Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

(no subject)
by hankee 26 May '07

26 May '07

hi, I want to compare the occipital lobe's cortical thickness in 2 groups,but I do't know how to do it? Athough I have seen some paper using FreeSurfer software to compare the thickness, it has no detail procedure. hankee，duhanjian(a)sohu.com 2007-5-26

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(no subject)
by hankee 26 May '07

26 May '07

Hi, I have finished 3 demension data management by the Freesurfer software, but I do’t know how to compare the cortical thickness of the occipital lobe between the patient group and the control group. Could you tell me the way to deal with that? Thank you very much! hankee，duhanjian(a)sohu.com 2007-5-26

2 1

White Matter Parcellation
by James Porter 25 May '07

25 May '07

Hello- In September of 2006 there was a post in which you mentioned that white matter parcellations were being fine-tuned but not yet ready. I'm really hoping to take advantage of the 3000 and 4000 level labels shown in FreeSurferColorLUT.txt, but I don't have them in my current parcellations that were created using FreeSurfer v3.0.3. Are there versions of the parcellation schemes available that I can upgrade to in order to obtain these finer white matter parcellations? Thanks, Jim Porter TRiCAM Lab Coordinator Elliott Hall N437 612.624.3892 www.psych.umn.edu/research/tricam

2 1

(no subject)
by hankee 25 May '07

25 May '07

1 0

Area measurement question
by Morgan Hough 25 May '07

25 May '07

I just wanted to check which surface was used to compute area and which reference would have this information. Thanks in advance. Cheers, -Morgan

2 4

Gammafit vs. SPMHRF
by Dan Dillon 21 May '07

21 May '07

Dear FreeSurfers, What exactly is the difference between the HRF function in gammafit vs. SPMHRF? Are there reasons to prefer one to the other? Thanks, Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 496-5222 E-mail: dillon(a)wjh.harvard.edu

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make_average_subject
by Furlong, Carolyn 21 May '07

21 May '07

Hi, I'm still having problems with make_average_subject, when I type the folowing command line in: >make_average_subject --debug --subjects 'subject1' 'subject2'..... --out PLP_average --no-symlink echo ERROR: Flag $flag unrecognized. echo ERROR: Flag --no-symlink unrecognized. ERROR: Flag --no-symlink unrecognized. echo $cmdline echo ....... exit 1 exit 1 and when I try to view the results by > tksurfer PLP_average lh inflated I get the message: surfer: current subjects dir: /disc2/Kate/Flatmap1 surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /disc2/Kate/Flatmap1 surfer: ### Could not find anatomical header information. The mri folder does not contain the same files that the tutorial example subject 'buckner fsaverage' does, what do you think is going wrong? Thanks for your help Best wishes Carolyn

2 1

reg -feat2anat error
by Furlong, Carolyn 21 May '07

21 May '07

Hi Doug Please find attached the logfile that you requested, sorry for the delay, I am only able to work on this one day a week. Best wishes Carolyn Actually, I wanted the log file found in featdir/reg/freesurfer/reg-feat2anat.log. doug Furlong, Carolyn wrote: > 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 >> > >-- >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 > > > >_______________________________________________ >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

2 1

RE: [Freesurfer] tkmedit
by Jenni Pacheco 21 May '07

21 May '07

Hi Martin, You should be fine not editing these regions routinely - only, of course, if they pose a problem for your surfaces. For the most part, also, you should be fine to run the entire stream and do any edits that may be needed after the fact - instead of running stepwise and checking each output along the way. Jenni -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Martin Chang Sent: Thursday, May 17, 2007 12:34 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] tkmedit >Hi, > >I have a question about using tkmedit. Up until now, our group has been >editing out the eye muscles after autorecon-1 and editing out the optic >nerve after autorecon-2. I know on earlier versions of freesurfer it was >highly recommended to do so because the program would sometimes crash >otherwise. However, using the newer version, the program seems to know to >not include eye muscles in the pial matter boundary, and the optic nerve >does create a region of high curvature at that point, but it doesn't crash >the program. > >I was wondering, in your own analyses, did you do editing at each step >(excluding situations that are obviously out of the norm), and would it be >a bad thing not to edit those regions in the majority of cases? > >Thanks, >Martin Chang _________________________________________________________________ PC Magazine's 2007 editors' choice for best Web mail-award-winning Windows Live Hotmail. http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migratio n_HM_mini_pcmag_0507 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 2

Where to get mri_binarize?
by Dan Dillon 18 May '07

18 May '07

I would like to use mri_binarize but don't seem to have it (running stable 3.0.3). Where can I get it? Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 496-5222 E-mail: dillon(a)wjh.harvard.edu

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Freesurfer