Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

T1-weighted quality
by Ahmed Abou Elseoud 30 Jun '10

30 Jun '10

Hello, We are starting to use FreeSurfer v4.5.0 for segmentation purposes and after running freesurfer and correcting the wm surfaces following the online instructions we still get abnormal surfaces (wm looks better after corrections, but gray matter still the same). We are suspecting the problem to be due to intensity problem in the original T1-weighted volumes and thus we would like to consult with you the T1 sequence we use to know if there is what we could fix/change about that. T1-weighted scans were imaged using 3D FSPGR BRAVO sequence (TR 12.1ms, TE 5.2 ms, slice thickness 1.0 mm, FOV 24.0 cm, matrix 256 x 256, and flip angle 20 º, parallel imaging factor 2, NEX 1). Thanks a lot in advance, Ahmed -- Ahmed Abou Elseoud MRI Research Unit, Department of Diagnostic Radiology, Oulu University Hospital(OYS), Finland.

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signal dropouts in 7T scanners
by Jose Luis Cantero Lorente 30 Jun '10

30 Jun '10

Dear Freesurfers, we are working with T1-MPRAGE images acquired in a siemens 7T scanner. Signal dropouts are a big problem with 7T scanner affecting drastically the white-grey matter contrast of temporal lobe structures. I was thinking to acquire two different MPRAGE images: one of them with excellent contrast on the top half of the brain, and the other with identical contrast in the bottom part of the brain (therefore improving the white/grey matter boundaries of temporal lobes). Would it be feasible by using Freesurfer to get a resultant image with homogeneous and improved contrast in the whole brain taking advantage of both MPRAGE acquisitions? If don't, do you know any other tool to make that possible? Thanks in advance. Best regards, Jose --- Jose L. Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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Re: [Freesurfer] mne_analyze unable to read inflated surface
by Onerva Korhonen 30 Jun '10

30 Jun '10

Hi, I get things to work with an older copy of data - maybe problem was just a corrupted file or something. Thanks for help, Onerva Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > usually that means you ran out of disk space. Did you check? > > cheers > Bruce > On Mon, 28 Jun > 2010, Onerva Korhonen wrote: > >> Hi all, >> >> I have problems with mne_analyze - I need to do the coordinate >> alignment, but when I try to load the inflated surface (or in fact any >> surface), I get error message: >> >> mne_read_float could not read data >> >> Inflated surface doesn't work with tksurfer either. Instead I get a message: >> >> freadFloat: fread failed >> >> I don't know if it would say something more later - there seems to be >> a loop, so I have killed the program at this point. >> >> I have no idea what to do - redoing recon-all doesn't seem to help. So >> I hope someone could help me with this. >> >> Many thanks, >> Onerva K. >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > 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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Surface-Area Weighted Average of Cortical Thickness
by Liang, Kelvin 29 Jun '10

29 Jun '10

Dear FreeSurfer Experts, I'd like to merge my cortical thickness measures across left and right hemispheres. Simple averaging of the ?h.thickness values would probably be the most straightforward method, but would it be more accurate to use a surface-area weighted average? i.e. entorhinal_combined = (lh_entorhinal_thickness * lh_entorhinal_area + rh_entorhinal_thickness * rh_entorhinal_area) / (lh_entorhinal_area * rh_entorhinal_area) Alternatively, the average could be weighted by the number of vertices (discussed in an old FreeSurfer mailing thread, but never quite concluded). Please let me know what you think. Thank you, Kelvin Liang The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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DODS vs DOSS
by Dankner, Nathan (NIH/NIMH) [F] 29 Jun '10

29 Jun '10

Hello all, I'm attempting to run a cortical thickness group differences test in qdec with a covariate, and have been told that in order for it to match up with similar anlyses in SPSS, amongst other things, I'll have to ensure that I match on "DODS" vs. "DOSS." What are these two options, and how would I go about ensuring that I'm matched on them?

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mri_vol2surf
by Oya, Hiroyuki 29 Jun '10

29 Jun '10

In mri_vol2surf , is it still valid to set -fwhm value less than 1? Thank you. Hiroyuki

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Brain atrophy assess
by Michele Placci 29 Jun '10

29 Jun '10

Dear FreeSurfer Experts, apart from the problem of my previous email I need to ask you more help, can you write the link of a FreeSurfer Manual please? I'm not able to find it in the site: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki My basic problem is: I have two CD (for each patients) with a 3D MRI image and I have to assess and quantify brain atrophy from the first CD (time one) to the second CD (time two, away from the first few months) during the growth of the patients. If there were a precise list of instructions for this assess I'd be really happy. Thanks a lot. Michele.

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Recon error
by Michele Placci 29 Jun '10

29 Jun '10

Hi all FreeSurfer Experts, I'm a young researcher, PhD student of the University of Padua with a degree in Mathematics. I'm trying to use FreeSurfer for analyze a 3D image MRI, NIFTI format (converted from DICOM) to calculate brain volume. I ran recon-all -autorecon1 -autorecon2 -subjid <..."file with extension.mgz, after the conversion with mri_convert from a unique file .nii" > and I obtained the errors that you can see in the attachments. Any suggestion? Thank you in advance. Michele.

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recon error
by Michele Placci 29 Jun '10

29 Jun '10

Hi all FreeSurfer Experts, I'm a young researcher, PhD student of the University of Padua with a degree in Mathematics. I'm trying to use FreeSurfer for analyze a 3D image MRI, DICOM format (I have NIFTI too) to calculate brain volume. I ran recon-all -autorecon1 -autorecon2 -subjid <..."file with extension .mgz, after the conversion with mri_convert from a unique file .nii" > and I obtained the errors that you can see in the attachments. Any suggestion? Thank you in advance. Michele.

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Re: [Freesurfer] mne_analyze unable to read inflated surface
by Onerva Korhonen 29 Jun '10

29 Jun '10

Him the disk space doesn't seem to be problem - at least mne_analyze and tksurfer are working fine with other subjects with the same space. Best regards, Onerva K. Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > usually that means you ran out of disk space. Did you check? > > cheers > Bruce > On Mon, 28 Jun > 2010, Onerva Korhonen wrote: > >> Hi all, >> >> I have problems with mne_analyze - I need to do the coordinate >> alignment, but when I try to load the inflated surface (or in fact any >> surface), I get error message: >> >> mne_read_int could not read data >> >> Inflated surface doesn't work with tksurfer either. Instead I get a message: >> >> freadFloat: fread failed >> >> I don't know if it would say something more later - there seems to be >> a loop, so I have killed the program at this point. >> >> I have no idea what to do - redoing recon-all doesn't seem to help. So >> I hope someone could help me with this. >> >> Many thanks, >> Onerva K. >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > 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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