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