Freesurfer May 2010

freesurfer@nmr.mgh.harvard.edu

98 participants
145 discussions

Using peak activation voxels to determine structural areas of interest
by Nathan Dankner 01 Jun '10

01 Jun '10

Hello all. I am considering using peak activation voxels (with coordinates either in talairach or MNI space) gleaned from fmri studies in our lab to determine a priori areas of interest for examining group differences in cortical thickness. Is this something that is possible in freesurfer? In particular, I would ideally like to be able to tell freesurfer how large of an area to examine around a particular peak voxel for each subject as opposed to tracing an ROI each time. I am not particularly well versed in the technical aspects of things such as blurring kernels, but I am assuming that the amount of blurring done by freesurfer will affect the ideal circumference of any sphere around this peak voxel. Any suggestions as to how to go about this? Please let me know if any more information is necessary. Thanks, Nathan

5 4

make_average_subject with large cohorts
by Marie Schaer 01 Jun '10

01 Jun '10

Hello everybody, I have a problem running make_average_subject for a large number of subjects (>400) on a Mac Intel. I tried with different Freesurfer versions (all the log outputs are attached). Using the freesurfer version 4.3 and 4.4 the make_average_subject script always stop at the 297th subject with the error "Cannot allocate memory". I already tried to uncomment the line "limit descriptors unlimited" or to set it to various values, as proposed in the mailing list, but without success (it always stop at the 297th subject). Then I tried with the Freesurfer version 4.5 (therefore I had to recompute the lh.inflated.H and lh.inflated.K which are not automatically produced in previous versions), but with the 4.5 version I got a strange "license error" message in the middle of the script (and my licence is certainly fine as I can run any other script without problems). Does anyone have an idea? Many thanks in advance for your precious help, Marie

3 7

using custom .tif files and .gcs files
by Danny Kim 01 Jun '10

01 Jun '10

Hi all, I was wondering if there are flags you can specify to use your own .tif and .gcs files in -autorecon3 processing pipeline. Currently, I am calling up individual processes to double check the results, but in the long run it would be useful to just automate this. Thanks Danny,

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Re: [Freesurfer] autorecon2 error
by Gabriel Go.Es. 31 May '10

31 May '10

Thank you so much Bruce and Martin, and I will be so glad to be able to download the files. Best, Gabriel > From: reuter(a)MIT.EDU > To: nicks(a)nmr.mgh.harvard.edu; gabriellbk(a)hotmail.com; fischl(a)nmr.mgh.harvard.edu > CC: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] autorecon2 error > Date: Mon, 31 May 2010 03:25:59 -0400 > > Yes, looks like the one I fixed. Nick can point you to a download for the > fixed files. > > Best, Martin > > > ----- Original Message ----- > From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> > To: "Gabriel Go.Es." <gabriellbk(a)hotmail.com> > Cc: "free surfer" <freesurfer(a)nmr.mgh.harvard.edu>; "Reuter, Martin -- > Martin Reuter" <mreuter(a)nmr.mgh.harvard.edu>; "Martin Reuter" > <reuter(a)mit.edu> > Sent: Sunday, May 30, 2010 4:50 PM > Subject: Re: [Freesurfer] autorecon2 error > > > Hi Gabriel, > > I think Martin fixed this bug, didn't you Martin? > > Bruce > > On Sun, 30 May 2010, Gabriel Go.Es. wrote: > > > > > > > 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 > > > 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. > _________________________________________________________________ Diseñar aplicaciones tiene premio. ¡Si eres desarrollador no esperes más! http://www.imaginemobile.es

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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

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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

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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

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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

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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

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Freesurfer May 2010