Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

(no subject)
by duhanjian＠sohu.com 18 Jun '07

18 Jun '07

hi, when I run the recon-all -s wangrong -qcache command, It goes wrong, show like that: -------- freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.5 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME     /usr/local/freesurfer/fsfast SUBJECTS_DIR    /usr/local/freesurfer/subjects MNI_DIR         /usr/local/freesurfer/mni GSL_DIR         /usr/local/freesurfer/lib/gsl FSL_DIR         /usr/local/freesurfer/fsl wangjian@linux-sner:~> recon-all -s wangrong -qcache ERROR: Flag -qcache unrecognized. -s wangrong -qcache wangjian@linux-sner:~> qdec & [1] 13325 bash: qdec: command not found [1]+  Exit 127                 qdec wangjian@linux-sner:~> Do I need to install some plug-in software to do Qdec? or what's wrong with my procedure? Thank you!

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FSFAST preproc-sess
by Doug Greve 18 Jun '07

18 Jun '07

I have made some changes in the default behavior of the FSFAST preproc-sess command in anticipation of pending updates to FSFAST. These will be live in the next update to dev (probably Monday): 1. It will now only run a stage if the input is newer than the output. Eg, if you are running MC and smoothing, it will check whether the raw data has changed before rerunning MC, and it will check whether MC has changed before rerunning smoothing. If the output of a stage does not exist, it will of course run that stage. Automatic update can be turned off with -force or -no-update. This feature can be quite convenient as you can pass preproc-sess all of your sessions and it will only rerun the stages that are needed. 2. INorm will NOT be run by default. The new version of selxavg (selxavg3-sess) performs intensity normalization in a different way that does not require the mean intensity (.meanval) to be computed in advance. You can turn on INorm with the -inorm flag. 3. In addtion to these default changes, I've added slice-timing correction to preproc-sess. It is not on by default. You turn it on by specifying a slice order with -sliceorder. See preproc-sess -help for more info. I'll keep you posted as I make more changes. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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subject limit for mri_glmfit
by Goldman, Aaron (NIH/NIMH) [C] 15 Jun '07

15 Jun '07

Hi, I was wondering if there was any way with mri_glmfit to override the limit of 500 subjects. I'm only barely above, but wanted to avoid arbitrarily excluding people if it's practical. Thanks, -Aaron-

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mris_anatomical_stats: differences in output between -a and -l flags
by Michael Harms 15 Jun '07

15 Jun '07

Hello, On Freesurfer 3.0.4, I used 'mri_annotation2label' to derive a set of labels from the Desikan atlas annotation file (lh.aparc.annot). If I then run mris_anatomical_stats using the label files, e.g., mris_anatomical_stat -l lh.bankssts.label $subj lh the resulting statistics that are output for that structure do not match those in lh.aparc.stats except for average thickness. Is a difference to be expected between the -a and -l approaches for obtaining statistics via mris_anatomical_stats? What is the source of this discrepancy? thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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talairach.lta
by Don Hagler 15 Jun '07

15 Jun '07

Can someone please explain what transformation matrix is contained in talairach.lta? Is this the registration matrix from atlas to subject or subject to atlas? Also, is this matrix for rigid body registration only, or does it have the affine registration? _________________________________________________________________ Get a preview of Live Earth, the hottest event this summer - only on MSN http://liveearth.msn.com?source=msntaglineliveearthhm

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Intel MacBook Pro Recommendations?
by Betty Ann Chodkowski 14 Jun '07

14 Jun '07

Hello All, I just joined this list so I want to say, 'Hello.' Also I see that some FreeSurfer users are working on the MacBook Pro with an Intel chip. We are considering purchasing a MacBook and I wish to solicit feedback as to how the MacBook Pro holds up under FreeSurfer. Our MPRAGE volume is 256 x 256 x 170, 16bit data (21.25MB). Any recommendations about cpu, ram, etc, would be appreciated. Currently, we are thinking about: MacBook Pro 2.4GHz Intel Core 2 Duo 2GB 667 DDR2 SDRAM - 2x1GB NVIDIA GeForce 8600M GT graphics with 256MB SDRAM 200GB Serial ATA Drive @ 4200 rpm 15inch Display (1440 x 900 resolution) Should we just get 4GB RAM right from the start or will 2GB be sufficient? Any other considerations? Your experiences? Thanks for any input. Regards, - BettyAnn _____________________________________ BettyAnn Chodkowski e: chodkowski(a)kennedykrieger.org v: 443.923.9524 f: 443.923.9279 F.M. Kirby Center Kennedy Krieger Institute 707 N. Broadway Baltimore, MD, USA 21205 Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Problem loading one subject's surface in tksurfer
by Robert Levy 14 Jun '07

