Freesurfer

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30057 discussions

Translate label file from average subject to all subjects
by Jonathan Wisco 16 Mar '06

16 Mar '06

Hi, I would like to translate a label created from an average subject inflated surface to all the subjects. How would I do that? Should I first use mri_surf2surf to resample the average subject inflated surface to all the other subjects? Would a label that was created on the average subject then automatically be translatable to the subjects? Thanks, Jon -- Jonathan J. Wisco, Ph.D. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Building 149, 13th St. Charlestown, MA 02129 E-mail: jjwisco(a)nmr.mgh.harvard.edu Tel: 617-851-8492 Fax: 617-726-7422

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Freesurfer & SuSE Linux
by Venkat subramanian 16 Mar '06

16 Mar '06

Dear Freesurfer Experts, Could youplease clarify whether the new freesurfer stable release version 3 is compatible with SuSE Linux 10.0 (kernel 2.6.13)? Many thanks, Venkat. Dr. Venkatasubramanian, Asst. Professor of Psychiatry, National Institute of Mental Health & Neurosciences, Bangalore, India. --------------------------------- Yahoo! Travel Find great deals to the top 10 hottest destinations!

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RE: [Freesurfer] cortical labels
by Kevin Teich 16 Mar '06

16 Mar '06

> but I would still like to know if there is anyway to build an mgz > image of the grey volume segmented accordingly to ?h.aparc.annot. I > hope you can help me. In tksurfer, you can import an annotation as a segmentation file. This will fill the voxels between surfaces with the label in the annotation file. Then you can save this segmentation as a new volume. -- Kevin Teich

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Testing FreeSurfer installation error
by Chunchun Ni 15 Mar '06

15 Mar '06

I installed the freesurfer following exactly as the instructions on the website. When I test it, "recon-all -s bert -all" doesn't work, it runs for a few min. and shows "flirt: Command not found. ERROR: running flirt". When I try to use my own data, convert dicom to mgt, "mri_convert" command shows "can't find dicom". What's the problem with the installation? Any help? Thanks Chunchun

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Autorecon1
by Martin Ystad 15 Mar '06

15 Mar '06

Hi, I have processed some of my subjects on a previously released dev-version (20060210). I have changed to the new stable release. Do I need to run the -autorecon1 step again, or will -autorecon2 and -3 suffice to bring the previously run subjects up to date? (the brainmask-volumes have been edited, so I'd like to keep these changes) Another question; if I run the -autorecon2-wm flag, will I save a lot of computing time if I manually remove the Optic Nerve before doing so? Thanks, Martin Ystad University of Bergen, Norway.

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cortical labels
by Pellegrini, Stefano (NIH/NINDS) [F] 15 Mar '06

15 Mar '06

Hi everybody, I have seen that the aseg.mgz file allows to see the segmentation of the whole brain volume in different areas. Is there any way to obtain an mgz file with the cortical gray matter volume labeled in such a way that every cortical region has a different intensity value? thanks, -stefano

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Re: surfcluster gives very different results run two ways on the same file
by Doug Greve 14 Mar '06

