[Freesurfer] 5.2 CENTOS x_64 ERROR tal_QC_AZS
Hi FS experts, I just downloaded the latest version again today: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0.tar.gz( 4.2 GB 1/28/13 9:47:00 PM, fsaverage has been copied to /subjects/myproject location) When running this command: recon-all -i -s x -qcache -hippo-subfields -all The system is giving me the following error: tal_QC_AZS /home/glerma/fs/52/freesurfer/subjects/TNT/S_03/mri/transforms/talairach_avi.log ERROR: tal_QC_AZS /home/glerma/fs/52/freesurfer/subjects/TNT/S_03/mri/transforms/talairach_avi.log failed! See logfile /home/glerma/fs/52/freesurfer/subjects/TNT/S_03/mri/transforms/talairach_avi_QA2.log The logfile talairach_avi_QA2.log is empty. This is the end of /mri/transforms/talairach_avi.log: start time Tue Jan 29 11:45:59 CET 2013 1661 end time Tue Jan 29 11:46:32 CET 2013 1662 1663 mpr2mni305 success 1664 1665 avi2talxfm orig_nu.mgz /home/glerma/fs/52/freesurfer/average/mni305.cor.mgz talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt transforms/talairach.auto.xfm 1666 avi2talxfm done 1667 1668 1669 Tue Jan 29 11:46:34 CET 2013 1670 talairach_avi done Is there something else I should check to make it work? thanks! Gari ___ 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] Post-doc position within the Collaborative Research Centre 940 Volition and Cognitive Control: Mechanisms, Modulators, and Dysfunctions
Post-doc position within the Collaborative Research Centre 940 Volition and Cognitive Control: Mechanisms, Modulators, and Dysfunctions at the Department of Child and Adolescent Psychiatry, University Hospital C. G. Carus, Dresden University of Technology, Germany Job Description: The Eating Disorder Section of the Department of Child and Adolescent Psychiatry, Dresden University of Technology, Germany (Prof. Stefan Ehrlich) invites applications for a postdoctoral research position in neuroimaging of eating disorders. The new project is part of the aforementioned Collaborative Research Centre (CRC, Steering Committee: Profs. T. Goschke, C. Kirschbaum, M. Smolka, A. Strobel, H.-U. Wittchen) and will focus on cognitive control, reward system and the processing of emotions in patients with anorexia nervosa. This is a full time position within the Translational Developmental Neuroscience Group. Responsibilities will include the coordination of our ongoing clinical research study and the acquisition and analysis of a range of behavioral and magnetic resonance imaging (MRI) data. Together with a doctoral student new functional MRI paradigms need to be implemented. Imaging sessions will take place on the Neuroimaging Center's 3T Siemens TIM-Trio scanner and data collected includes high-quality structural, diffusion, and functional MRI data. A variety of additional information will also be collected, including neuropsychological and psychiatric scales, physiological and endocrinological markers. Summarizing results and writing research articles will be another central aspect of the work. The successful applicant will work in a team of young investigators and also start to supervise doctoral students, interns and medical students working in the project. Thanks to the CRC the applicant will have ample opportunity to work with peers and senior scientists in similar project in the Medical School and the Psychology Department. Applicants for the position must hold (a) a PhD, MD or comparable degree in a relevant field (Psychology, Neurosciences or Medicine; if you have additional qualifications a degree in Biology, Biomedicine, Biophysics, Computer Science or Electrical Engineering may also be sufficient), (b) have had some exposure to cognitive and emotional neurosciences, (c) participated in research activities within the past years (d) published in peer-reviewed journals, e) possess strong organizational skills and (f) be able to communicate in basic German with non-scientific staff members. Some experience in computer programming (Linux/Unix shell scripting, Python and/or MATLAB), neuroimaging analysis methods (FSL, SPM, FreeSurfer or others), advanced statistical analyses and scientific publishing is necessary. The successful applicant will join a multidisciplinary team of researchers and clinicians, will receive further training and train doctoral students (informally). The position is available for a start date as soon as February 15th 2012 (to be confirmed). Review of applications will begin immediately and will continue until the position is filled. The position is guaranteed for two years with the possibility of renewal after positive evaluation. The CRC funding has been granted for 4 years. Salary will be consistent with levels in accordance with the German Research Foundation (100% TV-L: E 13). Compensation includes health insurance, and vacation time. To apply you can use our online portal (https://www.uniklinikum-dresden.de/Bewerbung/?id=5e0f53e16050a1fa4845830ba9a83433) The application should include a cover letter detailing professional objectives and interests, CV (with grades and language skills), and the names and email addresses of two references. The application can be written in German or English. The position is open to qualified international applicants but the knowledge of some German is necessary since the position includes the coordination of an ongoing clinical study. Applicants with a disability will be given preference in the selection process. Please refer to our homepage: http://www.kjp-dresden.de/en/Eating-disorders, http://www.kjp-dresden.de/en/Schizophrenia, http://tu-dresden.de/die_tu_dresden/fakultaeten/fakultaet_mathematik_und_naturwissenschaften/fachrichtung_psychologie/sfbo, and http://kjp-dresden.de/de/Publikationsliste-Prof-Dr-S-Ehrlich for more detailed information. *** PLEASE REPOST FOR INTERESTED PARTIES *** Für das Forschungsprogramm der Professur für Angewandte Entwicklungsneurowissenschaften (Prof. S. Ehrlich) wird für die Projekte zum Thema Increased volitional control of rewarding stimuli in eating disorders: Neural mechanisms and real-world costs im Rahmen des neuen Sonderforschungsbereichs (SFB) 940 Volition und kognitive Kontrolle ab frühestens dem 15. Februar 2012 ein Wissenschaftlicher
[Freesurfer] R: Re: R: Re: R: Re: R: R: Re: TRACULA
Hi list, I'm trying to run trac-all on one subject and have a problem with the bvecs file at the -prep stage. After dtifit is started an error massage occurs: Error: bvecs and bvals don't have the same number of entries: [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all -prep -c /Users/Stefano/Desktop/dmrirc_single_subject INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova INFO: Diffusion root is /Applications/freesurfer/subjects/subject_prova Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/dmrirc.local -log /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.log -cmd /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Mar 29 Gen 2013 13:51:50 CET mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz... cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvecs.txt /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvecs cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvals.txt /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvals flip4fsl /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -1 fslswapdim /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz x y z /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.nii.gz INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.mghdti.bvecs /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.mghdti.bvals /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals eddy_correct /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz 0 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0001 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0002 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0003 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0004 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0005 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0006 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0007 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0008 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0009 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0010 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0011 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0012 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0013 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0014 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0015 mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs.norot xfmrot /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.ecclog /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs.norot /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs fslroi /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz
Re: [Freesurfer] Delay
no, the longer time is probably because the mac version you are using is 32 bit. cheers Bruce On Tue, 29 Jan 2013, Varghese Chikku wrote: Dear All,I ran a test subject on VM and the process took 20 hrs to complete.But the same images on Mc pro took 58 hours.VM is 8GB and Mpro is 16 GB.I have noticed this delay happening in the past as well,where VM takes 20-24 for a single patient and Mc takes 24-30 for the same.But,this time ,its was so unexpected.Why is this happening?.Which would be more accurate,and does it mean that more time FS take,the better the results? Many thanks Chikku ___ 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.
Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: TRACULA
Hi Stefano - Are the files that you're attaching the ones from the dmri directory or are they the original files that you specified in your configuration file? I'm guessing they're not the dmri/bv??s files because then they'd be formatted in rows and not columns. Without seeing the bvecs from your dmri directory my best guess for what could be causing the error is this: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26026.html a.y On Tue, 29 Jan 2013, std...@virgilio.it wrote: Hi list, I'm trying to run trac-all on one subject and have a problem with the bvecs file at the -prep stage. After dtifit is started an error massage occurs: Error: bvecs and bvals don' t have the same number of entries: [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all -prep -c /Users/Stefano/Desktop/dmrirc_single_subject INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova INFO: Diffusion root is /Applications/freesurfer/subjects/subject_prova Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Applications/freesurfer/subjects/subject_prova/Diff01/scrip ts/dmrirc.local -log /Applications/freesurfer/subjects/subject_prova/Diff01/ scripts/trac-all.log -cmd /Applications/freesurfer/subjects/subject_prova/Di ff01/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Mar 29 Gen 2013 13:51:50 CET mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii. gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii. gz mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii. gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii. gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii .gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_o rig.nii.gz... cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvecs.txt /Applica tions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvecs cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvals.txt /Applica tions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvals flip4fsl /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ori g.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ori g_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -1 fslswapdim /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_o rig.nii.gz x y z /Applications/freesurfer/subjects/subject_prova/Diff01/dmri /dwi_orig_flip.nii.gz fslorient -forceradiological /Applications/freesurfer/subjects/subject_prova /Diff01/dmri/dwi_orig_flip.nii.gz INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ orig.mghdti.bvals, converting to FSL format INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ orig.mghdti.bvecs, converting to FSL format mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_f lip.mghdti.bvecs /Applications/freesurfer/subjects/subject_prova/Diff01/dmri /bvecs mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_f lip.mghdti.bvals /Applications/freesurfer/subjects/subject_prova/Diff01/dmri /bvals eddy_correct /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi _orig_flip.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmr i/dwi.nii.gz 0 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0001 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0002 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0003 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0004 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0005 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0006 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0007 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0008 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0009 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0010 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0011 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0012 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0013 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp0014 processing
Re: [Freesurfer] Delay
Hi Chikku note that because you have a 64 bit mac doesn't mean you are running 64 bit software. Until pretty recently we didn't have a 64 bit mac version, so unless you downloaded a beta in the last month or so, you are likely running a 32 bit version cheers Bruce On Tue, 29 Jan 2013, Varghese Chikku wrote: Thanks Bruce,Its 64 bit. On 29 January 2013 15:12, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: no, the longer time is probably because the mac version you are using is 32 bit. cheers Bruce On Tue, 29 Jan 2013, Varghese Chikku wrote: Dear All,I ran a test subject on VM and the process took 20 hrs to complete.But the same images on Mc pro took 58 hours.VM is 8GB and Mpro is 16 GB.I have noticed this delay happening in the past as well,where VM takes 20-24 for a single patient and Mc takes 24-30 for the same.But,this time ,its was so unexpected.Why is this happening?.Which would be more accurate,and does it mean that more time FS take,the better the results? Many thanks Chikku 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 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] mean cortical thickness of significant clusters in qdec
Dear FreeSurfer experts, I did a group analysis in qdec, found several significant clusters and would now like to extract the mean cortical thickness of each significant cluster. I know that I have to run mri_glmfit-sim to do this, but I do not understand which commands I need to get the xxx.y.ocn.dat as output by running mri_glmfit-sim. Any ideas? Any help is appreciated. :) Best wishes, Julia ___ 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] Job offer: Neuroimaging scientist or clinician in Frankfurt
Dear all, I'm attaching a job offer for a fully-funded neuroimaging position at Frankfurt University, available immediately. The position is based at the Brain Imaging Center of Goethe University, a facility that hosts two dedicated research MR scanners and an MEG facility. A full clinical salary is available for applicants with a medical degree. Best, Johannes Dr Johannes C Klein Goethe-University of Frankfurt Department of Neurology, Brain Imaging Center Schleusenweg 2-16 D-60528 Frankfurt/Main Germany email: kl...