Freesurfer June 2010

freesurfer@nmr.mgh.harvard.edu

97 participants
138 discussions

Re: [Freesurfer] Grey Matter Density?
by Matthew Ku 30 Jun '10

30 Jun '10

Dear Professor Fischl, Thank you for your support and the support from everyone else. It has been a really pleasant experience so far using Freesurfer and it’s great to know that such a great program has comparatively great support! We have accessed the NIH repository for normal pediatric brains, and have run the normative data through Freesurfer, then compared it to data outputted from the contracted NIH program, MINC. These are the results we have obtained so far: Left Right Calculated Total Frontal Occipital Parietal Temporal Frontal Occipital Parietal Temporal Freesurfer 108531 27381 80714 60177 106584 23498 85577 61030 553492 MINC 136241 35980 71381.4 84373.5 133588 32558.9 72250.5 86489.7 652863 By any chance, would you happen to know of any discrepancies between MINC and Freesurfer? In addition, since the NIH website reports their total through MINC as 820,000 while we summed it to be 652,863, do you know what MINC considers grey matter in comparison to what Freesurfer considers grey matter? Best, Matt From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, June 23, 2010 5:40 PM To: Schwartz, Carl R.E. Cc: mattku(a)seas.upenn.edu Subject: Re: [Freesurfer] Grey Matter Density? Sure, that would be great On Jun 23, 2010, at 5:21 PM, "Schwartz, Carl R.E." <carl_schwartz(a)hms.harvard.edu> wrote: Bruce, if you want I can answer this with a reference tonight and share a thread between you, me and Kagan re VBM vs. freesurfer that may help. Carl On 6/23/10 5:06 PM, "Matthew Ku" <mattku(a)seas.upenn.edu> wrote: Dear Professor Fischl, Thank you for your suggestions. We have used mri_binarize before with success and we are interested with both the cortical and subcortical volumes. However, we would appreciate it if you could clarify why you suggested for us to consider surface area and thickness independently, and how we should use those values in a reportable method. If possible, could you direct us to any relevant literature that would help us understand why we should use these values independently? Thanks for all the help. Best, Matt -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, June 23, 2010 3:47 PM To: Matthew Ku Cc: freesurfer(a)nmr.mgh.harvard.edu; dchinapp(a)seas.upenn.edu Subject: Re: [Freesurfer] Grey Matter Density? Hi Matt, you could use mri_binarize to extract a gray matter binarization then go from there, although we've never put together scripts to do it since the biological intepretation is always hard. Are you interested in subcortical volumes or just cortical? If cortical, why not look at surface area and thickness independently? cheers Bruce On Wed, 23 Jun 2010, Matthew Ku wrote: > Dear Professor Fischl, > > Thanks a lot for your prompt response. > > We are trying to compute the grey matter density because we are > analyzing the maturation of grey matter, as referred to by N. Gogtay > et al. (Dynamic mapping of human cortical development during childhood > though early adulthood). > > From Freesurfer's output, we have only noticed grey matter volume. > However, would there be a way to obtain the grey matter mass through > an ROI mask without having to use SPM or FSL? > > Thanks again, > Matt > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Wednesday, June 23, 2010 3:20 PM > To: Matthew Ku > Cc: dchinapp(a)seas.upenn.edu; freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Grey Matter Density? > > Hi Matt, > > density is really just average gray matter per unit volume. Why would > you want to compute such a thing? I think the way SPM/FSL does it is > to take a binary segmentation and smooth it, but you can check with them. > > cheers > Bruce > On Wed, 23 > Jun 2010, Matthew Ku wrote: > >> Hi Freesurfer Experts, >> >> >> >> I have been running Freesurfer to calculate the grey matter volume of >> pediatric brains but I was wondering if there was a method to >> determine grey matter density using Freesurfer? I have read a >> question previously posted asking a similar question, but there had >> been no replies or answers. If there is no command to calculate the >> density of grey matter, is there any alternate method to determine >> the density from > the volume data? >> >> >> >> Thanks, >> >> Matt >> >> _________________________________________ >> >> Matthew Ku >> >> University of Pennsylvania >> >> School of Engineering Class of 2013 >> >> (845) 596-3840 >> >> mattku(a)seas.upenn.edu >> >> >> >> > _______________________________________________ > 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. > > > > _______________________________________________ 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

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tksurfer bus error
by Nai Ding 30 Jun '10

30 Jun '10

Hi everyone, We installed Freesurfer on our Mac system. freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0-full Everything works except tksurfer. When we try > tksurfer bert rh pial Freesurfer returns > surfer: current subjects dir: /Applications/freesurfer/subjects > Bus error How could we fix the problem? Thanks a lot, Nai

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mri_glmfit-sim of qdec
by Joana Braga Pereira 30 Jun '10

30 Jun '10

Dear all, I'm running the mri_glmfit script that has been automatically generated in qdec: mri_glmfit-sim \ --glmdir /home/joana/subjects/qdec/results_2sample \ --sim mc-z 10000 2 mc-z.abs.2 \ --sim-sign abs \ --overwrite Because i want to get the clusters, area size and hopefully z or p values of my results. I made a comparison of cortical thickness between 2 groups, with 2 covariates and in qdec this analysis shows that there are some clusters corrected at FDR. Is the script that i'm using correct? It has been running for a week now, which is the average time that it takes? Many thanks for your help, Joana

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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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Freesurfer June 2010