Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

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

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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

2 1

sub-cortical segmentation
by Durastanti, Valentina (NIH/NINDS) [F] 30 Oct '06

30 Oct '06

Hi, I'd like to know where I can find a detailed description of the sub-cortical segmentation stages thanks Valentina

3 11

mri_annotation2label
by Dahlia Sharon 30 Oct '06

30 Oct '06

Hi, I have two annotations, ?h.aparc.annot and ?h.aparc.a2005s.annot, created by recon-all with the -cortparc and -cortparc2 command options. I would like to convert each of these to a set of labels. For aparc.a2005s.annot I run (hopefully this is correct): mri_annotation2label --subject subj04_bay2 --hemi rh --annotation aparc.a2005s --labelbase $SUBJECTS_DIR/subj04_bay2/label/aparc2005-rh --table $FREESURFER_HOME/Simple_surface_labels2005.txt But for aparc.annot I don't know what table file I should specify (there are two other files in the $FREESURFER_HOME folder that could potentially be correct: Simple_surface_labels200s.txt and surface_labels.txt). Could you tell me which table to use for aparc.annot? Thanks, Dahlia.

2 2

average T1's before correcting for inhomogeneity?
by Stephen Towler 30 Oct '06

30 Oct '06

Greetings all, I'm new to freesurfer, so apologies if this has been covered. Two questions about early processing: 1) It looks like the recon-all script averages multiple T1's prior to correcting inhomogeneity. If processing T1's acquired on different days, and/or on different scanners, might it be advantageous to manually run mri_nu_correct.mni on each individually before averaging? Other than CPU time, why average first and then correct for inhomogeneity? 2) Is freesurfer's use of MNI_N3 over FSL's fast inhomogeneity correction algorithmic, empirical, historical, or other? Thanks! Stephen -- Stephen Towler stowler(a)mbi.ufl.edu 352-294-0048 office 352-258-6409 mobile 352-392-8347 fax Leonard Lab Department of Neuroscience PO Box 100244 University of Florida HSC Gainesville, FL 32610

2 1

Head Points data files
by Juranek, Jenifer 30 Oct '06

30 Oct '06

Hi, What are the file format requirements for the 2 files called to load head points - *.hpts and *.trans into tkmedit or tksurfer? We have a whole-head neuromagnetometer (4-D Neuroimaging 3600 Magnes MEG system) with 248 sensor channels. I'd like to co-register my dipole locations with FreeSurfer's aseg+aparc.mgz to efficiently localize dipoles x ROIs. I have already co-registered index points and headshape files to each subject's aMRI within 4D's software. Any advice is greatly appreciated! Jenifer ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ Jenifer Juranek, PhD Assistant Professor University of Texas MEG Lab 1333 Moursund St, Ste H114 Houston, TX 77030 Phone: 713.797.7574 Fax: 713.797.7590

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