@med.uni-frankfurt.de http://www.bic.uni-frankfurt.de/ The Department of Neurology and Brain Imaging Center (BIC) at the Goethe-University Frankfurt am Main invites applications for a full-time position as Clinician scientist (m/f) Or Doctoral/Postdoctoral researcher (m/f) We are seeking to recruit a highly motivated individual to develop a programme of research into imaging biomarkers of neurological diseases. Topics include the evolution of lesions in Multiple Sclerosis, the differentiation of neurodegenerative diseases, and the evaluation of target sites for deep brain stimulation (DBS) in movement disorders. Essential qualifications and interests include · a background in medicine, neuroscience, or a related field (e.g., a degree in psychology, engineering, physics, biology) · programming skills (Linux shell scripting, MATLAB) · an interest in biomedical questions and systems neuroscience · interpersonal skills when dealing with research subjects and colleagues Additionally, the ideal applicant · has experience with imaging software packages (e.g. FSL, SPM) · enjoys inter-disciplinary interactions with physicists and clinicians · has experience with conducting MRI scans · speaks (basic) German to interact with study subjects The successful candidate should have a demonstrated capacity for independent work and be capable of initiating research in a lively research environment. The post will involve collecting MRI data from patients with neurological conditions and normal volunteers. The post will also involve data analysis and writing of manuscripts for submission to peer-reviewed journals, as well as writing ethics applications for research projects. For Doctoral researchers, Goethe-University provides the opportunity to obtain a PhD degree. The Brain Imaging Center offers excellent imaging facilities, with two research-only 3T Siemens MRI scanners, MEG, various stimulus presentation methods, and an active physics group. The position is available immediately and can be split up. The appointment will be initially for 2 years, with the possibility of extension. Salary will be based on TV-Ä Hessen for Clinicians, and up to TVÖD-E13 for Postdoctoral Researchers. Goethe University is an equal opportunity employer. Applications from female candidates are encouraged. Where qualifications are equal, preference will be given to applicants with disabilities. Candidates should submit their applications (as a PDF including CV, names of at least two referees, and a brief letter of motivation outlining their interests and explaining how they meet the qualifications listed above) to Dr Johannes Klein (kl...@med.uni-frankfurt.de). Dr Klein is also available for informal enquiries. Applications will be considered until the post is filled. ___ 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.
Re: [Freesurfer] mean cortical thickness of significant clusters in qdec
Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not? doug On 01/29/2013 11:03 AM, Richter, Julia wrote: Dear FreeSurfer experts, I did a group analysis in qdec, found several significant clusters and would now like to extract the mean cortical thickness of each significant cluster. I know that I have to run mri_glmfit-sim to do this, but I do not understand which commands I need to get the xxx.y.ocn.dat as output by running mri_glmfit-sim. Any ideas? Any help is appreciated. J Best wishes, Julia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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.
Re: [Freesurfer] QDEC ERROR ANALYSE
You have either too many effects that you are trying to fit or you don't have enough subjects. Decrease one or increase the other! doug On 01/28/2013 01:00 PM, Pablo Emanuel wrote: Hi, My name is Pablo. I am using the freesurfer in my analyses, but when I try use the QDEC to statistical analyses the follwing ERROR, attached, arise. What I have to do to fix it? Thank you so much. Pablo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19
When I run recon-all using freesurfer 5.2 latest beta it will segment crash. Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /home/knutjbj/freesurfer/ernie mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz Segmentation fault Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ernie exited with ERRORS at ti. 29. jan. 19:25:15 +0100 2013 For more details, see the log file /home/knutjbj/freesurfer/ernie/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Knut J -- SUBJECT ernie DATE ti. 29. jan. 19:28:17 +0100 2013 USER knutjbj HOST mypc PROCESSOR x86_64 OS Linux Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.54 2013/01/15 22:31:19 nicks Exp $ /usr/local/freesurfer/bin/recon-all PWD /home/knutjbj/freesurfer/ernie CMD mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz ti. 29. jan. 19:28:13 +0100 2013 /home/knutjbj/freesurfer/ernie /usr/local/freesurfer/bin/recon-all -i /usr/local/freesurfer/subjects/sample-001.mgz -i /usr/local/freesurfer/subjects/sample-002.mgz -s ernie -debug subjid ernie setenv SUBJECTS_DIR /home/knutjbj/freesurfer FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 maxlocks unlimited maxsignal192659 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 24683456 24399144 284312 0 654024 20092400 -/+ buffers/cache:3652720 21030736 Swap: 49337340 3796 49333544 program versions used $Id: recon-all,v 1.379.2.54 2013/01/15 22:31:19 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:13-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:13-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:13-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:13-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:13-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:13-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64
Re: [Freesurfer] Delay
Chikku, Can you send us your recon-all.log and recon-all.cmd files? I'd like to investigate why it ran so slowly. Nick On Tue, 2013-01-29 at 06:53 +0100, Varghese Chikku wrote: Dear All, I ran a test subject on VM and the process took 20 hrs to complete.But the same images on Mc pro took 58 hours.VM is 8GB and Mpro is 16 GB.I have noticed this delay happening in the past as well,where VM takes 20-24 for a single patient and Mc takes 24-30 for the same.But,this time ,its was so unexpected.Why is this happening?.Which would be more accurate,and does it mean that more time FS take,the better the results? Many thanks Chikku ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19
Hi Knut does it segfault on other systems? Can you email me the 001.mgz and I'll see if it works here? thanks Bruce On Tue, 29 Jan 2013, Knut J Bjuland wrote: When I run recon-all using freesurfer 5.2 latest beta it will segment crash. Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /home/knutjbj/freesurfer/ernie mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz Segmentation fault Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ernie exited with ERRORS at ti. 29. jan. 19:25:15 +0100 2013 For more details, see the log file /home/knutjbj/freesurfer/ernie/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Knut J ___ 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.