14 Jun '07

Hello, I have been unable to load one subject's surface, for purposes of viewing a functional mask on the surface. I noticed this warning in the text output: "surfer: WARNING: fov was ~0, setting to 0.256". The warning, and subsequent failure to load the surface, occurred when I called surf-sess using the same parameters I had used successfully to load all other subjects' mask data. The surface did not load, and instead a red rectangle and a blue rectangle were rendered. The warning I mentioned was the only suspicious line in the text output from surf-sess. The other output (including the "can't find tal...") was present for the subjects where the command was successful, not just for this subject. Here is the command I used (accessing a list of subjects, one of which was the one that did not load): surf-sess -sf Subject_Lists/bw-group-error-5 -analysis EMerror -contrast dACC_rh_pos_0_ASce68 -map mask -hemi rh -fthresh .5 Here is the context of the warning: can't find talairach file '/space/ventzl/1/users/SUBJECTS_DIR/mano011/mri/T1/COR-.info/../transforms/talairach.xfm' surfer: Reading header info from /space/ventzl/1/users/SUBJECTS_DIR/mano011/mri/T1/COR-.info * surfer: WARNING: fov was ~0, setting to 0.256* surfer: vertices=95942, faces=192364 can't find talairach file '/space/ventzl/1/users/SUBJECTS_DIR/mano011/surf/../mri/orig/COR-.info/../transforms/talairach.xfm' surfer: ### redraw failed: no gl window open Do you know what might cause a problem like this? Thanks in advance for any help or advice, Rob -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2656 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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Is there any easy way to make freesurfer work on animal data?
by lan lin 13 Jun '07

13 Jun '07

Is there any easy way to make freesurfer work on animal data? Such as monkey or mouse.

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Question about volume measurements in aseg.stats
by Mehul Sampat 13 Jun '07

13 Jun '07

Hi all, We have a mismatch in the volumes given in the aseg.stats by freesurfer0 and the volumes computed from the aseg.mgz with other programs like Slicer and Matlab I will use the data of subject bert that is already segmented in freesurfer. In the aseg.stats file (for the subject bert) the volume of the Brain Stem is 24490 mm^3 ( 24490 voxels ; segmentation id = 16) If I measure the volume of the brain-stem in matlab i get 25075 voxels the code used for this is : ---------------------------------------------------------------------------------------------------------------------------------------- [data,m] = load_mgh('/Applications/freesurfer/subjects/bert/mri/aseg.mgh'); temp = (data ==16); sum(sum(sum(temp))) --------------------------------------------------------------------------------------------------------------------------------------- When I measure the brain stem volume with Slicer 2.6, it gives 25.075 mL which matches exactly with the Matlab result. (A colleague also tried it using Analyze and the result matches those of Matlab and Slicer) Similar trends is seen for other structures also: (for example for the left Amygdala aseg.stats reports 1723 while with matlab we get 1728). Question is: Which measurement is more accurate ? I can see that the Matlab measurement is an approximation (for example the structure may only cover half the voxel but with matlab we assume it covers the entire voxel). Does freesurfer use a sophisticated method for measuring the volumes ? If this is true then it implies that the volume measurements in Slicer and Analyze are sub-optimal... Thanks Mehul

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Re: 回复:RE: [Freesurfer] (no subject)
by Jenni Pacheco 13 Jun '07

13 Jun '07

Hi, The instructions for this are on the wiki page you indicated previously, https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis When you run mris_preproc you specify thickness as the measure you are looking at. We have a new group analysis tool, with a GUI interface, that is now available. Tutorials on that are available here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis The new tool, Qdec, performs the same analyses - but it is hopefully more user friendly. Jenni On Wed, 13 Jun 2007 duhanjian(a)sohu.com wrote: > Which command to specify the thickness, can you tell me how to use? Thank you very much!

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