_register)

mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_em_register)

mri_em_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_em_register)

mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_normalize)

mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_normalize)

mri_ca_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_ca_normalize)

mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_register)

mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_register)

mri_ca_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_ca_register)

mri_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_label)

mri_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_label)

mri_ca_label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_ca_label)

mri_pretess: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_pretess)

mri_pretess: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_pretess)

mri_pretess: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_pretess)

mri_fill: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_fill)

mri_fill: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_fill)

mri_fill: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_fill)

mri_tessellate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_tessellate)

mri_tessellate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_tessellate)

mri_tessellate: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_tessellate)

mri_concatenate_lta: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_concatenate_lta)

mri_concatenate_lta: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_concatenate_lta)

mri_concatenate_lta: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_concatenate_lta)

mri_normalize_tp2: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_normalize_tp2)

mri_normalize_tp2: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_normalize_tp2)

mri_normalize_tp2: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_normalize_tp2)

mris_smooth: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_smooth)

mris_smooth: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_smooth)

mris_smooth: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_smooth)

mris_inflate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_inflate)

mris_inflate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_inflate)

mris_inflate: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_inflate)

mris_curvature: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_curvature)

mris_curvature: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_curvature)

mris_curvature: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_curvature)

mris_sphere: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_sphere)

mris_sphere: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_sphere)

mris_sphere: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_sphere)

mris_fix_topology: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_fix_topology)

mris_fix_topology: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_fix_topology)

mris_fix_topology: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_fix_topology)

mris_topo_fixer: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_topo_fixer)

mris_topo_fixer: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_topo_fixer)

mris_topo_fixer: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_topo_fixer)

mris_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_ca_label)

mris_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_ca_label)

mris_ca_label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_ca_label)

mris_euler_number: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_euler_number)

mris_euler_number: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_euler_number)

mris_euler_number: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_euler_number)

mris_make_surfaces: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_make_surfaces)

mris_make_surfaces: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_make_surfaces)

mris_make_surfaces: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_make_surfaces)

mris_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_register)

mris_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_register)

mris_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_register)

mris_volmask: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_volmask)

mris_volmask: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_volmask)

mris_volmask: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_volmask)

mris_anatomical_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_anatomical_stats)

mris_anatomical_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_anatomical_stats)

mris_anatomical_stats: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_anatomical_stats)

mrisp_paint: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mrisp_paint)

mrisp_paint: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mrisp_paint)

mrisp_paint: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mrisp_paint)

mris_curvature_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_curvature_stats)

mris_curvature_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_curvature_stats)

mris_curvature_stats: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_curvature_stats)

mris_calc: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_calc)

mris_calc: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_calc)

mris_calc: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_calc)

mri_robust_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_robust_register)

mri_robust_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_robust_register)

mri_robust_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_robust_register)

mri_robust_template: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_robust_template)

mri_robust_template: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_robust_template)

mri_robust_template: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_robust_template)

mri_and: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_and)

mri_and: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_and)

mri_and: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_and)

mri_or: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_or)

mri_or: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_or)

mri_or: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_or)

mri_fuse_segmentations: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_fuse_segmentations)

mri_fuse_segmentations: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_fuse_segmentations)

mri_fuse_segmentations: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_fuse_segmentations)

mri_segstats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_segstats)

mri_segstats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_segstats)

mri_segstats: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_segstats)

/****************/***444

 mri_convert /********************/***_mp.nii /*******************/****444/mri/orig/001.mgz 

mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert)

mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert)

mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_convert)

Linux ************************************ ************************ SMP Fri Mar 22 ******** EDT 2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s ***444 exited with ERRORS at Mon Feb 17 02:24:00 EST 2014

For more details, see the log file **********************/***444/scripts/recon-all.log

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.