Re: [Freesurfer] bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19
Knut, I noticed in the log that there was only 284KB of free memory available, which is not enough to run freesurfer, although it would seem like it should be enough to run the mri_convert command. Can you free-up more memory and re-run? Also, I noticed that you're running the Centos6 build, what OS are you running? Fedora 18? Does the v5.2 Centos4 freesurfer build work on that? Nick On Tue, 2013-01-29 at 19:30 +0100, Knut J Bjuland wrote: When I run recon-all using freesurfer 5.2 latest beta it will segment crash. Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /home/knutjbj/freesurfer/ernie mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz Segmentation fault Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ernie exited with ERRORS at ti. 29. jan. 19:25:15 +0100 2013 For more details, see the log file /home/knutjbj/freesurfer/ernie/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Knut J ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19
it's probably not enough to run gunzip, which for some reason takes *lots* of ram On Tue, 29 Jan 2013, Nick Schmansky wrote: Knut, I noticed in the log that there was only 284KB of free memory available, which is not enough to run freesurfer, although it would seem like it should be enough to run the mri_convert command. Can you free-up more memory and re-run? Also, I noticed that you're running the Centos6 build, what OS are you running? Fedora 18? Does the v5.2 Centos4 freesurfer build work on that? Nick On Tue, 2013-01-29 at 19:30 +0100, Knut J Bjuland wrote: When I run recon-all using freesurfer 5.2 latest beta it will segment crash. Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /home/knutjbj/freesurfer/ernie mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz Segmentation fault Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ernie exited with ERRORS at ti. 29. jan. 19:25:15 +0100 2013 For more details, see the log file /home/knutjbj/freesurfer/ernie/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Knut J ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19
Hi Nick I reran dicom import from /usr/local/freesurfer/subject/sample*. I had 24254940 kB free memory but I still got a segmentation error.I used sample data from /usr/local/freesurfer/subject. Do you think it is a glibc bug in Fedora 18. It contain glibc-2.16-28.fc18.x86_64. This error showed up in my dmesg log. [ 175.413292] mri_convert[1350]: segfault at 0 ip 0037e092fbda sp 7fff0a9dc2c8 error 4 in libc-2.16.so[37e080+1ad000] Knutj On 29. jan. 2013 19:47, Nick Schmansky wrote: Knut, I noticed in the log that there was only 284KB of free memory available, which is not enough to run freesurfer, although it would seem like it should be enough to run the mri_convert command. Can you free-up more memory and re-run? Also, I noticed that you're running the Centos6 build, what OS are you running? Fedora 18? Does the v5.2 Centos4 freesurfer build work on that? Nick On Tue, 2013-01-29 at 19:30 +0100, Knut J Bjuland wrote: When I run recon-all using freesurfer 5.2 latest beta it will segment crash. Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /home/knutjbj/freesurfer/ernie mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz Segmentation fault Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ernie exited with ERRORS at ti. 29. jan. 19:25:15 +0100 2013 For more details, see the log file /home/knutjbj/freesurfer/ernie/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Knut J ___ 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. Tue Jan 29 20:26:29 CET 2013 /home/knutjbj/freesurfer/ernie /usr/local/freesurfer/bin/recon-all -i /usr/local/freesurfer/subjects/sample-001.mgz -i /usr/local/freesurfer/subjects/sample-002.mgz -s ernie subjid ernie setenv SUBJECTS_DIR /home/knutjbj/freesurfer FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 192659 maxlocks unlimited maxsignal192659 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 24683456 455644 24227812 0 66580 77648 -/+ buffers/cache: 311416 24372040 Swap: 49337340 0 49337340 program versions used $Id: recon-all,v 1.379.2.54 2013/01/15 22:31:19 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-19:26:29-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: root Machine: super-knut Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-19:26:29-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: root Machine: super-knut Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-19:26:29-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: super-knut Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC
Re: [Freesurfer] bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19
does v5.1 work on this system? does the centos4_x86_64 v5.2 build work? n. On Tue, 2013-01-29 at 20:33 +0100, Knut J Bjuland wrote: Hi Nick I reran dicom import from /usr/local/freesurfer/subject/sample*. I had 24254940 kB free memory but I still got a segmentation error.I used sample data from /usr/local/freesurfer/subject. Do you think it is a glibc bug in Fedora 18. It contain glibc-2.16-28.fc18.x86_64. This error showed up in my dmesg log. [ 175.413292] mri_convert[1350]: segfault at 0 ip 0037e092fbda sp 7fff0a9dc2c8 error 4 in libc-2.16.so[37e080+1ad000] Knutj On 29. jan. 2013 19:47, Nick Schmansky wrote: Knut, I noticed in the log that there was only 284KB of free memory available, which is not enough to run freesurfer, although it would seem like it should be enough to run the mri_convert command. Can you free-up more memory and re-run? Also, I noticed that you're running the Centos6 build, what OS are you running? Fedora 18? Does the v5.2 Centos4 freesurfer build work on that? Nick On Tue, 2013-01-29 at 19:30 +0100, Knut J Bjuland wrote: When I run recon-all using freesurfer 5.2 latest beta it will segment crash. Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /home/knutjbj/freesurfer/ernie mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz Segmentation fault Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ernie exited with ERRORS at ti. 29. jan. 19:25:15 +0100 2013 For more details, see the log file /home/knutjbj/freesurfer/ernie/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Knut J ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] diluting a mask using inflated brain
Dear Freesurfer users and experts, We are attempting to grow a mask that we have created in FSL, to expand it into white matter. At first, we tried this in FSL using the dilM command which dilated the size of the mask by n voxels. We then multiplied this by a segmented white matter mask (again, created in FSL) so only the white matter voxels were included. However, a problem with this method, is that if a mask is over a gyri (as most of our masks are), then diluting the mask in a non-inflated brain causes some voxels from an adjacent gyri to be included. What we would like to be able to do, is to dilute the mask using the inflated white matter brain created by Freesurfer, and then to take this back into FSL space; thereby, allowing us to create a mask of which includes the true surrounding white matter rather than white matter from adjacent gyri. Hope this makes sense!? Does anyone know how to do this or could point us in the right direction? Cheers, Jodie - --- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC, V5Z 3N9 Canada Tel: 604-875-4111Tel:604-875-411 ext 69003 ___ 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.
