Freesurfer January 2007

freesurfer@nmr.mgh.harvard.edu

51 participants
74 discussions

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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single set of DICOMS
by Catherine Alexandra Hartley 21 Jan '07

21 Jan '07

Hi, I'm just beginning to use FreeSurfer and I have a very basic question. I'm doing a reanalysis of an existing data set looking at behavioral correlates of cortical thickness in a particular ROI. I only have one set of DICOMS for each subject. Is it ok to do the analysis on a single set of structural data or would the level of inaccuracies resulting from not averaging across multiple scans be undesirable? Thanks, Cate

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RE: [Freesurfer] control points and white matter edits
by Tanji, Kazuyo (NIH/NIMH) [F] 18 Jan '07

18 Jan '07

Dear List, I have a similar problem with getting accurate pial and white matter surfaces in monkey inferior temporal, frontal and occipital regions. In those areas surfaces are not recognized properly. I tried putting control points with limited success. In my case most of the missed white matter voxels have the intensity value of 110. As was mentioned somewhere in the list, is it useless to have control points on the voxels with the value of 110? I would very much appreciate it if you could suggest any other ways to correct this problem. Thanks, Kazu > Hi Paul, > > The inferior temporal regions are the trickiest, especially in low > quality scans - without seeing any images, you may have achieved as > close as you are going to get. > > Be careful with control points, more is not always better, quality > over quantity, you want to be sure you have put them in correct > locations, not on partial volumed voxels, and only in regions that are supposed to be wm. > > While adding voxels to the wm volume will have some impact on where > the final surface lays, it is also dependant on finding the best > intensity gradient. If your scans are lower quality with intensity > troubles that will likely trump any edits you've made. > > If you'd like to upload one of your subjects I am happy to take a look > at it > - although I will be out of town all next week so it might take me a > while to get to it. > > Jenni > > > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Paul Greenberg > Sent: Friday, January 05, 2007 7:04 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: [Freesurfer] control points and white matter edits > > Hi all, > > I'm having trouble getting accurate white and pial surfaces in > inferior temporal regions on a few lower quality scans with > significant intensity variation. I've added hundreds of control > points and drawn in white matter in these regions when control points > failed to recover unlabeled cortex, but when re-running the scripts > with either -autorecon2-wm, or -autorecon2-cp, followed by -autorecon3 > the surfaces are still not accurate. Are there other interventions I > can to to get more accurate surfaces? If you manually add white > matter why will the regenerated white matter surfaces not always extend around the hand drawn parts? > > Thanks, > Paul

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buckner data set
by joel-bruss＠uiowa.edu 18 Jan '07

18 Jan '07

Just a quick question. Is the vitamin E capsule (or whatever the bright artifact outside the skull/skin is) denoting the right or left hemisphere for the Buckner 40-brain data (look at subject buckner_data/group_study/004/mri/rawavg.mgz)? Thanks, Joel

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Freesurfer January 2007