Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

RE: [Freesurfer] interpret analysis results
by Reschke, Cole 23 Jan '07

23 Jan '07

Thank you, I have three follow up questions: Threshold is -log10(p), why are negative values showing up on the display? I am using fsaverage to display my results, would it make any difference if I created my own average subject based on the analysis? Is it possible to export the voxel-by-voxel intensities (or the brain surface data) used in Freesurfer's analysis; and then re-import the some external analysis results back to Freesurfer format for display purposes? Cole ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Doug Greve Sent: Monday, January 22, 2007 11:56 AM To: Reschke, Cole Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] interpret analysis results The values are -log10(p), so p < .01 would require a threshold of 2, etc. I don't use t, z, or F because I have not memorized the various tables that convert them to p:). The sig will map to any surface, including pial. doug Reschke, Cole wrote: First, thanks to Doug for all his help up to this point. Next, I have three questions. In my analysis, I used the -paired-diff and -osgm options in mris_preproc and mri_glmfit, respectively. I have successfully loaded sig.mgh onto the inflated surface. Are the values from the color chart [-5,5] representative of a t-score or an F-score (t^2)? I adjust the threshold by changing the 'Min' value in the 'Configure Overlay Display'? Ex. If Min ==3, then p < 0.001 ? Is the sig.mgh created solely for the inflated surface, or is it able to be uploaded on others (pial, wm, etc.)? Thank you, Cole Cole Reschke Data Manager, PET Center Banner Alzheimer Institute Banner Good Samaritan Medical Center Phone: (602) 239-4868 ________________________________ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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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the dorsolateral prefrontal cortex
by wan＠vt.edu 23 Jan '07

23 Jan '07

Hello All, We want to get the information about the dorsolateral prefrontal cortex. However, two parcellation maps (?h.aparc.annot and ?h.aparc.a2005s.annot)didn't show this structure directly. Can you please tell me how to draw the ROI for the dorsolateral prefrontal cortex in the Final Surface of the brain? and how to get values for thickness and volume for this structure? Thanks, Li

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thickness reproducibility-longitudinal?
by Chacko Cherian 23 Jan '07

23 Jan '07

Hello all, http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility Is this page on thickness reproducibility intended for longitudinal analysis or is it just a general group analysis procedure? THanks in advance, Chacko. ____________________________________________________________________________________ Want to start your own business? Learn how on Yahoo! Small Business. http://smallbusiness.yahoo.com/r-index

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Freesurfer usage on Ubuntu 6.06
by Binyam Nardos 22 Jan '07

22 Jan '07

Hello All, I just installed Freesurfer, the Red Hat 9 version for Ubuntu 6.06. I followed all the instructions and made the changes as directed to my .bashrc and .bash_profile files to include the two lines as follows: export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh Upon running the test command recon-all --help, I get the following message: bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory and indeed there is no tcsh dir in the /bin folder. I'm assuming that reference should have been /bin/bash instead of /bin/tcsh. Any help would be appreciated, Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 4444 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments.

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Longitudinal analysis
by Chacko Cherian 22 Jan '07

22 Jan '07

Hello users, Is there a typo on the longitudinal analysis page on the wiki.. does the command go like this?? recon-all-long -long -subjid tp1 -subjid tp2 Thanks Chacko. ____________________________________________________________________________________ Expecting? Get great news right away with email Auto-Check. Try the Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/newmail_tools.html

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single set without skull -- help
by yanxia 22 Jan '07

22 Jan '07

Dear All, I have a MRI dataset without skull (did skull-stripping with FSL), and try to reconstruct the surface. I run: recon-all -s $subject_name -autorecon-all But the program stops because "nu_correct: Command not found"! Question: 1> whether installation was not correct so not to find "nu_correct"? 2> what is best way or command to reconstruct the surface with a skull-stripped data set? Thanks. Best Regards, Yan

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RE: [Freesurfer] -noaseg
by Nick Schmansky 22 Jan '07