Re: [Freesurfer] ERROR: aparcstats2table
Hello again! Thank you for all your help so far. Just one more question now... is there a way to specify these values to be pulled using a script: GausCurv FoldInd CurvInd ...?? Thanks, Catherine On 1/23/13, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: They must be in a single folder and the $SUBJECTS_DIR env variable must be set to that folder. If you know a little unix, you can set up folders with symbolic links to subjects' true directories. doug On 01/23/2013 02:58 PM, Nucleos P wrote: Thank you for your help Doug! I was trying to specify the path to get to the subjects. Do I have to have all the subjects in a folder called 'subjects'? I know the naming conventions are important. Thanks again, Catherine On Fri, Jan 18, 2013 at 6:31 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: actually, looking at your cmd line more I see that you have slashes (/) in the subject names. The argument to --subjects should just be a list of name. See the help (aparcstats2table -h) for examples. doug On 01/18/2013 04:58 PM, Nucleos P wrote: Hello experts: Can someone please help me understand what I am doing wrong? This is the first time I am trying this command and it will not work... COMMAND: aparcstats2table --subjects /RGS4_31p/rgs0868_raw /RGS4_31p/rgs0871_raw /RGS4_31p/rgs0883_raw/ /RGS4_31p/rgs1194_raw144/ /RGS4_31p/rgs1311a/ /RGS4_31p/rgs1370a/ /RGS4_31p/rgs1383a/ -t RGS4_31p/aparc.volume.rh -m volume --hemi=rh PATH: [/usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats]:pwd /usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats ERROR: SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files ERROR: The stats file /RGS4_31p/rgs0868_raw/stats/rh.aparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Thank you, Catherine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ERROR: aparcstats2table
yes, use the -m or --meas flags. If you run it with -h, you will get help and examples doug On 01/29/2013 04:12 PM, Nucleos P wrote: Hello again! Thank you for all your help so far. Just one more question now... is there a way to specify these values to be pulled using a script: GausCurv FoldInd CurvInd ...?? Thanks, Catherine On 1/23/13, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: They must be in a single folder and the $SUBJECTS_DIR env variable must be set to that folder. If you know a little unix, you can set up folders with symbolic links to subjects' true directories. doug On 01/23/2013 02:58 PM, Nucleos P wrote: Thank you for your help Doug! I was trying to specify the path to get to the subjects. Do I have to have all the subjects in a folder called 'subjects'? I know the naming conventions are important. Thanks again, Catherine On Fri, Jan 18, 2013 at 6:31 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: actually, looking at your cmd line more I see that you have slashes (/) in the subject names. The argument to --subjects should just be a list of name. See the help (aparcstats2table -h) for examples. doug On 01/18/2013 04:58 PM, Nucleos P wrote: Hello experts: Can someone please help me understand what I am doing wrong? This is the first time I am trying this command and it will not work... COMMAND: aparcstats2table --subjects /RGS4_31p/rgs0868_raw /RGS4_31p/rgs0871_raw /RGS4_31p/rgs0883_raw/ /RGS4_31p/rgs1194_raw144/ /RGS4_31p/rgs1311a/ /RGS4_31p/rgs1370a/ /RGS4_31p/rgs1383a/ -t RGS4_31p/aparc.volume.rh -m volume --hemi=rh PATH: [/usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats]:pwd /usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats ERROR: SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files ERROR: The stats file /RGS4_31p/rgs0868_raw/stats/rh.aparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Thank you, Catherine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Postdoctoral Position in Australia
Post-doc position available immediately within the Centre for Research on Ageing, Health and Wellbeing, College of Medicine, Biology and the Environment, Australian National University, Canberra, Australia. We are seeking a junior Postdoctoral Fellow to join a small collaborative team working on research aimed at characterising normal brain ageing in mid-life and into old age. This research includes using large neuroimaging datasets, studying cognitive correlates of age-related brain changes, identifying predictors and risk factors for brain and cognitive ageing, and test theoretical models of neuro-cognitive ageing. Working closely with Dr Nicolas Cherbuin, the research involves, processing and analysing structural brain scans and conducting research with a dynamic multi-disciplinary team. The successful applicant will hold a PhD in Psychology or equivalent and will have a research record in a field relevant to the project with demonstrated experience in processing and analysing neuroimaging data using FSL/Freesurfer or equivalent. An interest in ageing/lifespan development research will be highly regarded. Applications are required to be lodged online, please submit a summary of claims against the selection criteria along with your CV. Full details can be found here: http://jobs.anu.edu.au/PositionDetail.aspx?p=3120 Enquiries: Dr Nicolas Cherbuin Phone: 02 61253858 Email: nicolas.cherb...@anu.edu.au Nicolas Cherbuin PhD ARC Research Fellow Director of the NeuroImaging and Brain Lab Centre for Research on Ageing, Health and Wellbeing College of Medicine Biology and Environment 62A Eggleston Road Australian National University Canberra ACT 0200 P:+61 2 6125 3858 F:+61 2 6125 1558 E:nicolas.cherb...@anu.edu.au W: ageing.anu.edu.au/research/projects/nimbl.php CRICOS Provider #00120C ___ 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.
