Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

autorecon2 error
by Gabriel Go.Es. 30 May '10

30 May '10

Dear FreeSurfers I run an autorecon1 using the flag -no-wsgcaatlas for skullstripping, I'm using freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0, you may find attached the recon-all_status log for any information you may need Then I was trying to run the autorecon2: recon-all -subjid -autorecon2 when it gives the following error message: ------------------------------------------------------ Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ /root/trabajo/freesurfer/bin/recon-all PWD /root/trabajo/freesurfer/subjects/MP2RAGE_2/mri CMD mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /root/trabajo/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Left_Cerebellum_Cortex based on Right_Cerebellum_Cortex = 1.05 x + 0 estimating mean gm scale to be 1.16 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.43 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri May 28 14:57:45 CEST 2010 ------------------------------------------------------------------- any suggestions and help will be so appreciated Best Gabriel ¿Sabes que La Gente de Hoy tiene GUARDAESPALDAS contra el Spam? Con las alertas de Hotmail no perderás detalle de tu correo. ¡Contrátalo ya! _________________________________________________________________ ¿Quieres conocer trucos de Windows 7? ¡Los que ya lo usan te los cuentan! http://www.sietesunpueblodeexpertos.com/index_windows7.html

2 1

scalp mesh
by Marcel Heers 30 May '10

30 May '10

Dear all, while I am doing my first steps using freesurfer, I am searching for a scalp mesh, which I could use for the brainstorm toolbox. Is there a scalp mesh produced during recon-all, which I can use for this purpose? Thanks for every hint! Marcel

2 2

?h.aparc.stats - GrayVol
by Houman Ebrahimi 30 May '10

30 May '10

Hi, Regarding information in the ?h.aparc.stats files; for a purely surface based structure such as the entorhinal cortex, why is there a discrepancy between the "GrayVol" value and the derived value of "ThickAvg" x "SurfArea"? Also the values for entorhinal "GrayVol" that we are getting are somewhat (up to 2x) larger than those presented in the recent paper published by your group (Dickerson, BC et al. Differential effects of aging and Alzheimer's disease on medial temporal lobe cortical thickness and surface area. Neurobiol Aging 2007). Is the standard (v4.5.0) segmentation map different to that used in your study? or is there some manual manipulation/segmentation that is required and not part of recon-all? Thank you dearly for all your help! Houman

1 0

FW: autorecon2 failture
by Gabriel Go.Es. 28 May '10

28 May '10

Dear FreeSurfers I run the autorecon1 using the flag -no-wsgcaatlas for skullstripping, I'm using freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0, you may find attached the recon-all_status log for any information you may need Then I was trying to run the autorecon2: recon-all -subjid -autorecon2 when it gives the following error message: ------------------------------------------------------ Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ /root/trabajo/freesurfer/bin/recon-all PWD /root/trabajo/freesurfer/subjects/MP2RAGE_2/mri CMD mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /root/trabajo/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Left_Cerebellum_Cortex based on Right_Cerebellum_Cortex = 1.05 x + 0 estimating mean gm scale to be 1.16 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.43 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri May 28 14:57:45 CEST 2010 ------------------------------------------------------------------- any suggestions and help will be so appreciated Best Gabriel ¿Sabes que La Gente de Hoy tiene GUARDAESPALDAS contra el Spam? _________________________________________________________________ Consejos para seducir ¿Puedes conocer gente nueva a través de Internet? ¡Regístrate ya! http://contactos.es.msn.com/?mtcmk=015352

1 0

QDEC Multigroupal analysis
by Jordi Delgado 28 May '10

28 May '10

Dear Experts, I'm trying to use QDEC for a Multigroupal analysis. I've read in the wiki that QDEC uses a GLM method to perform the analysis, but when I load a table with 43 subjects aprox. of three different groups and I run the analysis, at 70% QDEC shows me the following error: Error in Analyze: command failed: mri_glmfit --y ../path/qdec/qdecUntitled/y.mgh --fsgd ../path/qdec/Untitled/qdec.fsgd dods --glmdir ../path/qdec/Untitled --surf fsaverage lh --label ../path/fsaverage/label/lh.cortex.label Any idea? Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html

2 1

Motion Correction
by Houmran Ebrahimi 28 May '10

28 May '10

Hi, We are planning to conduct a retrospective study on subjects that have only had 1 MP-RAGE run each. What will be the effect of running recon-all without motion correction? Is there any way of quantifying any possible error/variation? Will this be the same across the whole subject set? For design of a future prospective study, we are limited in scanner time. How essential is it to have 2 or more runs per subject? Thanks, Houman Dr Houman Ebrahimi BSc MBBS(Hons) Radiology Registrar John Hunter Hospital Phone: +61 2 4921 3434 Fax: +61 2 4927 0848 Mobile: +61 420 98 93 98 Email: Houman.Ebrahimi(a)hnehealth.nsw.gov.au

2 1

autorecon2 failture
by Gabriel Go.Es. 28 May '10

28 May '10

Dear FreeSurfers I was running the autorecon2: recon-all -subjid -autorecon2 and it gives the following error message: Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ /root/trabajo/freesurfer/bin/recon-all PWD /root/trabajo/freesurfer/subjects/MP2RAGE_2/mri CMD mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /root/trabajo/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri May 28 14:57:45 CEST 2010 the autorecon1 was perform by using the flag -no-wsgcaatlas for skullstripping you may find attached the recon-status log for any information you may need any suggestions and help will be so appreciated Best Gabriel _________________________________________________________________ ¿Quieres conocer trucos de Windows 7? ¡Los que ya lo usan te los cuentan! http://www.sietesunpueblodeexpertos.com/index_windows7.html

1 0

GM and thickness
by Kelly Silva 28 May '10

28 May '10

Hello, I'm doing regression analyses with cortical thickness at the level of voxel. Should I correct the total GM volume by introducing this parameter as a confounding variable? Shoud I include the intracranial volume as an additional nuisance variable? If positive, I assume that these variables can only be introduced as covariates if they differ between groups. Am I correct? I saw in one message that we should not corret for thickness. Why not? Thanks in advance and best regards, Kelly

3 2

monkey segmentation error query
by Jason Connolly 28 May '10

28 May '10

Dear Freesurfer experts, We are attempting to segment a template monkey brain. The following is the command line input: recon-all -i /usr/local/freesurfer/subjects/template_2/mri/orig/MonkTempl_w81096_T1.nii.gz -s template -all -notal-check -force -noaseg It runs for a few hours and then we get the following error: "cannot find seed region for corpus collosum" Do we have to manually mark this somehow in tkmedit? Any advice would be appreciated! Thank you, Jason.

2 1

data conversion
by Yvonne.Fonken＠mpi.nl 28 May '10

28 May '10

Hi all, I've just started using Freesurfer and the software works fine (with .mnc extensions). However, my data has a .mri format. I couldn't find how to convert this data with Freesurfer. Does anyone know whether this format is supported within Freesurfer of how to convert it to a format that can be used in Freesurfer? Best wishes, Yvonne Fonken

2 1

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