Freesurfer

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30076 discussions

(no subject)
by duhanjian＠sohu.com 11 Jun '07

11 Jun '07

  <p>Thank you for previous help.</p><p>Now I want to compare the cortical thickness of the two groups. Mr Pacheco tells me to use the group analysis to compare. When I read the manual of the group analysis (<a href="https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis">https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis</a>), I meet some problem. When writing the FSGD file, I don't how to input another group thickness (eg, control group) in to the FSGD. If not use method, how to compare the cortical thickness between the two group?</p>

2 1

volume to use for control points
by syc2114＠columbia.edu 08 Jun '07

08 Jun '07

Hi, I recently started using Freesurfer and I have a quick question about adding control points. I want to add control points to a stretch of white matter which was excluded - can I add them to the wm.mgz volume by referring to the T1 aux or do they need to be added to the brainmask volume only?

3 2

Where can I find global and local thickness / volume measures for individual subjects?
by Burmicz, Ryszarda 08 Jun '07

08 Jun '07

Hi! I am new to Freesurfer; I have run reconstruction steps with recon-all. I can find no reference to thickness values calculated as part of this process, apart from visualising them in Freesurfer - is there a specific file from which I can extract this information without running the GUI? I am comparing data from a single subject across different scanning protocols in order to look at variation in thickness. So ultimately I would like to produce tabulated data of global and local thicknesses. Many thanks for your help, Rysia

2 1

FRD in ROI
by Marie Schaer 07 Jun '07

07 Jun '07

Hello everybody, Following the question of Jorge Luis yesterday, I was wondering if the option "marked only" in "Set threshold using FDR" could be an option to get FDR corrected results on parcells of the cortical surface? However, when I load ROI and click on "marked only", the terminal window shows: "surfer: Error calculating threshold with FDR". Any hint would be very appreciated, many thanks, Marie Schaer

1 0

F-Test and directed contrasts
by Juergen Haenggi 07 Jun '07

07 Jun '07

Dear Freesurfer users We have done a cortical thickness group comparison, but we are not absolutely sure which color corresponds to which contrast. In our *.mat file we specified -1 1 0 0 0 0, but the sig.mgh file shows both directed contrasts (group1 > group2 and group1 < group2). Where can we look which color corresponds to which contrast? We searched for the answer in the archives, but did not find it! Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of 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(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

2 1

w file to label
by Robert Levy 07 Jun '07

07 Jun '07

Hello, I am trying to convert a w file into a label file, and the best way I came up with seems like it is too complicated to be the actual best way. What I am doing below is reading a list of subjects, and then for each subject, 1.) running mri_surfcluster, 2.) merging its output into a new label, and 3.) removing the component labels that went into it. # entered in bash shell # generate the .w file paint-sess -sf Subject_Lists/bw-group-error-5 -analysis EMerror -contrast rACC_lh_pos_0_ASce68 -map mask -hemi lh # merge labels cat Subject_Lists/bw-group-error-5 | while read subject; do mri_surfcluster --in $subject/bold/EMerror/rACC_lh_pos_0_ASce68/mask-0-lh.w --thmin 0.5 --sign pos --subject $subject --hemi lh --surf orig --annot aparc --minarea 1 --sum $subject/bold/EMerror/rACC_lh_pos_0_ASce68/mask-0-h-label.sum --olab $subject/label/rACC_lh_pos_0_ASce68 ; cd $subject/label; mri_mergelabels $(ls rACC_lh_pos_0_ASce68*.label | sed 's/rACC/\-i rACC/g') -o rACC_lh_pos_0_ASce68.label; rm rACC_lh_pos_0_ASce68-0*.label; cd $SUBJECTS_DIR; done #check in tksurfer surf-sess -s mano001 -analysis EMerror -contrast rACC_lh_pos_0_ASce68 -map mask -hemi lh -fthresh 1 It seems to work, but if there is a more direct way, it may be better just because there is potential room for error the way I am doing it. Thanks, 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

3 3

Turn Off Verbose Output
by James Porter 07 Jun '07

07 Jun '07

Howdy- I didn't see any flags in the help files, but are there some 'hidden' commands I could use to attenuate the verbosity of reg-feat2anat and aseg2feat? Thanks, Jim Porter TRiCAM Lab Coordinator Elliott Hall N437 612.624.3892 www.psych.umn.edu/research/tricam <http://www.psych.umn.edu/research/tricam>

3 3

mapping aseg.mgz to group FEAT analyses
by Eric Feczko 07 Jun '07

07 Jun '07

Hey, I noticed on the freesurfer wiki a workflow for registering an individual's subcortical segmentation(aseg.mgz) to individual feat sessions using aseg2feat. Are there any scripts for registering an individual's subcortical segmentation to a group feat session (.gfeat directory)? -Eric

2 1

Re: [Freesurfer] reg- feat2anat error
by Furlong, Carolyn 06 Jun '07

06 Jun '07

Hi niiRead(): unsupported timing pattern in Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz sorry for the delay, Best wishes Carolyn can you send the log file? Furlong, Carolyn wrote: Hi, When I try to register my functional data to anatomical data using reg-feat2anat --feat feat_directory --subject subject_name I get the following error message ERROR: could not read ///example_func.nii.gz as 24 What does this mean? And how can I fix this? Best wishes Carolyn ________________________________ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://owa.liv.ac.uk/exchweb/bin/redir.asp?URL=https://mail.nmr.mgh.harvar…> -- 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

3 11

Cortical ROIs analysis
by jorge luis 06 Jun '07

06 Jun '07

Hello all I have a question: How to threshold a thickness statistical parametric map by using FDR just in one specific label of the fsaverage cortical surface parcelation? In advance thank you a lot Jorge ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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