Re: [Freesurfer] diluting a mask using inflated brain
Hi Jodie you can do this on the surface, then project the resulting label 1mm into the white matter if I understand what you want correctly. You might also check out the wmparc.mgz and see if it already does what you want. cheers Bruce On Tue, 29 Jan 2013, Jodie Davies-Thompson wrote: Dear Freesurfer users and experts, We are attempting to grow a mask that we have created in FSL, to expand it into white matter. At first, we tried this in FSL using the dilM command which dilated the size of the mask by n voxels. We then multiplied this by a segmented white matter mask (again, created in FSL) so only the white matter voxels were included. However, a problem with this method, is that if a mask is over a gyri (as most of our masks are), then diluting the mask in a non-inflated brain causes some voxels from an adjacent gyri to be included. What we would like to be able to do, is to dilute the mask using the inflated white matter brain created by Freesurfer, and then to take this back into FSL space; thereby, allowing us to create a mask of which includes the true surrounding white matter rather than white matter from adjacent gyri. Hope this makes sense!? Does anyone know how to do this or could point us in the right direction? Cheers, Jodie - --- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC, V5Z 3N9 Canada Tel: 604-875-4111 ext 69003 ___ 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] mris_pmake
Dear all, I am trying to calculate the distance from a reference vertex to all other vertices in a surface mesh (or ideally to a subset of vertices), moving along the actual surface (e.g. smoothwm). I am able to loop through the pairs of vertices in which I'm interested, using mris_pmake in each loop, but this is quite time consuming. I have tried using '--mpmProg autodijk' as described in the mris_pmake help file, but have been unsuccessful at getting this command to work. The current code I am using for each pair is: mris_pmake --subject subject --surface0 smoothwm --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:###,endVertex:### Any suggestions to cut down my processing time, while still calculating along the surface, would be greatly appreciated. Andrew ___ 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.
Re: [Freesurfer] diluting a mask using inflated brain
Jodie, you might also look into using the white matter parcellation. That would allow you to select the WM from a particular gyrus. doug On 01/29/2013 03:31 PM, Jodie Davies-Thompson wrote: Dear Freesurfer users and experts, We are attempting to grow a mask that we have created in FSL, to expand it into white matter. At first, we tried this in FSL using the dilM command which dilated the size of the mask by n voxels. We then multiplied this by a segmented white matter mask (again, created in FSL) so only the white matter voxels were included. However, a problem with this method, is that if a mask is over a gyri (as most of our masks are), then diluting the mask in a non-inflated brain causes some voxels from an adjacent gyri to be included. What we would like to be able to do, is to dilute the mask using the inflated white matter brain created by Freesurfer, and then to take this back into FSL space; thereby, allowing us to create a mask of which includes the true surrounding white matter rather than white matter from adjacent gyri. Hope this makes sense!? Does anyone know how to do this or could point us in the right direction? Cheers, Jodie - --- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC, V5Z 3N9 Canada Tel: 604-875-4111 Tel:604-875-411 ext 69003 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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.
Re: [Freesurfer] TRACULA
Are there commas in the dmri/bvecs file? If so, do setenv LANG en_US.UTF-8 as described in the archive post that I sent you. Does this solve the error about bvecs and bvals not having the same size? On Tue, 29 Jan 2013, std...@virgilio.it wrote: Hi Anastasia, I put my files in a folder /Application/freesurfer/subjects/subject_prova/Diff01/ File are these: data.nii.gz (DWI data, 16 directions) TI_CON_01.nii.gz (T1 structural images) bvals.txt and bvecs.txt (as you can see in the previously attacked files). Could error depends from the use of the . or , that was used to separate the decimal? Is corrects the name of the 4 files in the Diff01 folder (FSL.nii.gz and its directory) I have previously used this data in FSL for TBSS. I only inverted the matrix of bvals (FLS:1x16, fs:16x1) and (FSL:3x16; fs:16x3) Is the configuration file good? Thank you very much for you kindness and avaibility. Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 29-gen-2013 15.42 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: TRACULA Hi Stefano - Are the files that you're attaching the ones from the dmri directory or are they the original files that you specified in your configuration file? I'm guessing they're not the dmri/bv??s files because then they'd be formatted in rows and not columns. Without seeing the bvecs from your dmri directory my best guess for what could be causing the error is this: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26026.html a.y On Tue, 29 Jan 2013, std...@virgilio.it wrote: Hi list, I'm trying to run trac-all on one subject and have a problem with the bvecs file at the -prep stage. After dtifit is started an error massage occurs: Error: bvecs and bvals don' t have the same number of entries: [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all -prep -c /Users/Stefano/Desktop/dmrirc_single_subject INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova INFO: Diffusion root is /Applications/freesurfer/subjects/subject_prova Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Applications/freesurfer/subjects/subject_prova/Diff01/scrip ts/dmrirc.local -log /Applications/freesurfer/subjects/subject_prova/Diff01/ scripts/trac-all.log -cmd /Applications/freesurfer/subjects/subject_prova/Di ff01/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Mar 29 Gen 2013 13:51:50 CET mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii. gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii. gz mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii. gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii. gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii .gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_o rig.nii.gz... cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvecs.txt /Applica tions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvecs cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvals.txt /Applica tions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvals flip4fsl /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ori g.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ori g_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -1 fslswapdim /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_o rig.nii.gz x y z /Applications/freesurfer/subjects/subject_prova/Diff01/dmri /dwi_orig_flip.nii.gz fslorient -forceradiological /Applications/freesurfer/subjects/subject_prova /Diff01/dmri/dwi_orig_flip.nii.gz INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ orig.mghdti.bvals, converting to FSL format INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ orig.mghdti.bvecs, converting to FSL format mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_f lip.mghdti.bvecs /Applications/freesurfer/subjects/subject_prova/Diff01/dmri /bvecs mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_f lip.mghdti.bvals /Applications/freesurfer/subjects/subject_prova/Diff01/dmri /bvals eddy_correct /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi _orig_flip.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmr i/dwi.nii.gz 0 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t mp processing
Re: [Freesurfer] entorhinal cortex volume question
Hi Folks, I have a question about entorhinal cortex volume. The entorhinal cortex is listed in ?h.aparc.stats and ?h.entorhinal_exvivo.stats. In a previous post on the mailing list, it was mentioned that we should use the volume measurement from ?h.entorhinal_exvivo.stats. We would like to make manual corrections to the entorhinal cortex segmentation (when required). For this task I can create a entorhinal volume from ?h.entorhinal_exvivo.label using mri_label2vol This entorhinal volume will be different from the one in aparc+aseg.mgz My question is: Has anyone published any protocols to somehow combine the two entorhinal volumes ? Or is recommend to take the take the entorhinal volume created from ?h.entorhinal_exvivo.stats. and overlay it on norm.mgz and edit manually (when required). One limitation of this approach is that it would be hard to integrate this entorhinal volume back into aparc+aseg.mgz... Thanks Mehul On Wed, Dec 7, 2011 at 10:50 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Catherine I guess I would recommend the ex vivo one since it is based explicitly on architecontics and not on guessing locations from folds. cheers Bruce On Wed, 7 Dec 2011, Cat Chong wrote: Hello experts, I am very new to freesurfer so please excuse my basic question: We want to get measurements of entorhinal cortex volumes on a group of people. I found these results listed in ?h.aparc.stats. I also noticed another ?h.entorhinal_exvivo.stats, with different results. Which should I use for a group analysis of entorhinal volume and surface area, and why are the results very different? very best regards, catherine ___ 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 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.
