Freesurfer

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30132 discussions

patch present-label missing
by maahmed＠mappi.helsinki.fi 29 Aug '11

29 Aug '11

Hi, I did the recon-all using the same case and the same freesurfer edition twice. The second processing I did was missing the label : Medial_wall-rh.label I have the same problem with 20 other cases. I uploaded an image of the first and second attempt here : http://tinyurl.com/3p52zrj You will notice that in the second one, the patches definition is poor around the medial surface of the hemisphere.Is this the problem ?and if so, how can i tackle it ? Can i label the medial patch manually ? Thank you, Mostafa Abdelgawad

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tkmedit: Extending white matter and pial surfaces
by Michelle Umali 27 Aug '11

27 Aug '11

Hi Freesurfers, When looking at the surfaces in tkmedit, I noticed that quite a bit of the tip of the temporal lobe was not included in pial/wm surfaces. I need to extend both surfaces. In what order does one do the edits? Does one paint in wm voxels first or pial first? Thanks. Michelle

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Re: [Freesurfer] Hippocampal volumes measured by Freesurfer 4.3.0 vs 4.5
by Thomas Yeo 27 Aug '11

27 Aug '11

I might be wrong, but it's generally not recommended to compare data across different freesurfer versions. --Thomas On Sat, Aug 27, 2011 at 5:08 PM, Thomas Yeo <yeoyeo02(a)gmail.com> wrote: > I might be wrong, but it's generally not recommended to compare data across > different freesurfer versions. > > --Thomas > > On Sat, Aug 27, 2011 at 6:59 AM, Bayley, Peter J. <Peter.Bayley(a)va.gov>wrote: > >> Hi,**** >> >> ** ** >> >> I would like to merge two datasets containing volumetric data from two >> different versions of Freesurfer (4.3.0 and 4.5). I am only interested in >> looking at volumes of hippocampus, entorhinal cortex, and whole brain. A >> cursory look at the release notes for versions 4.4 and 4.5 suggests that v. >> 4.3.0 and v. 4.5 are quite similar as most updates involved bug fixes. >> However, v 4.5 involved an updated C.Destrieux atlas. Does anyone know of >> any problems when comparing data generated by v. 4.3.0 and v. 4.5 ?**** >> >> ** ** >> >> Thanks**** >> >> ** ** >> >> Peter Bayley**** >> >> _______________________________________________ >> 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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Hippocampal volumes measured by Freesurfer 4.3.0 vs 4.5
by Bayley, Peter J. 26 Aug '11

26 Aug '11

Hi, I would like to merge two datasets containing volumetric data from two different versions of Freesurfer (4.3.0 and 4.5). I am only interested in looking at volumes of hippocampus, entorhinal cortex, and whole brain. A cursory look at the release notes for versions 4.4 and 4.5 suggests that v. 4.3.0 and v. 4.5 are quite similar as most updates involved bug fixes. However, v 4.5 involved an updated C.Destrieux atlas. Does anyone know of any problems when comparing data generated by v. 4.3.0 and v. 4.5 ? Thanks Peter Bayley

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about correction of inhomogeneity
by Xiaoying Tang 26 Aug '11

26 Aug '11

Hi All, I am now trying to do inhomogeneity correction for T1 images. I find that there are two commands: nu_correct and mri_nu_correct.mni in Freesurfer. I am not sure about the difference between these two commands. To me, they seem to be the same.... I would be glad if someone could answer my question. Best, Xiaoying

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Freesursfer versions and Linux CentOS versions
by Alexopoulos, Dimitrios 26 Aug '11

26 Aug '11

I have a few questions related to Freesursfer versions and Linux CentOS versions. We have we processed some data (i.e. generated surfaces using -autorecon 1 -autorecon2, and then GM and WM surface-based volumes using mris_anatomical_stats and mris_wm_volume, respectively), using the build 'freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0' on our linux server that was running CentOS 4. We have recently upgraded the server OS to CentOS 5.6. We now would like to modify the segmentations/surfaces and was wondering whether we can use the same build (freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0) on CentOS5.6 or do we need to install 'freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0' ? Are there any issues with processing data using 'freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0' on CentOs4 then modifying this data with 'freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 on CentOs5 Comments? Thanks. The materials in this email are private and may contain Protected Health Information. 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 email in error, please immediately notify the sender via telephone or return email.

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DTI and Fresurfer
by Antonella Kis 26 Aug '11

26 Aug '11

Dear All, I would like to do DTI analysis on my subjects data. I finished the pre-processing using recon-all and also I used GLm for the group study. Can you please let me know how I can do DTI analysis using FSL in Freesurfer? What steps I need to follow? Many thanks, Antonella

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free surfer group analysis how to get cache-in thickness.fwhm10.fsaverage ?
by xian zhang 26 Aug '11

26 Aug '11

Dear Freesurfer: I am new in freesurfer. I have done recon-all for my subjects and the results are good. however in this tutorial the commands between recon-all the mirs-process are missing. Please advice what I have to after recon-all to have thickness.fshm10.fsaverage available? Appreciate your help. Xian http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Assemblet… Previously Cached (qcached) Data When you have run recon-all with the -qcache option, recon-all will resample data onto the average subject (fsaverage) and smooth it at various FWHM (full-width/half-max), usually 0, 5, 10, 10, 20, and 25mm. This can speed later processing. The data for this tutorial have been cached, so run: mris_preproc --fsgd gender_age.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi lh \ --out lh.gender_age.thickness.10.mgh

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help for further distribution (fwd)
by Bruce Fischl 26 Aug '11

26 Aug '11

FYI ---------- Forwarded message ---------- Date: Fri, 26 Aug 2011 15:48:33 +0200 From: Jorge Jovicich <jorge.jovicich(a)unitn.it> To: Jorge Jovicich <jorge.jovicich(a)unitn.it> Subject: help for further distribution Dear All, I'd appreciate your help to further distribute the attached advert for two MRI methods postdoctoral positions, or to bring it to the attention of potentially interested and qualified candidates. Below is the list of places where I have already posted the advert. Thanks!! jorge -ISMRM site, as well as the UK and German chapters -EEGlab list -MGH-all email list -- Jorge Jovicich, Ph.D. MR Lab Co-Director Center for Mind Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich(a)unitn.it http: //www.cimec.unitn.it/ http: //polorovereto.unitn.it/~jovicich

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Reference for tracula and enable mpi in tracula?
by Knut J Bjuland 26 Aug '11

26 Aug '11

Hi I am having trouble finding all reference to Tracula in the wiki. Could you please add them. I read in (Postelnicu, Zollei et al. 2009) that combined surface and volumetric algorithm could use MPI . Is the same true for tracula? Knut J Postelnicu, G., L. Zollei, et al. (2009). "Combined Volumetric and Surface Registration." Medical Imaging, IEEE Transactions on 28(4): 508-522. In this paper, we propose a novel method for the registration of volumetric images of the brain that optimizes the alignment of both cortical and subcortical structures. In order to achieve this, relevant geometrical information is extracted from a surface-based morph and diffused into the volume using the Navier operator of elasticity, resulting in a volumetric warp that aligns cortical folding patterns. This warp field is then refined with an intensity driven optical flow procedure that registers noncortical regions, while preserving the cortical alignment. The result is a combined surface and volume morph (CVS) that accurately registers both cortical and subcortical regions, establishing a single coordinate system suitable for the entire brain.

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