Freesurfer June 2007

freesurfer@nmr.mgh.harvard.edu

59 participants
82 discussions

slice thickness
by T. Song 21 Jun '07

21 Jun '07

Hi All: I have a question about the slice thickness. To get a "good" freesurfer reconstruction, especially the "accurate" statistic analysis, what it the maximum slice thickness can I use when acquire the DICOM image? Thanks! Tao

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ICV / brain volumes
by Nurunisa Neyzi 21 Jun '07

21 Jun '07

Hi. does it matter whether I use the total brain volumes or the ICVs from the aseg. stats in order to normalize individual brain structure volumes?

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Correction: Re: [Freesurfer] Q: masking statistical overlays
by raij＠nmr.mgh.harvard.edu 20 Jun '07

20 Jun '07

Correction: We want to use func_print_timecourse_selection (not labl_save) to output the tables that contain the means across the label (with the bad vertex points excluded by previously done masking). However I think the time course functions are not compatible with the .w file format? Right, Doug? Then, I guess the question is, how do we mask the bad vertex points out of the time course volumes? -Tommi --- Hi Bruce & Surfers, OK, we created a .w file and it looks at is should so part (a) below is solved. However we cannot seem to extract a list of functional overlay values of vertex points included in a label, which was why we needed to do this in the first place. Our goal is to get rid of some bad vertex points points in our functional overlay by creating a mask that excluded them, then load a label, and use labl_save to create a list of overlay values contained within the label (that does not include the vertex points that were masked away). Bruce, Kevin, Doug, any suggestions? Bests, Tommi > Hi Tommi, > > the w-file format is sparse and doesn't have to cover the surface, but the .mgz does. > > Bruce > > On Tue, 19 Jun 2007 raij(a)nmr.mgh.harvard.edu wrote: > >> Dear Fellow Surfers, >> >> Is there a FreeSurfer way to mask a stat map overlay, on the inflated cortical surface, in a way that the masked vertex points >> >> (a) are transparent in the overlay display (just the underlying dark gray/light gray curvature is showing)? >> >> (b) do not effect label-specific HDR time courses (i.e., only unmasked vertex points are taken into account when calculating the HDR curve)? >> >> We can edit the stats map with our custom script to generate the mask (e.g., mark all masked vertex points as 0 in the overlay), but it seems that in a stats map every vertex point needs to have an overlay value (i.e., we cannot just skip the vertex points we want to omit - right?). >> >> Thanks! >> >> -Tommi >> >> --- >> Tommi Raij, M.D., Ph.D. >> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St >> Charlestown, MA 02129 >> U.S.A. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > >

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Q: masking statistical overlays
by raij＠nmr.mgh.harvard.edu 20 Jun '07

20 Jun '07

Dear Fellow Surfers, Is there a FreeSurfer way to mask a stat map overlay, on the inflated cortical surface, in a way that the masked vertex points (a) are transparent in the overlay display (just the underlying dark gray/light gray curvature is showing)? (b) do not effect label-specific HDR time courses (i.e., only unmasked vertex points are taken into account when calculating the HDR curve)? We can edit the stats map with our custom script to generate the mask (e.g., mark all masked vertex points as 0 in the overlay), but it seems that in a stats map every vertex point needs to have an overlay value (i.e., we cannot just skip the vertex points we want to omit - right?). Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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incorrect slice orientations
by Catherine Hartley 19 Jun '07

19 Jun '07

Hi, I just ran autorecon1 on a batch of data and when I view the brainmask in tkmedit, selecting the coronal orientation actually displays the sagittal orienation and vice versa (horizontal is fine). Also, when I check the talairach using tkregister, the talairach comparison volume comes up with a strange diagonal orientation. Some illustrative images are attached. Any suggestions for how to correct this would be welcome. Thank you, Cate

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Problems converting SPM functionals to bshort
by Lars Kuchinke 19 Jun '07

19 Jun '07

Hi all, is it possible to convert my functional SPM images (3d) to bshort (or bfloat) format using mri_convert? Is still get stucked here, since mri_convert only allows me to convert one image instead of the full time series... Is there an option to convert a list of old SPM 3d images? I'm a bit confused so I would appreciate any kind of help. Thanks. Lars -- Lars Kuchinke, PhD Freie Universität Berlin Allgemeine Psychologie Habelschwerdter Allee 45 14195 Berlin kuchinke(a)zedat.fu-berlin.de www.fu-berlin.de/allgpsy Tel: 030 838 55776

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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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Freesurfer June 2007