Re: [Freesurfer] entorhinal cortex volume question
Hi Mehul the entorhinal label in the aparc was drawn by Rahul based on gyral landmarks. The one in the _exvivo.stats is based on being able to see the layer II islands in ex vivo MRI and hence we believe it is more accurate. Not sure why you need to integrate the ex vivo one back into the aparc+aseg, can you clarify? cheers Bruce On Tue, 29 Jan 2013, Mehul Sampat wrote: Hi Folks, I have a question about entorhinal cortex volume. The entorhinal cortex is listed in ?h.aparc.stats and ?h.entorhinal_exvivo.stats. In a previous post on the mailing list, it was mentioned that we should use the volume measurement from ?h.entorhinal_exvivo.stats. We would like to make manual corrections to the entorhinal cortex segmentation (when required). For this task I can create a entorhinal volume from ?h.entorhinal_exvivo.label using mri_label2vol This entorhinal volume will be different from the one in aparc+aseg.mgz My question is: Has anyone published any protocols to somehow combine the two entorhinal volumes ? Or is recommend to take the take the entorhinal volume created from ?h.entorhinal_exvivo.stats. and overlay it on norm.mgz and edit manually (when required). One limitation of this approach is that it would be hard to integrate this entorhinal volume back into aparc+aseg.mgz... Thanks Mehul On Wed, Dec 7, 2011 at 10:50 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Catherine I guess I would recommend the ex vivo one since it is based explicitly on architecontics and not on guessing locations from folds. cheers Bruce On Wed, 7 Dec 2011, Cat Chong wrote: Hello experts, I am very new to freesurfer so please excuse my basic question: We want to get measurements of entorhinal cortex volumes on a group of people. I found these results listed in ?h.aparc.stats. I also noticed another ?h.entorhinal_exvivo.stats, with different results. Which should I use for a group analysis of entorhinal volume and surface area, and why are the results very different? very best regards, catherine ___ 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 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.
Re: [Freesurfer] entorhinal cortex volume question
Thanks for quick response Bruce. We will use the volume from ex-vivo stats.. Regarding the need to integrate the ex vivo one back into aparc+aseg. We noticed the entorhinal volume in aparc is larger than that in exvivo.stats. So do the extra entorhinal voxels in aparc need to be re-labelled as unkown or as cortical-gray-matter? We plan to make manual correction on aparc (when required): So would it be a good approach to use the entorhinal labels from exvivo.stats to guide the corrections on aparc ? In this case, the question is, what should the end-user re-label the extra entorhinal voxels as ? Thanks Mehul On Tue, Jan 29, 2013 at 6:02 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Mehul the entorhinal label in the aparc was drawn by Rahul based on gyral landmarks. The one in the _exvivo.stats is based on being able to see the layer II islands in ex vivo MRI and hence we believe it is more accurate. Not sure why you need to integrate the ex vivo one back into the aparc+aseg, can you clarify? cheers Bruce On Tue, 29 Jan 2013, Mehul Sampat wrote: Hi Folks, I have a question about entorhinal cortex volume. The entorhinal cortex is listed in ?h.aparc.stats and ?h.entorhinal_exvivo.stats. In a previous post on the mailing list, it was mentioned that we should use the volume measurement from ?h.entorhinal_exvivo.stats. We would like to make manual corrections to the entorhinal cortex segmentation (when required). For this task I can create a entorhinal volume from ?h.entorhinal_exvivo.label using mri_label2vol This entorhinal volume will be different from the one in aparc+aseg.mgz My question is: Has anyone published any protocols to somehow combine the two entorhinal volumes ? Or is recommend to take the take the entorhinal volume created from ?h.entorhinal_exvivo.stats. and overlay it on norm.mgz and edit manually (when required). One limitation of this approach is that it would be hard to integrate this entorhinal volume back into aparc+aseg.mgz... Thanks Mehul On Wed, Dec 7, 2011 at 10:50 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Catherine I guess I would recommend the ex vivo one since it is based explicitly on architecontics and not on guessing locations from folds. cheers Bruce On Wed, 7 Dec 2011, Cat Chong wrote: Hello experts, I am very new to freesurfer so please excuse my basic question: We want to get measurements of entorhinal cortex volumes on a group of people. I found these results listed in ?h.aparc.stats. I also noticed another ?h.entorhinal_exvivo.stats, with different results. Which should I use for a group analysis of entorhinal volume and surface area, and why are the results very different? very best regards, catherine __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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 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.