14 Mar '06

Frida has helped find another bug (thanks Frida!). When running mri_surfcluster with average7 inside your csd file, make sure to specify --subject average7 --really-use-average7 or else it will underestimate the clustersize and cause the significances to be too low. I'll mod the code when I get back from CA. doug On Tue, 14 Mar 2006, Frida Polli wrote: > yes, that indeed fixes it - you might want to put some of this stuff in the > documentation or send out an email or something b/c i spent two weeks running > another analysis b/c i thought my clusters weren't meeting significance, and > only discovered this discrepancy when i did a regular mri_surfcluster :). so > i can imagine since many people are still using average7, this would be > really importnat for them to know. i am cc'ing nurit from moshe;s lab, as i > know she's been using it - there are probably others. that having been said, > thanks for the tool - its great. > thanks, frida > On Monday, March 13, 2006, at 04:44 PM, Doug Greve wrote: > >> >> >> Oh, I know what happened. It only fixes the vertex area when you pass >> average7 in explicitly. When you use a csd, it get's the subject name >> from the csd. The ratio of the areas is 1.5. I think it will work if >> you specify --subject average7 with the csd (and >> --really-use-average7). Can you try that and let me know? >> >> doug >> >> >> On Mon, 13 Mar 2006, Frida Polli wrote: >> >>> hi doug >>> i am very confused. i used mri_surfcluster on one file in two different >>> ways, and for one cluster, got two different sizes for all the clusters >>> (see example of one cluster below). the first way is just the standard >>> way, the second way is using csd files and having it output CWPs. >>> >>> for one cluster, the first way gave me the following result: >>> 4 3.230 71230 1065.25 8.0 12.9 25.4 1788 >>> >>> the second way gave me the following result: >>> 4 3.230 71230 710.17 8.0 12.9 25.4 0.36277 >>> 0.35092 0.37500 1788 >>> >>> as you can see, this is the same cluster, but with two wildly discrepant >>> values for surface area. what is going on, and which is correct? >>> >>> the first way, i ran: >>> mri_surfcluster --really-use-average7 --src >>> BG3b_glmfit/rh.ASevASc_6s_BwGroup3b.fsfast.glmdir/ >>> BwGroupError3b_NvSZ_contrast/sig.mgh --hemi rh --srcsubj average7 --thmin >>> 1.3 --minarea 100 --sum rh.BG3_6s.sum >>> >>> the second way i ran: >>> mri_surfcluster --src >>> BG3b_glmfit/rh.ASevASc_6s_BwGroup3b.fsfast.glmdir/ >>> BwGroupError3b_NvSZ_contrast/sig.mgh --csd >>> csdfiles/BG3b_ASevASc_6s_rh_MCSIMz-BwGroupError3b_NvSZ_contrast.csd --sum >>> BG3b_glmfit/rh.ASevASc_6s_BwGroup3b.fsfast.glmdir/ >>> BwGroupError3b_NvSZ_contrast/sig.cluster.sum --ocp >>> BG3b_glmfit/rh.ASevASc_6s_BwGroup3b.fsfast.glmdir/ >>> BwGroupError3b_NvSZ_contrast/sig.cluster.mgh --thmax infinity >>> >>> in /space/ventzl/1/users/SUBJECTS_DIR >>> >>> thanks, frida >>> >>> >>> >>> >> >> -- >> 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 >> >> >> > Frida Polli > PhD Candidate, Suffolk University > Research Fellow in Psychiatric Neuroimaging > Massachusetts General Hospital > CNY 149-2608, 13th Street > Charlestown, MA 02129 > phone: (617) 724 4604 > fax: (617) 726 4078 > email: fpolli(a)nmr.mgh.harvard.edu > > > -- 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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talairach
by Durastanti, Valentina (NIH/NINDS) [F] 13 Mar '06

13 Mar '06

I tried to check the talairach transformation after the autorecon1 typing: tkregister2 --mgz --s "sunject name" --fstal But I haven't a surface at this step and I can't see the green line Can you tell me what's happening?

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fix vertex area
by Sasha Wolosin 13 Mar '06

13 Mar '06

Dear all, I ran the 'mris_make_surfaces' script after running recon-all, but I forgot to include 'setenv FIX_VERTEX_AREA' in my set up file. I saved a back-up of the surf folder created by recon-all. Will I need to re-run mris_make_surfaces? Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin(a)kennedykrieger.org Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Recon All
by Frederick Powell 13 Mar '06

13 Mar '06

Hello all, I am new to Freesurfer and would like to know what is the new command to perform the automated process for this software. I have created a subject directory and my files are dicom. If anyone could please give me as much information because I just started to use this and I am running X11 on my mac. Any help would be much appreciated. Thanks -- Frederick G. Powell Boston University School of Medicine MD/PhD candidate 617-593-7183

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