Freesurfer

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30132 discussions

Re: [Freesurfer] R: RE: Info FreeSurfer
by Azeez Adebimpe 26 Nov '12

26 Nov '12

17 is the intensity value for left hippocamus, and 53 for the right hippocamus. Then you can view with tkmedit ( to view aseg.mgz) for more clearance. Then use matlab to extract this label base on the intensities value. Azeez Adebimpe Date: Mon, 26 Nov 2012 13:48:09 +0100 From: andrea.tateo(a)virgilio.it To: ayobimpe2004(a)hotmail.com Subject: R: RE: [Freesurfer] Info FreeSurfer Hi Azeez Adebimpe, thanks for your quick answer. I open the text file that you recommended me. What means these three numbers in the following string: 17 Left_Hippocampus 1.20 0.0 80 ? How can I use these information in MatLab? Andrea Tateo ----Messaggio originale---- Da: ayobimpe2004(a)hotmail.com Data: 26-nov-2012 13.19 A: <andrea.tateo(a)virgilio.it> Ogg: RE: [Freesurfer] Info FreeSurfer Hi AndreaYou cant restrict ouput of the freesurfer to only hippocamus but after the segmentation you can select the hippocamus both right and left base on intensity value ( check this doc inside mri subfolder: aseg.auto_noCCseg.label_intensities.txt). You can use matlab or any program to extract the hippocamus. Azeez Adebimpe Date: Mon, 26 Nov 2012 13:06:48 +0100 From: andrea.tateo(a)virgilio.it To: Freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Info FreeSurfer Hello, I am working on segmentation of the hippocampus and I need a comparing method. I am approaching for the first time to FreeSurfer method. I would like your courteous help. I have three questions for you: 1 - I have input a MRI-image.nii showing all head. As output I would like a binary image showing only left and right hippocampus. I used the following command: ### mri_convert FILE_NAME.nii path/directory/NAME_OUTPUT.mgz recon-all -s SUBJECT_name -autorecon-all ### How can I extract the required binary image? 2 - Is it possible to comput only hippocampus region (to reduce the processing time)? 3 - Is it possible to give as input only an ristrected region of the subject's head? Best regards Andre Tateo _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Missing tracts in final TRACULA results
by Arman Eshaghi 26 Nov '12

26 Nov '12

Dear all, Following successful runs of 3 stages of trac-all script on an MS brain, I get the following result. As you might see right inferior longitudinal fasciculus (parital) and right uncinate fasciculus are missing. I was wondering at which stage the problem is most likely (prep, bedpostx, or the last step)? (recon-all results seem to be alright.) All the best, -Arman [image: Inline image 1]

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aseg.mgz not automatically upated after topological correction
by 嘉逸劉 24 Nov '12

24 Nov '12

Hi FreeSurfer experts, I have a question regarding how to update aseg.mgz after topological correction. I hope to use the labels in aseg.nii as the definition of ROIs (including the definition of white matter). After topological correction, the surfaces of white matter and pia are fine; the filled.mgz looks good. However, when I go back to check aseg.mgz, I notice that the boundary of white matter of aseg.mgz is not updated. Any suggestion is appreciated. Thanks, JoJo

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Please help: nu_correct crash problem
by Negar Memarian 24 Nov '12

24 Nov '12

Dear all, I'm very new to FreeSurfer and really appreciate your help: I installed FreeSurfer very recently and it's the first time that I need to run recon-all but unfortunately it crashes at the nu_estimate_np_and_em step with this error message: nu_estimate_np_and_em: crashed while running spline_smooth (termination status = 6) nu_correct: crashed while running nu_estimate_np_and_em (termination status = 65280) ERROR: nu_correct FYI, the recon-all.log file is attached. Also, not sure if it makes any difference or not, but I need to run recon-all for a subject whose images were imported from DICOM to mgz using recon-all -i Looking forward to your response. Thank you, Negar

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bad reconstructions; why?
by Catherine Bois 23 Nov '12

23 Nov '12

Hello, I have a question re reconstructing brains (ie after doing the edits and running them again to ensure the edits went through). Before the reconstruction, the whole brain was there, however afterwards, large chunks of the brain is missing. Im worried whether this is something to do with the edits i have done; ie can control points/white matter edits actually make parts of the brain "go missing"? Or is it more likely that somewhere along the process the watershed parameters changed/gone wrong? Has anybody else experienced this problem? Thank you so much for your help Regards Cathy

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optic radiation ROI
by Ritobrato Datta 22 Nov '12

22 Nov '12

Hi All, Is there an Optic Radiation ROI in freesurfer or some other program ? Please let me know. Thank you Ri

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wm vol mismatch
by Gabriel Gonzalez Escamilla 22 Nov '12

22 Nov '12

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Tool for incorporating T2-SPACE data in pial surface recons?
by Winter, Warren 22 Nov '12

22 Nov '12

Hi all, Back in January and October Bruce mentioned that he had under development some scripts designed to utilize T2-SPACE images for better pial surface reconstruction in the presence of dura -- I was just wondering if any of that is ready for trial? Thanks! Warren -- Warren Winter Research Coordinator Boston Children's Hospital Sheridan Laboratory of Cognitive Neuroscience Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224

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intrinsic curvature
by irene.mat＠libero.it 22 Nov '12

22 Nov '12

Hi FS Developers,I would like to know if the measures of intrinsic curvature of FS are quite reliable; I would like to launch a project with this parameter, but I've never used this.Which is your experience? Thanks,IreneResident in Neurology, Italy

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Re: [Freesurfer] tksurfer crashes
by Johan Carlin 22 Nov '12

22 Nov '12

On the off chance that you are using a Mac - I had a similar issue with X11 and tksurfer becoming unresponsive at the tkoInitWindow stage. I think this is because a recent OS X update broke X11. This update (from X11 2.5.4 to 2.6.5) fixed the problem for me: http://support.apple.com/kb/DL1605 Cheers, Johan Dear Freesurfer experts, I have a problem with Tksurfer. Whereas this worked previously fine it suddenly crashes every time I try to start it. This happens with every subject or fsaverage. A similar problem was reported before with similar terminal output but unfortunately I could not find a solution to this problem in the mailing list. Any suggestions are welcome! Ruthger Righart Hi Michelle, hmmm, no idea. Do you want to upload the the subject and we'll see if we can replicate the problem? Do you have enough memory on that machine? Bruce On Mon, 19 Mar 2012, Michelle Umali wrote: Hi Freesurfers, I've been using Freesurfer for a while, and have had no trouble with launching tksurfer. But recently I have tried to view an inflated hemisphere of a subject I have had no problem viewing before. The window no longer opens. This the case for all of my subjects, with whom I have had no previous problems. Any suggestions would be most welcome. Thanks very much. Michelle Below is the terminal output. After this it just returns to the prompt without any error message.. /usr/local/freesurfer/subjects> tksurfer ld07 lh inflated subject is ld07 hemi is lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects checking for nofix files in 'inflated' Reading image info (/usr/local/freesurfer/subjects/ld07) Reading /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: vertices=160638, faces=321272 surfer: double buffered window surfer: tkoInitWindow(ld07) _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Johan Carlin, PhD Research Associate MRC Cognition & Brain Sciences Unit 15 Chaucer Road Cambridge CB2 7EF UK johan.carlin(a)mrc-cbu.cam.ac.uk +44 (0)1223 355294 ext 278

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