Freesurfer August 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
152 discussions

File Format for talairach.m3z
by Soon Hock Wei 10 Aug '10

10 Aug '10

Dear All: I am a new user of FreeSurfer and I am wondering what is the file format for talairach.m3z (i.e. the output of mri_ca_register)? I couldn't find this information in FreeSurfer Wiki. In addition, I would like to know how can I use this talairach.m3z to check the accuracy of non-linear mapping to the atlas space? And if I wanted to replace this non-linear transform (i.e. talairach.m3z) by another non-linear transform (without affecting the other process flow), how should I do that? Appreciate if anyone could kindly show me some guidance. Thanks! Best Regards, Soon National University of Singapore

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surface-based aal template
by Zhangyuanchao 10 Aug '10

10 Aug '10

hi, expert I need a surface-based aal template which is compatible with freesurfer surface files. Is there any way I can obtain such a surface-based aal template? Thanks!

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region seeding and growing
by Eriksen, Jeffrey (Portland) 09 Aug '10

09 Aug '10

I have looked at the web site and gone through much of the available documentation (without downloading the installer yet) and cannot find if FreeSurfer offers low-level region seeding and growing capabilities. Anyone able to confirm or deny such a feature? Thanks, Jeff Eriksen, PhD Senior Research Associate Oregon Brain Imaging Research Lab (OBIRL) Portland VA Research Foundation kjeffrey.eriksen2(a)va.gov 503-220-8262, x54117

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[freesurfer] a puzzling installation error
by Glen Lee 09 Aug '10

09 Aug '10

Dear freesurfer experts, I'm running into installation failure and can't quite figure this out (I'm a novice Linux user too). It complains there is no such file or directory although I've downloaded the file and move that to the usr/local directory, so there clearly is the file. Would anybody help me how to resolve this issue? Below is the error message and platform info. Many thanks! -GL ------------------------------------------------------------------------------- glen@ubuntu:/usr/local$ uname -a Linux ubuntu 2.6.32-24-generic-pae #39-Ubuntu SMP Wed Jul 28 07:39:26 UTC 2010 i686 GNU/Linux. tar: freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.ifh: Cannot open: No such file or directory freesurfer/average/surf/ tar: freesurfer/average/surf: Cannot mkdir: No such file or directory freesurfer/average/surf/lh.sphere.reg tar: freesurfer/average/surf/lh.sphere.reg: Cannot open: No such file or directory freesurfer/average/surf/rh.sphere.reg tar: freesurfer/average/surf/rh.sphere.reg: C

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Exec format error. Wrong Architecture.
by Kristina Fanucci 09 Aug '10

09 Aug '10

Hello all, I finished running autorecon1 pbsubmit -m kfanucci -l nodes=1:opteron -c "recon-all -i /autofs/cluster/mscat/users/kristina/MS-freesurfer/ms-dicom/MS_pt20_dicom/MEMPRAGE_4e/008/255000-000008-000049.dcm -subjid MS_pt20_recon -autorecon1" and then tried to look at the skull strip tkmedit MS_pt20_recon brainmask.mgz -aux T1.mgz but received this error: /autofs/cluster/mscat/users/kristina/MS-freesurfer/frozen-freesurfer-vers03082010/stable/bin/tkmedit.bin: Exec format error. Wrong Architecture. Where did I go wrong? Thanks, Kristina

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Make_average failure
by Lena Palaniyappan 09 Aug '10

09 Aug '10

Following a bug-fix to enable processing large number of scans in make_average_surface ( see http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14122.html ) Something odd has happpened and I am not able to run the make_average as before. I am trying to make an average map of a single subject using make_average_subject --out aMPRAGE01 --subjects MPRAGE01 But after few minutes I get the following error message +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ make_average_surface --out aMPRAGE04 --subjects MPRAGE04 $Id: make_average_surface,v 1.39.2.2 2009/07/30 23:33:52 nicks Exp $ Mon Aug 9 16:32:52 BST 2010 /Applications/freesurfer/subjects/areamap setenv SUBJECTS_DIR /Applications/freesurfer/subjects/areamap ni305.cor.mgz INFO: extension is mgz output ddir is /Applications/freesurfer/subjects/areamap uid=501(Lena) gid=20(staff) groups=20(staff),98(_lpadmin),81(_appserveradm),101(com.apple.sharepoint.gro up.1),79(_appserverusr),80(admin),102(com.apple.access_ssh) ==================== make_average_surface ==================== Mon Aug 9 16:32:52 BST 2010 /Applications/freesurfer/subjects/areamap /Applications/freesurfer/bin/make_average_surface --out aMPRAGE04 --subjects MPRAGE04 input subjects: MPRAGE04 output subject: aMPRAGE04 mri_add_xform_to_header -c auto /Applications/freesurfer/subjects/areamap/aMPRAGE04/mri/mni305.cor.mgz /Applications/freesurfer/subjects/areamap/aMPRAGE04/mri/mni305.cor.mgz #@# Making lh registration template --------- /Applications/freesurfer/subjects/areamap/aMPRAGE04 mris_make_template -norot -annot aparc lh sphere.reg MPRAGE04 lh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization... processing subject MPRAGE04 (1 of 1) reading spherical surface /Applications/freesurfer/subjects/areamap/MPRAGE04/surf/lh.sphere.reg... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_fin al.txt) ripping medial wall... computing parameterization for surface /Applications/freesurfer/subjects/areama/MPRAGE04/surf/lh.inflated.H... curvature mean = -0.027, std = 1.004 computing parameterization for surface /Applications/freesurfer/subjects/areamap/MPRAGE04/surf/lh.sulc... computing parameterization for surface /Applications/freesurfer/subjects/areamap/MPRAGE04/surf/lh.smoothwm... writing updated template with 1 subjects to lh.reg.template.tif... curvature mean = -0.004, std = 0.594 curvature mean = -0.066, std = 0.792 #@# Making lh annotation --------------------- Mon Aug 9 16:33:07 BST 2010 mris_ca_label -ml-annot lh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs 7 label/lh.aparc.annot /Applications/freesurfer/subjects/areamap/aMPRAGE04 ML Label: lh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs 7 label/lh.aparc.annot Reading icosahedron /Applications/freesurfer/lib/bem/ic7.tri Reading gcsa from /Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killi any.2007-06-20.gcs reading color table from GCSA file.... average std = 2.1 using min determinant for regularization = 0.044 0 singular and 372 ill-conditioned covariance matrices regularized Building most likely labels Filtering labels 2 filter iterations complete (2 requested, 378 changed) writing colortable into annotation file... mris_ca_label -ml-annot lh.destrieux.simple.2009-07-29.gcs 7 label/lh.aparc.a2009s.annot /Applications/freesurfer/subjects/areamap/aMPRAGE04 ML Label: lh.destrieux.simple.2009-07-29.gcs 7 label/lh.aparc.a2009s.annot Reading icosahedron /Applications/freesurfer/lib/bem/ic7.tri Reading gcsa from /Applications/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized Building most likely labels Filtering labels 2 filter iterations complete (2 requested, 1605 changed) writing colortable into annotation file... #@# Making average lh.orig surface --------------------- Mon Aug 9 16:33:21 BST 2010 /Applications/freesurfer/subjects/areamap/aMPRAGE04 mris_make_average_surface -i 7 -o orig -sdir-out /Applications/freesurfer/subjects/areamap lh orig_avg sphere.reg aMPRAGE04 MPRAGE04 /Applications/freesurfer/bin/mris_make_average_surface: Permission denied. mris_average_surface failed ERROR: make_average_surface +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Any help will be much appreciated, Thanks Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Re: [Freesurfer] question abt Destrieux atlas
by Christophe Destrieux 09 Aug '10

