Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Top Quartile of Active Voxels
by Dave Brohawn 08 Jan '09

08 Jan '09

Hello, I ran the following analysis to target task-specific voxels at a certain contrast and offset. func2roi-sess -roidef dACC10_lh -analysis EMerror -anatlabel dACC-lh -maskcontrast ASevfix -maskframe 5 -maskthresh 1 -masktail pos -maskmap sig -sf Subject_files/MTHFRn18-list -d $SUBJECTS_DIR I would like to create a functional constraint including only the 25% most active voxels (top quartile). Is there a command that can achieve this? Thanks, Dave Brohawn

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Problem running tksurfer
by Yigal Agam 08 Jan '09

08 Jan '09

tksurfer fsaverage lh inflated surfer: current subjects dir: /autofs/space/ventzl_001/users/SUBJECTS_DIR surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/space/schnook_001/users/yigal/projects/functional surfer: Reading header info from /autofs/space/ventzl_001/users/SUBJECTS_DIR/fsaverage/mri/T1.mgz reading group avg surface area 822 cm^2 from file surfer: vertices=163842, faces=327680 Loading /usr/local/freesurfer/stable4/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(fsaverage) surfer: using interface /usr/local/freesurfer/stable4/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/stable4/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/stable4/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/stable4/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/stable4/lib/tcl/tkUtils.tcl Error loading icon_disk_multiview: couldn't open "/usr/local/freesurfer/stable4/lib/images/icon_disk_multiview.gif": no such file or directory Error sourcing /usr/local/freesurfer/stable4/lib/tcl/tksurfer.tcl: image "icon_disk_multiview" doesn't exist reading white matter vertex locations...

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File cnr.mgh
by Jürgen Hänggi 08 Jan '09

08 Jan '09

Dear FS experts I am not sure whether the file cnr.mgh represents the contrast-to-noise ration (CNR) on one hand and how to interpret it. When I loaded the cnr.mgh in tkmedit, there is actually no image visible and only one value is shown e.g., 0.355 or -0.965. What do these values mean? In my opinion, these values are to small for a classical CNR, isn't it? Can I use the cnr.mgh file to control the CNR (and also the SNR) of the FS surfaces derived from images acquired on two different scanners? Is there another way in FS to check whether the SNR and CNR is comparable between surfaces derived from images acquired on different scanners? Thanks in advance Kindly regards Jürgen ---------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------------------

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Subcortical Label
by Kelly Silva 08 Jan '09

08 Jan '09

Hello, I´d like to know if there is some way to create a ROI-label of a subcortical structure. If there is a way, please tell me how to do. Thanks, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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mri_vol2surf - MNI subject
by Yigal Agam 08 Jan '09

08 Jan '09

Hi, If I have volume data in MNI subject space (produced using --tal option in mri_vol2vol), how do I project it onto the surface in the same subject space? There does not seem to be an equivalent tal option in mri_vol2surf. Thanks, Yigal

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Trouble Creating label
by Zeidan, Mohamed A. 07 Jan '09

07 Jan '09

Hello all, I'm creating a label on a volume in tkmedit and as I do it, tkmedit will unexpectedly close and give me the following error message in the terminal window: =================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to analysis-bugs(a)nmr.mgh.harvard.edu : : Now exiting... Any thoughts? Thanks, Moe

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Averaging two SPGR
by antonio cerasa 07 Jan '09

07 Jan '09

Dear List Does anyone know how to get more detailed information on the specifics of the method used to average two SPGR (or MPRAGE) sequences ? -------------------------------------------------------------------------- Antonio Cerasa PhD Laboratory of Neuroimaging Institute of Neurological Sciences National Research Council (CNR) Cosenza, Italy.

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Parameter comparison in native vs. template space
by Christine Ecker 06 Jan '09

06 Jan '09

I would like to export cortical thickness measures and compare the data across subjects in a vertex-by-vertex fashion. Please could you confirm that similar functions such as mri_glmfit are based on the parameters in template space e.g. lh.thickness.fsaverage.mgh and not on the parameters in native space e.g. lh.thickness. So for a group comparison I would have to export the files in template space (e.g. lh.thickness.fsaverage.mgh) and could then map the output back onto the template? Also, why are the parameters not the same in native and template space? Finally, in order to compare groups on the basis of the parcellated regions (e.g. lh.aparc.stats). Are parameters such as area, volume, curvature etc comparable across groups or would they still have to be corrected for whole-brain volume? I would be very grateful if you could help me further. Thank you!

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Loading Projects Files
by Bramen, Jennifer E. 06 Jan '09

06 Jan '09

Dear Freesurfer Community I have been unable to load any of my saved Project files , and I cannot find any explanation in the tutorial or in the list arcives. I have been saving the project files inside of the qdec/<Design Name> directory as <?h_description>.qdec. However, when I try to load them, I get an error. I am using Qdec 1.1. Any ideas about what is wrong? Thank you. Best regards -- Jennifer Bramen, Ph.D. Postdoc David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)267-5116 Fax: (310)206-5518 Email: jbramen(a)mednet.ucla.edu Campus Mail Code 176919 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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How to overlap FSL statistical map onto surface in Matlab?
by Yunjie Tong 06 Jan '09

06 Jan '09

Hi I was able to view the statistical maps (from FSL) on the subject's surface following the tutorial (FsTutotial/FSLFeatFreeSurfer). I would like to see the same image in Matlab. I could show the subject's surface as well as the the cortical parcellation in Matlab by modifying the functions freesurfer_read_surf.m and read_annotation.m. I do not know how to overlap the statistical map onto the surface then. Is there any Matlab function I can use? Thanks. Best, Yunjie

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