22 Jan '07

Kazu, This is for a non-human primate, right? If so, you will need to manually define seed points for the corpus callosum and pons. To do so, open the white matter volume in tkmedit: tkmedit <subjid> wm.mgz and using the cursor, identify the 'volume index' of the point where you think the corpus callosum is located and make a note of it (for instance, in an example subject 'bert', its around 128 117 123). Also make a note of where the pons is located. Then, restart recon-all from mri_fill, passing those coordinates, for example: recon-all -s bert -autorecon2-wm -noaseg \ -cc-crs 128 117 123 \ -pons-crs 128 154 108 Nick ps, i've posted this to the list as others may have a better suggestion. On Mon, 2007-01-22 at 12:55 -0500, Tanji, Kazuyo (NIH/NIMH) [F] wrote: > Hi Nick, > > Thank you so much. It worked. > Now I got an error message at 'mri_fill'. > > The message says: > mri_fill: could not find corpus callosum > INFO: Modifying dst c_(r,a,s), using the transform dst > find_cutting_plane:seed point not in structure! Searching neighborhood... > recon-all exited with ERRORS at Mon Jan 22 10:57:43 EST 2007 > > Is this error due to -noaseg flag? What should I do next? > > Kazu > -----Original Message----- > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > Sent: Sun 1/21/2007 6:38 PM > To: Tanji, Kazuyo (NIH/NIMH) [F] > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] -noaseg > > Kazu, > > It looks like the -noaseg option does make use of norm.mgz (a change > that seems to have occurred since the option was created and tested). > > As a work-around, you should be able to do this: > > ln -s brainmask.mgz norm.mgz > > and then run the -autorecon2 -noaseg flags. brainmask.mgz is a close > enough stand-in for norm.mgz. > > Nick > > > On Sun, 2007-01-21 at 17:45 -0500, Tanji, Kazuyo (NIH/NIMH) [F] wrote: > > Hi, > > > > I have a question on how to use -noaseg option. > > > > I tried a script: recon-all -autorecon2 -noaseg -subjid xxx. > > > > This seems to skip several steps of autorecon2 and start from 'mri_normalize' . This results in an error because norm.mgz is not existing. > > > > Could you suggest better ways to use -noaseg? > > > > Thanks, > > Kazu > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > >

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interpret analysis results
by Reschke, Cole 22 Jan '07

22 Jan '07

First, thanks to Doug for all his help up to this point. Next, I have three questions. In my analysis, I used the -paired-diff and -osgm options in mris_preproc and mri_glmfit, respectively. I have successfully loaded sig.mgh onto the inflated surface. Are the values from the color chart [-5,5] representative of a t-score or an F-score (t^2)? I adjust the threshold by changing the 'Min' value in the 'Configure Overlay Display'? Ex. If Min ==3, then p < 0.001 ? Is the sig.mgh created solely for the inflated surface, or is it able to be uploaded on others (pial, wm, etc.)? Thank you, Cole Cole Reschke Data Manager, PET Center Banner Alzheimer Institute Banner Good Samaritan Medical Center Phone: (602) 239-4868

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info about ?h.cortex.label
by David Ziegler 22 Jan '07

22 Jan '07

Hello all, I recently noticed that one of the labels that appears to be standard output from recon-all is "?h.cortex.label." I can't seem to find any documentation about this label on the wiki, and I was hoping someone could tell me what exactly this label is (e.g. does it exclude the entire medial wall, callosum, etc), how it is generated, and when during the recon-all process it is generated. Finally, is there a command line that I can use to generate this label automatically for a set of recons? Thanks! David

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-noaseg
by Tanji, Kazuyo (NIH/NIMH) [F] 21 Jan '07

21 Jan '07

Hi, I have a question on how to use -noaseg option. I tried a script: recon-all -autorecon2 -noaseg -subjid xxx. This seems to skip several steps of autorecon2 and start from 'mri_normalize' . This results in an error because norm.mgz is not existing. Could you suggest better ways to use -noaseg? Thanks, Kazu

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