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