Freesurfer

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30076 discussions

New recon-all "Files vs Steps" doc posted
by Graham Wideman 19 Jun '07

19 Jun '07

Folks: If you need to know what recon-all and its many steps are really doing you may be interested in a doc I've just posted tabulating file create/read/write/delete for each step: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps In case you've seen my previous similar effort, this one's a considerable improvement because it's based on monitoring an actual run (bert to the rescue!), rather than on documentation. Hope it shortens a few learning curves :-). Graham

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question re: low contrast images
by Turner, Jessica 18 Jun '07

18 Jun '07

Hi experts-I have some very low-contrast images from an older dataset and the Freesurfer segmentation completely misses the lower and posterior bits of the occipital lobe on many of the subjects (see attached images from an example subject). What is the recommendation in this case? Can I fix this with control points? It's a much more extensive failure than I'm used to seeing fixed with control points. Thanks, Jess ------------------------ Jessica Turner, Ph.D. Project Scientist, FBIRN (www.nbirn.net) Department of Psychiatry and Human Behavior University of California, Irvine Phone: (949) 824-3331 Fax: (949) 824-3324

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analyze orientation
by Leila BH 18 Jun '07

18 Jun '07

Hello, I have some analyze images (128*128*68), and I did not understand the way to read them correctly (with mri_convert). For the moment I am using : 'mri_convert chuv70 -it img -ot mgz 001.mgz'. This command works but gives me INFO: could not find .mat file for direction cosine info. In the end of my processing I have to get my output (coming from mri_label2vol command) according to a template that I have made 128*128*128 (empty_cube.img), then convert it to my orientation with a software (imageconverter) then cut the additional slices to obtain the FreeSurfer output in the same referential as my original data to continue my processing in matlab (windows). I also open one of dicom (axial slice) file with matlab and see the ImageOrientationPatient field: it is -0.0173 0.9999 -0.0005 0.0302 0.0000 -0.9995 I also tried to convert this with mri_convert : Mri_convert chuv70 -it dicom -ot mgz 003.mgz It works and gives me.. Spatial information first image position 72.7981 -128.026 125.594 last image position 72.7981 -128.026 125.594 image orientation -0.0172556 0.999851 -0.000521332 0.0301985 1.35525e-19 -0.999544 ------------------------------------------------- TR=9.99, TE=4.60, TI=0.00, flip angle=8.00 i_ras = (0.0172556, -0.999851, -0.000521332) j_ras = (-0.0301985, -1.35525e-19, -0.999544) k_ras = (0.999395, 0.0172635, -0.030194) writing to 003.mgz... but I don't know how to use these informations to get my output in the correct orientation ? Could some one help me!! Thanks Leila

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Problems with intensity/final volumes/wm segm?
by Inês Souta 18 Jun '07

18 Jun '07

Hi, After running -autorecon2, I checked the output images and I found that either the intensity normalization or the wm segmentation was not done well. I don't really know what to do or where to start. I've already tried adding some control points and editing wm.mgz, but it doens't seem to improve much. What should I do? I send some of the images in atachment, Thanks, Ines

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fsaverage
by Stacy Chu 18 Jun '07

18 Jun '07

Hi Freesurfer community, I'm curious about fsaverage and the nature of the subjects used to create it: ie how many subjects/where they are from/age group/gender/other general stats. Is there somewhere I can find out this information, or if anyone just knows, can you send me an email? Thank you in advance! Best, Stacy Chu stacy.chu(a)med.nyu.edu ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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(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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