[Freesurfer] ERROR: could not find ribbon.mgz
Dear Freesurfer community, I am conducting cortical-thickness analysis using freesurfer 5.3.0. The error during: recon-all –autorecon1 –subjid BB53_mdeft, where mri_segstats could find ribbon.mgz, appeard after eliminating Dura mater and N.opticus. Below, we provide the details of our setup and the exact error message for one subject. Feel free to ask for more information. Thank you very much for your help! Yours sincerely, Jana Dinges FREESURFER_HOME: /apps/prod/i486/freesurfer-5.3.0 Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Debian version: 5.0.6 Kernel info: Linux 2.6.27.39-1-ql-beowulf i686 $ which freesurfer -> /apps/prod/i486/freesurfer-5.3.0/bin/freesurfer Used command: recon-all –autoreco1 –subjid BB53_mdeft. Error Message: INFO: mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file /data/projects/oertelmatura/Neurodegeneration_MCI/BB53_mdeft. mri_segstats—seg mri/aseg.mgz—sum stats/aseg.stats—pv mri/norm.mgz—empty—brainmask mri/brainmask.mgz—brain-e norm—in-intensity-units MR—etiv—surf-wm-vol—surf-ctx-vol—totalgray—euler—ctab /apps/prod/x86_64/freesurf $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats—seg mri/aseg.mgz—sum stats/aseg.stats—pv mri/norm.mgz—empty—brainmask mri/brainmask.mgz -ity-name norm—in-intensity-units MR—etiv—surf-wm-vol—surf-ctx-vol—totalgray—euler—ctab /apps/prod/x86_64/f sysname Linux hostname beo-05 machine x86_64 user jdinges UseRobust 0 atlas_icv (eTIV) = 1723578 mm^3 (det: 1.130268 ) mghRead(/data/projects/oertelmatura/Neurodegeneration_MCI/BB53_mdeft./mri/ribbon.mgz, -1): could not open file Computing euler number orig.nofix lheno = -70, rheno = -38 orig.nofix lhholes = 36, rhholes = 20 -- Getting Brain Volume Statistics Linux beo-05 2.6.32.59-ql-beowulf-54 #1 SMP Fri Nov 2 12:47:48 CET 2012 x86_64 GNU/Linux recon-all -s BB53_mdeft. exited with ERRORS at Fri Nov 1 03:55:37 CET 2013 ___ 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.
[Freesurfer] Betreff: Error “mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file”
Dear freesurfer community, unfortunately there was a mistake in the previous mail. Please find attached the current valid mail and ignore previous mail from my adress. Dear freesurfer community, We are conducting cortical-thickness analysis using freesurfer 5.3.0 and have been experiencing problems with the computation after eliminating dura mater and optical nerve. For several subjects we ran the command “recon-all –autorecon2 –subjid _mdeft.” and received the error message “mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file”. Below, we provide the details of our setup and the exact error message for one subject. Feel free to ask for more information. Thank you very much for your help! Yours sincerely, Jana Dinges FREESURFER_HOME: /apps/prod/i486/freesurfer-5.3.0 Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Debian version: 5.0.6 Kernel info: Linux 2.6.27.39-1-ql-beowulf i686 $ which freesurfer -> /apps/prod/i486/freesurfer-5.3.0/bin/freesurfer Used command: recon-all –autorecon2 –subjid BB53_mdeft. Error Message: INFO: mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file /data/projects/oertelmatura/Neurodegeneration_MCI/BB53_mdeft. mri_segstats—seg mri/aseg.mgz—sum stats/aseg.stats—pv mri/norm.mgz—empty—brainmask mri/brainmask.mgz—brain-e norm—in-intensity-units MR—etiv—surf-wm-vol—surf-ctx-vol—totalgray—euler—ctab /apps/prod/x86_64/freesurf $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats—seg mri/aseg.mgz—sum stats/aseg.stats—pv mri/norm.mgz—empty—brainmask mri/brainmask.mgz -ity-name norm—in-intensity-units MR—etiv—surf-wm-vol—surf-ctx-vol—totalgray—euler—ctab /apps/prod/x86_64/f sysname Linux hostname beo-05 machine x86_64 user jdinges UseRobust 0 atlas_icv (eTIV) = 1723578 mm^3 (det: 1.130268 ) mghRead(/data/projects/oertelmatura/Neurodegeneration_MCI/BB53_mdeft./mri/ribbon.mgz, -1): could not open file Computing euler number orig.nofix lheno = -70, rheno = -38 orig.nofix lhholes = 36, rhholes = 20 -- Getting Brain Volume Statistics Linux beo-05 2.6.32.59-ql-beowulf-54 #1 SMP Fri Nov 2 12:47:48 CET 2012 x86_64 GNU/Linux recon-all -s BB53_mdeft. exited with ERRORS at Fri Nov 1 03:55:37 CET 2013 ___ 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.
[Freesurfer] minimal freesurfer pieces for recon-all
hi folks, has anybody on this list: a. built or extracted the necessary pieces (binaries, libraries, atlases) for running vanilla recon-all only? b. or better still, has a package file for any linux distro? i know the neurodebian folks are building one, but that's not fully ready yet. cheers, satra ___ 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.
[Freesurfer] difference in atlas size
hi i noticed a big discrepancy in size between these two, but not among other lh and rh gcs files. > 28769857 May 13 17:21 rh.DKTatlas100.gcs > 6883965 May 13 17:21 lh.DKTatlas100.gcs are these the intended sizes? this is from the 5.3 centos6_x86_64 distro cheers, satra ___ 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.
[Freesurfer] A question as to subcortical volumetric measurement
Dear Doug and experts I've analyzed structural changes of the subcortical GM by using both VBM (DARTEL in SPM8) and subcortical volumemetric measurement using FreeSurfer 5.1. While there is no significant volumetric difference between the groups in VBM (corrected p<0.05), FS results showed that some subcortical GM had significant volume reductions in patients relative to controls (MANCOVA controlling for the effect of ICV, age, gender, followed by Bonferroni correction). One of the referees raised the question regarding this discrepancy between the VBM and FS findings. How can I cope with it? Thank you in advance for your help. Kim ___ 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.
