Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Neonatal brain
by Schneider, Jacques 02 Dec '09

02 Dec '09

Hello to the freesurfer group, I would like to analyze neonatal cortices with freesurfer. I ran a test data with a 10 yo child which came through wihtout problem. But a neonatal data set failed the recon at the level of talairach transformation. I suspect that the adult template is inconsistent with the neonatal immature folding and makes the transformation impossible. Now, Kazemi et al in NeuroImage 2007 published a neonatal template, and gave me the files on a research basis. My question is: how to replace the talairach coordinates in freesurfer with these neonatal data to make it work for this population ? I suspect the answer is not easy. But we are willing to give it a try, or perhaps are you already working on it ? Cheers Jack Dr. J.F. Schneider Head of Pediatric Radiology University Children's Hospital UKBB CH-4005 Basel Switzerland Phone +41 61 685 6282 Fax +41 61 685 6015 e-mail: jacques.schneider(a)ukbb.ch Diese Mitteilung ist vertraulich. Sie kann durch das Berufsgeheimnis geschuetzte Informationen enthalten und dient nur zum Gebrauch durch den Adressaten. Sollte diese Mitteilung irrtuemlich an Sie erfolgt sein, informieren Sie uns bitte und loeschen Sie diese Mitteilung sowie allfaellige Anhaenge unverzueglich. Jedes Verbreiten, Weiterleiten oder Vervielfaeltigen dieser Mitteilung ist verboten. This message is confidential and may contain confidential information which is covered by legal or professional privilege. If you are not the intended addressee and have received this e-mail by error, please advise the sender and immediately delete this message and any attachments. Any dissemination, distribution or copying of this communication is prohibited.

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Incorrect hemispheres
by Mayuresh Korgaonkar 02 Dec '09

02 Dec '09

Hello Freesurfer authors, I have processed a few datasets without realising that the hemispheric orientation was provided incorrectly i.e the labelled left hemisphere is actually the right hemisphere. Does this mean all the analysis is incorrect and unusable? What should I do to correct for this hemispheric flip? Thanks in advance, Mayuresh The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/

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(no subject)
by Guang Zeng 01 Dec '09

01 Dec '09

Hi, there, I have made our own template using 20 subjects follwoing the instruction in FreeSurfer WIKI. (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) I have a quesition now, Does the quality of the new template depends on the first subject I picked to built the tempalte? Maybe I do not interpret my question clearly, I think I'd like to ask is: If we pick different subject to built a template at the fist step of the all procedure, will the output templates have big difference? If yes, is there a way in FS to pick one subject which is most similar to others, and use it at the first s tep of the build own template procedure? Thanks a lot! Guang _________________________________________________________________ Chat with Messenger straight from your Hotmail inbox. http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?o…

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Problem with mri_aparc2aseg
by Jürgen Hänggi 01 Dec '09

01 Dec '09

Dear FS experts I run recon-all -long on 12 subjects (3-4 time points each) and there is a problem with mri_aparc2aseg. The processor is running, but the the number of labeling slices does not increase (hangs by 4 slices since hours). The other time points of this subject as well as the cross-sectional analysis worked fine. The .log file shows following: #@# WMParc Sat Nov 28 02:34:54 CET 2009 /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04 \n mri_aparc2aseg --s thomas_sub04_tp3.long.thomas_sub04 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz \n reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_fin al.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_fin al.txt) SUBJECTS_DIR /Applications/freesurfer/subjects subject thomas_sub04_tp3.long.thomas_sub04 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/mri/apa rc+aseg.mgz Reading lh white surface /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/surf/l h.white Reading lh pial surface /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/surf/l h.pial Loading lh annotations from /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/label/l h.aparc.annot Reading rh white surface /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/surf/r h.white Reading rh pial surface /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/surf/r h.pial Loading rh annotations from /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/label/r h.aparc.annot Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/mri/rib bon.mgz Loading filled from /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/mri/fil led.mgz Ripping vertices labeled as unkown Ripped 6730 vertices from left hemi Ripped 6931 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/mri/ase g.mgz Loading Ctx Seg File /Applications/freesurfer/subjects/thomas_sub04_tp3.long.thomas_sub04/mri/apa rc+aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 Any idea? I repeated the analysis several times and always the same problem occured. Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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colin27 skullstrip problem
by Mishkin Derakhshan 01 Dec '09

