Freesurfer October 2006

freesurfer@nmr.mgh.harvard.edu

41 participants
61 discussions

aseg, aparc regions reference table (aka "data dictionary")?
by Graham Wideman 22 Dec '06

22 Dec '06

Folks: It would be *really* great if there was a page somewhere (or just a file) giving some info on the various measures that are captured in the aseg and aparc files. For each measure (in the table or the "comments" above the table): -- Description of what it includes -- some are obvious from the name, others not. -- Whether it's deprecated. -- Whether FS V-whatever actually produces this value, or just zero. (Very useful, and probably not too much work? Plus I'd like to adapt this info so as to pull only the non-inert rows from the data file). (Or is there some other way to determine this?) -- Some suggestions on what numbers need to be added to get popular subtotals. I've just read through the last six months of freesurfer list traffic, and I see numerous questions along these lines... and replies with some clues here and there. Also references to papers, but these don't detail the nitty gritty of what FS V-something actually does. Probably numerous users would get a lot of use out of having this info in one place. Thanks, Graham

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new Intel Mac freesurfer distribution
by Nick Schmansky 04 Dec '06

04 Dec '06

Intel Mac owners, A distribution of Freesurfer is now available for the new Intel- processor Macs. It can be downloaded here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ Look for the file: freesurfer-Darwin-apple-i686-dev3-20061004.tar.gz To install it, copy it to /Applications, and then: tar zxvf freesurfer-Darwin-apple-i686-dev3-20061004.tar.gz To setup: setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh This distribution is from our 'dev' (development) code base, so it is slightly different from the normal publicly distributed 'stable' release. A stable build release of this Intel Mac distribution (with associated install GUI) will coincide with the next stable build release (next month, hopefully). Nick

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editing pre-existing annotations
by Eric Feczko 09 Nov '06

09 Nov '06

Hey, Is there a way to add structures/labels to a pre-existing annotation file? I sampled an annotated atlas onto a subjects surface. But when I load the annotation and try to create a new label, I can't export the edited annotation without eliminating the new label. I tried to create a new color lookup table with the new structure included, and I can load the table in tksurfer just fine. However, when I also try to import the pre-existing annotation(in order to edit it), the color table existing in the annotation overrides the color lookup table I load. If it try to load the table after importing the annotation, the new structure/label does not show up in the label window. If anyone can help me with this issue, that would be great, thanks! -Eric

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mris_anatomical_stats error
by Johannes Klein 01 Nov '06

01 Nov '06

Hi everyone, I'm trying to calculate surface areas for some labels I've drawn on an averaged subject created with mrake_average_surface, and mris_anatomical_stats seems the way to go. Unfortunately, it needs a file called wm.mgz, which doesn't exist for my averaged subject. The mri subdir contains T1, brain, mni305.cor and orig.mgz, but no wm.mgz. Is there a way to create this file from the data I've got? Thanks for your help, Johannes

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recon-all autorecon2 error.
by Mithra 31 Oct '06

31 Oct '06

Hello, I ran autorecon1 this step worked fine. The transform obtained from this step looked good. When I run autorecon2, I get a segmentation fault error. Can anybody tell me whats wrong. Thanks a whole bunch. Error: Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86 _64 x86_64 x86_64 GNU/Linux WM removal version #------------------------------------- #@# EM Registration Tue Oct 31 14:32:46 CST 2006 /usr/pubsw/freesurfer/subjects/sub02/mri mri_em_register -mask brainmask.mgz nu.mgz /usr/pubsw/freesurfer/average/RB_all _2006-02-15.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/pubsw/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... Segmentation fault Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86 _64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Oct 31 14:32:57 CST 2006

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mri_convert options
by Derin Cobia 31 Oct '06

31 Oct '06

Hi, Currently we've been converting from .img to .mgz format using the following syntax: mri_convert -TI 20 -te 4 -tr 9.7 -flip_angle 0.174532925199433 -ot mgz s1501p.img mri/orig/001.mgz It came to my attention today that the values we used for TI, TE, and TR are all actually in ms, and correspond to the Siemen's Vision use of the terms TI and TR for the MRPAGE sequence. This is quite different from how TI and TR are used for the MPRAGE sequence on the Symphony, Sonata, and Trio Siemens platform. Furthermore, we have actually been applying these values to Vision FLASH data as well, for which TI is irrelevant, and the TR and flip were different. Basically, we have just been confused in our use of mri_convert. So, this raises a couple questions: 1) Are the TI, TE, TR and flip parameters important to mri_convert? How are they used? Are they used in any manner in the subsequent Freesurfer processing stream? We wonder if they are not important, since the current documention lists TR as an option, but doesn't mention TI, TE, or flip as options. 2) If these parameters are important in some manner how would the use of such grossly incorrect values affect the results? So basically, we are wondering what parameters, if any, are truly necessary as part of mri_convert? And do we (gasp) need to consider rerunning the stream from stage 1... Thanks! Derin

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automatic processing
by Nicolas Cherbuin 31 Oct '06

31 Oct '06

Hi, I have to process more than 500 good quality scans (1mm isotropic) for an epidemiological study and have limited time resources. Initial processing of 20 scans seems promising but I am new to freesurfer and therefore I am not quite sure how significant small defects might be in the big picture (where they will be averaged over a large number of subjects). I would be interested to hear the experience of others in using autoreconall for processing most scans and only reprocessing a small portion of scans with obvious substantial defects (mostly on the inflated surface). With good quality scans would most people reprocess most scans? Thanks for sharing your experiences. Nic

2 1

ROI group analysis
by Cameron Ellis 31 Oct '06

31 Oct '06

Hi, I am trying to run mri_volcluster on a group ROI and am having some trouble. I was hoping someone had suggestion. I created individual ROIs and wanted to average them to obtain a group ROI. I ran isxavg-re-sess for each ROI but there is no registration file for mri_volcuster to reference. Have I hit a dead end? Does anyone know another way of creating a group ROI that I can apply the mri_volcluster command to? Thanks, Cameron

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Morphological measures
by Juergen Haenggi 31 Oct '06

31 Oct '06

Dear Freesurfer users after running Freesurfer, I got 11 colums (without structure name) in the recon_all.log file with the different morphological indices: e.g. 208 122 451 3.056 0.740 0.125 0.024 2 0.6 15 0.179 G_cingulate-Isthmus but actually there should be only 9 colums (without structure name). further I am confused because in another subject there are only 10 colums (without structure name) e.g. 188 124 272 2.121 0.641 0.107 0 18 1.966 0.12 G_cingulate-Isthmus and in the second example, the 7th colum (Gaussian curvature) is always zero!!! What happens? Thanks in advance for clarification Best regards Juergen ---------------------------------------------- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi(a)bli.unizh.ch (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------

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Quality of Surface
by Paul Greenberg 30 Oct '06

30 Oct '06

Hello, I've attached a tif image showing the results of an inflated hemisphere viewed in Tksurfer and was wondering a) how would you rate this inflation on a scale of 1-5 with 5 being the best? and b) given that there are many brains to process, are any of the visible defects worth fixing? Thanks, Paul

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Freesurfer October 2006