Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

Next Release
by Michael Harms 31 May '07

31 May '07

Hello, There have been several mentions on this list of the intent to release a new FS version later this summer. As an aid to those trying to decide whether it is worthwhile to wait for the next version to start an analysis of a new group of subjects, I thought it would be helpful to know the following: 1) Can anyone comment on the target month, and how likely that target will "stick"? 2) At what stage of the processing would you have to begin reprocessing the data in order for the results to completely reflect v3.1? -- the very beginning? Somewhere in the middle of autorecon2? [I see from http://surfer.nmr.mgh.harvard.edu/fswiki/NextReleaseNotes? action=highlight&value=next+release that there is going to be a corrected aseg in v3.1. So, am I correct in assuming that everything following the creation of the aseg.mgz would have to be reprocessed?] thanks, Mike H.

2 1

Freesurfer mri_surf2surf-smoothing error
by Susanne Mueller 31 May '07

31 May '07

Hi, I am relatively new to freesurfer and trying to do my first group analysis. Following the web tutorial -although with my own data set- I was able to do the pre-processing incl. mris_preproc which created the desired output without any error message. However, when I try to perform the next step, i.e. smoothing the data, I get the following error message mri_surf2surf --hemi lh --s average --sval lh.ADvsContr ols.thickness.mgh --fwhm 10 --tval lh.ADvsControls.thickness.10.mgh srcsubject = average srcval = lh.ADvsControls.thickness.mgh srctype = trgsubject = average trgval = lh.ADvsControls.thickness.10.mgh trgtype = surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 Reading source surface reg /cind/00/FAD/subjects/average/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject reading group avg surface area 922 cm^2 from file Segmentation fault I also tried to run the smoothing as a part of the mris_preproc with the same result. I am using the v3.0.5 version of freesurfer. Any help to figure out what I am doing wrong or what else is going on would be greatly appreciated. Susanne

2 1

tksurfer time course window
by Elaine Leung 30 May '07

30 May '07

Hello Freesurfer, Is there a way to adjust or set the y-axis of the time course window in tksurfer? Thanks in advance, Elaine

2 1

white matter surface leakage
by Paul Aparicio 29 May '07

29 May '07

Dear List, I am having a problem with mri_normalize. The problem is that after normalization the white matter areas in my volume have expanded and leaked into area that should be grey matter, is there a way to place control points for grey matter? Thanks paul

1 0

(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

2 1

(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

2 1

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