01 Dec '09

Hi, I'm trying to get the surfaces for the colin27 brain that is included with the mni packages. Has anyone managed to do this before? I thought I would have an easy time given that this linear average of 27 brains has very good signal to noise and nice contrasts, and even though recon-all completes without errors, the surfaces are way off. The main problem appears to be the skull stripping. My input volume is here: http://opus.bic.mni.mcgill.ca/public/colin27_t1_tal_lin.mnc.gz These are the steps I took and where I think the problem might be: 1. gunzip colin27_t1_tal_lin.mnc.gz 2. recon-all -i colin27_t1_tal_lin.mnc -subjid colin27 3. tkmedit conlin27 orig/001.mgz At this point the image the brightness and contrast levels of the image look very washed out. I am hoping this is only a display issue and that the underlying intensities of the image are still intact and is not a result of something going on in mri_convert, but maybe this is what is causing the downstream skull strip to fail. Can someone take a look? http://opus.bic.mni.mcgill.ca/public/001.mgz 4. recon-all -autorecon1 -subjid colin27 5. tkregister2 --mgz --s colin27 --fstal Results are not perfect but reasonable ie. about the same as many other runs I've had that have passed so I don't think it is the registration. 6. tkmedit colin27 brainmask.mgz -aux T1.mgz It is clear this is where the problem is. http://opus.bic.mni.mcgill.ca/public/brainmask.mgz http://opus.bic.mni.mcgill.ca/public/T1.mgz 7. I have subsequently tried: recon-all -skullstrip -wsthresh 10 -clean-bm -no-wsgcaatlas -subjid colin27 (basically extract the entire head) recon-all -skullstrip -wsthresh 5 -clean-bm -no-wsgcaatlas -subjid colin27 (basically extracted the entire head) recon-all -skullstrip -wsthresh 5 -clean-bm -subjid colin27 (extracted the brain, but left large chunks of skull) recon-all -skullstrip -wsthresh 2 -clean-bm -subjid colin27 (extracted the brain, but left quite a few chunks of skull) I'm concerned that the -wsthresh is so low in order to get a reasonable result, that's why I think the intensities might be off (see step 3). I'm re-running -autorecon2/3 now to see if the surfaces are better, but if someone could take a look at my input file and the converted 001.mgz to see if it isn't a problem there it would be much appreciated. thanks, mishkin

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recon-all -qcache question
by Guang Zeng 01 Dec '09

01 Dec '09

Hi, there, I have 60 subjects which have been FS analyzed without the flag -qcache. Now, I wan to do group analysis using QDEC. I need run recon-all -s subjectid -qcache for each of my subjects. Just want to know how it will take to finish the recon-all -s subjectid -qcache command for one subject? Will it go through the whole -autorecon1, 2, 3 process again? Thanks a lot! Guang _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/

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Comments in paradigm files
by Yigal Agam 30 Nov '09

30 Nov '09

Hi, Can you add comments to a paradigm file? Thanks, Yigal

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TKSURFER error- open GL in Fedora
by Massieh Moayedi 30 Nov '09

30 Nov '09

Hi, I can't seem to run tksurfer in Fedora 7. We are using a Wacom Tablet monitor, and since we installed it, we cannot run tksurfer. We get the following error: surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(fsaverage) Can't create a context! surfer: failed, trying double buffered window Can't create a context! surfer: failed, no suitable display found Does anyone know how to go about this? massih

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T1 and T2 in one recon-all
by Samuel Inverso 30 Nov '09

30 Nov '09

Hi Freesurfers, Looking through the mail archives it seems T1 and T2 runs for a single subject should not be combined when doing recon-all. Is this still the case? Thank you for your time, Cheers, -Sam

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Re: [Freesurfer] convert/reconstructing with mrdc
by Jesse Bledsoe 29 Nov '09

29 Nov '09

I have T1volume+org.BRIK - should I use those with mri_convert? Thanks again, Jesse On Tue, Nov 24, 2009 at 4:23 PM, Saad, Ziad S. (NIH/NIMH) [E] < saadz(a)mail.nih.gov> wrote: > mri_convert usually work with BRIK files. > > Alternately, 3dAFNItoNIFTI could turn BRIK files to nifti format > which FreeSurfer can read fine. > > cheers, > ziad > > On Nov 24, 2009, at 3:28 PM, Bruce Fischl wrote: > > > These are not the standard .BRIK files? Ziad (ccd) will know. > > > > Bruce > > > > > > On Tue, 24 Nov 2009, Jesse Bledsoe wrote: > > > >> Hello, > >> > >> So far I have had no problems running recon-all with .mnc files but > >> could > >> use some guidance converting/reconstructing brains processed with > >> AFNI > >> (MRDC). > >> > >> There are 120 MRDC files in the T1 directory. > >> > >> I believe I need to run mri_convert on these MRDC files but am > >> unsure of > >> what the correct command would be? > >> > >> Thanks in advance, > >> > >> Jesse > >> > > -- Jesse Bledsoe, M.A. Clinical Psychology Assistant Director, Center for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.

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