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 <dura...@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 > > > >
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