Re: [Freesurfer] TRACULA
Hello Anastasia and Stefano, Maybe is of little help but I wanted to let you know that I've experienced the same problem. Using exactly the same data, and using 5.1 in both cases, and having the locale set up as specified according to a solution in the mailing list: - in cent os 4 it is working - in mac os x mountain lion it is not working. Same error (don't have same number of entries) If you can try your data and config files on a Linux box and it works, at least you will know that the problem is not your data but the fs/os interaction. Br, Gari On 30/01/2013, at 01:00, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Are there commas in the dmri/bvecs file? If so, do setenv LANG en_US.UTF-8 as described in the archive post that I sent you. Does this solve the error about bvecs and bvals not having the same size? On Tue, 29 Jan 2013, std...@virgilio.it wrote: Hi Anastasia, I put my files in a folder /Application/freesurfer/subjects/subject_prova/Diff01/ File are these: data.nii.gz (DWI data, 16 directions) TI_CON_01.nii.gz (T1 structural images) bvals.txt and bvecs.txt (as you can see in the previously attacked files). Could error depends from the use of the . or , that was used to separate the decimal? Is corrects the name of the 4 files in the Diff01 folder (FSL.nii.gz and its directory) I have previously used this data in FSL for TBSS. I only inverted the matrix of bvals (FLS:1x16, fs:16x1) and (FSL:3x16; fs:16x3) Is the configuration file good? Thank you very much for you kindness and avaibility. Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 29-gen-2013 15.42 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: TRACULA Hi Stefano - Are the files that you're attaching the ones from the dmri directory or are they the original files that you specified in your configuration file? I'm guessing they're not the dmri/bv??s files because then they'd be formatted in rows and not columns. Without seeing the bvecs from your dmri directory my best guess for what could be causing the error is this: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26026.html a.y On Tue, 29 Jan 2013, std...@virgilio.it wrote: Hi list, I'm trying to run trac-all on one subject and have a problem with the bvecs file at the -prep stage. After dtifit is started an error massage occurs: Error: bvecs and bvals don' t have the same number of entries: [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all -prep -c /Users/Stefano/Desktop/dmrirc_single_subject INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova INFO: Diffusion root is /Applications/freesurfer/subjects/subject_prova Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Applications/freesurfer/subjects/subject_prova/Diff01/scrip ts/dmrirc.local -log /Applications/freesurfer/subjects/subject_prova/Diff01/ scripts/trac-all.log -cmd /Applications/freesurfer/subjects/subject_prova/Di ff01/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Mar 29 Gen 2013 13:51:50 CET mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii. gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii. gz mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii. gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii. gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii .gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_o rig.nii.gz... cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvecs.txt /Applica tions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvecs cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvals.txt /Applica tions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvals flip4fsl /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ori g.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ori g_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -1 fslswapdim /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_o rig.nii.gz x y z /Applications/freesurfer/subjects/subject_prova/Diff01/dmri /dwi_orig_flip.nii.gz fslorient -forceradiological /Applications/freesurfer/subjects/subject_prova /Diff01/dmri/dwi_orig_flip.nii.gz INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ orig.mghdti.bvals, converting to FSL format INFO: found
Re: [Freesurfer] Delay
Thanks Nick, Please find the attached. On 29 January 2013 19:33, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Chikku, Can you send us your recon-all.log and recon-all.cmd files? I'd like to investigate why it ran so slowly. Nick On Tue, 2013-01-29 at 06:53 +0100, Varghese Chikku wrote: Dear All, I ran a test subject on VM and the process took 20 hrs to complete.But the same images on Mc pro took 58 hours.VM is 8GB and Mpro is 16 GB.I have noticed this delay happening in the past as well,where VM takes 20-24 for a single patient and Mc takes 24-30 for the same.But,this time ,its was so unexpected.Why is this happening?.Which would be more accurate,and does it mean that more time FS take,the better the results? Many thanks Chikku ___ 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. recon-all-status.log Description: Binary data ___ 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.
Re: [Freesurfer] bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19
On 29. jan. 2013 21:16, Nick Schmansky wrote: does v5.1 work on this system? no does the centos4_x86_64 v5.2 build work? no. I have filed a bug report on https://bugzilla.redhat.com/show_bug.cgi?id=905638 . It might be problem with mri_convert and glibc interaction. Knut J n. On Tue, 2013-01-29 at 20:33 +0100, Knut J Bjuland wrote: Hi Nick I reran dicom import from /usr/local/freesurfer/subject/sample*. I had 24254940 kB free memory but I still got a segmentation error.I used sample data from /usr/local/freesurfer/subject. Do you think it is a glibc bug in Fedora 18. It contain glibc-2.16-28.fc18.x86_64. This error showed up in my dmesg log. [ 175.413292] mri_convert[1350]: segfault at 0 ip 0037e092fbda sp 7fff0a9dc2c8 error 4 in libc-2.16.so[37e080+1ad000] Knutj On 29. jan. 2013 19:47, Nick Schmansky wrote: Knut, I noticed in the log that there was only 284KB of free memory available, which is not enough to run freesurfer, although it would seem like it should be enough to run the mri_convert command. Can you free-up more memory and re-run? Also, I noticed that you're running the Centos6 build, what OS are you running? Fedora 18? Does the v5.2 Centos4 freesurfer build work on that? Nick On Tue, 2013-01-29 at 19:30 +0100, Knut J Bjuland wrote: When I run recon-all using freesurfer 5.2 latest beta it will segment crash. Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /home/knutjbj/freesurfer/ernie mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz Segmentation fault Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ernie exited with ERRORS at ti. 29. jan. 19:25:15 +0100 2013 For more details, see the log file /home/knutjbj/freesurfer/ernie/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Knut J ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