09 Aug '10

Hi Rito The answer for the second question is yes : the stable 4.5.0 version includes the 2009 parcellation atlas (see http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) For the first one I'm not quite sure if running recon-all with the -cortparc2 <http://surfer.nmr.mgh.harvard.edu/fswiki/cortparc> -parcstats2 <http://surfer.nmr.mgh.harvard.edu/fswiki/parcstats> -aparc2aseg <http://surfer.nmr.mgh.harvard.edu/fswiki/aparc2aseg> is methodologically correct if yours subjects were reconstructed with 4.4.0 version ; Nick or Bruce could you answer this part? cheers > Hello Christophe > > My name is Rito and I am an avid freesurfer user. I realised that our freesurfer version is not the latest one and doesnt create the parcellations contained in Destrieux2009 atlas. > > I have run a lot of data using the 4.4 release. I have installed the latest release of freesurfer but my question to you is > > 1) How do I get the 2009 parcellations on the data that I already ran through with the 4.4 release ? > > 2) Also does the latest freesurfer release contain the parcellations reported in you latest paper "Destrieux et al. Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. NeuroImage (2010)" ? > > Any help will be highly appreciated. > > Thanks > > Rito > > Ritobrato Datta, Ph.D. > Post Doctoral Fellow > Department of Neurology > Center for Functional Neuroimaging > University of Pennsylvania School of Medicine > 3rd Floor Gates Building > 3400 Spruce St. > Philadelphia > Pa 19104 > > > -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=120065115… Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07

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Re: [Freesurfer] smoothed data stats
by raka maitra 09 Aug '10

09 Aug '10

Dear Doug Thanks for the clarification. I was using files in the standard fsaverage surface space. Thanks again! Raka ________________________________ From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: raka maitra <rakamaitra(a)yahoo.com> Cc: freesurfer_mailing_list <freesurfer(a)nmr.mgh.harvard.edu> Sent: Mon, August 9, 2010 4:02:11 PM Subject: Re: [Freesurfer] smoothed data stats It should work. How are you smoothing the thickness file? You need to smooth it in the native surface space. doug raka maitra wrote: > Dear all > > I would like to look at the change in the average values of thickness > after smoothing. > But mris_anatomical_stats does not work on the smoothed files as the > no of vertices of the annot files and the smoothed files are very > different. > > I tried recreating annot files using the flag -surf pial and the > aparc+aseg.mgz but I got following error message: > could not open translation file > /Applications/freesurfer/cma_parcellation_colors.txt > could not open translation file > /Applications/freesurfer/Simple_surface_labels2002.txt > > Your help would be appreciated. > Thanks in advance > Raka > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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 _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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smoothed data stats
by raka maitra 09 Aug '10

09 Aug '10

Dear all I would like to look at the change in the average values of thickness after smoothing. But mris_anatomical_stats does not work on the smoothed files as the no of vertices of the annot files and the smoothed files are very different. I tried recreating annot files using the flag -surf pial and the aparc+aseg.mgz but I got following error message: could not open translation file /Applications/freesurfer/cma_parcellation_colors.txt could not open translation file /Applications/freesurfer/Simple_surface_labels2002.txt Your help would be appreciated. Thanks in advance Raka

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the difinition about VentralDC
by leemon albert 09 Aug '10

09 Aug '10

Dear Pedro, Dear Bruce, Dear all, In the previous discussion about VentralDC in the aseg stats file, I learned that it's the the acronym stands for ventral diencephalon. And Dr. Fischl said that It's a mismash of a bunch of different stuff and the CMA pubs have more details on it. However, anyone can give me any more hints about the CMA pubs? I'm very interested in it. Thanks a lot in advance. -- Meng

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Freesurfer August 2010