Freesurfer

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30132 discussions

Rejoindre mon réseau sur LinkedIn
by Paula Diniz via LinkedIn 01 Jul '11

01 Jul '11

LinkedIn ------------ Paula Diniz souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Paula Diniz http://www.linkedin.com/e/-wptfe6-gpl23w9p-41/vLfSn8bYH8_5DFBPLmfTK84Tj6M6D… Voir l'invitation de Paula Diniz http://www.linkedin.com/e/-wptfe6-gpl23w9p-41/vLfSn8bYH8_5DFBPLmfTK84Tj6M6D… ------------------------------------------ SAVEZ-VOUS que vous pouvez être le premier informé quand un membre de votre réseau change de poste ? Les "Nouvelles du réseau" sur votre page d'accueil LinkedIn vous informe des évolutions de carrière dans votre réseau. Soyez informé(e) en premier ! http://www.linkedin.com/ -- (c) 2011, LinkedIn Corporation

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error in qdec design analyze
by Sophy Zhu 01 Jul '11

01 Jul '11

Hi Freesurfers, There existed an error "Error in Analyze: Couldn't open file /usr/local/freesurfer/subjects/PD1/surf/lh.thickness.fwhm10.fsaverage.mgh", when I clicked on the button "Analyze" in qdec design. I have only done "recon-all" with my data (PD-MPR group and Controled-MPR group). Did I miss one step before qdec analysis? Thanks

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queue software and routine to remove dura from brain
by Knut J Bjuland 30 Jun '11

30 Jun '11

Hi What kind of queue software is used for Freesurfer to enable multiple instance across several CPU in mulit-core system? Is thesse software available in either Fedora or Ubuntu? I am working with 14 years old image which has enlarged ventricles. What is the recommend setting to remove non-brain tissue like dura from the MRI pictures? Cheers Knut J Bjuland

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Trouble downloading freesurfer v4.4
by Rachel Steinhorn 30 Jun '11

30 Jun '11

My lab uses freesurfer v4.4, and I'd like to install it on my PC, but the download doesn't seem to be available from the Archives. When I click on any version of the archived file or try to save it to disk, I get a page saying "The connection was reset, The connection to the server was rest while the page was loading." Trying to download other releases, such as v5.0 and v4.0.5, produces the same message. The mirror offered for some releases gives me a blank page. Are the files available elsewhere, or will they be put back up at some point? The version I'm looking for is for Mac OS 10.6 (freesurfer-Darwin-leopard-i686-stable-pub-v4.4.0-full.dmg) Thank You, Rachel Steinhorn

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Re: [Freesurfer] pet partial volume correction
by Douglas N Greve 30 Jun '11

30 Jun '11

Actually, I think it only will affect the volume measurement for each structure, so that's no good. There is not a flag to mri_segstats that will do this. If you have a registration between your native pet data and the FS anat, then you can use mri_compute_volume_fractions regfile.dat pet.nii pvf This will create pvf.{gm,wm,csf}.mgz You can then correct the pet with something like fscalc pet.nii div pvf.gm.mgz pet.pvf.nii You can map the aparc+aseg into the pet space using mri_label2vol (and the reg from above), then use mri_segstats with the files in the native pet space. doug corinna bauer wrote: > Hi Doug, > I will give that a try. How will this account for the p.v. in pet > data? Does it remove the voxels that are mixed tissue classes? Does it > account for partial volume effects between neighbouring grey matter > structures? > Corinna > > On Wed, Jun 8, 2011 at 1:06 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Corinna, > try adding --pv mri/norm.mgz > doug > > corinna bauer wrote: > > Hi all, > I am wondering if partial volume is taken into account when > calculating average uptake values of pet data. I know that > aseg.stats takes partial volume into account and I am > wondering if there is something similar in place for pet data? > From what I gather, most people when using FreeSurfer correct > for partial volume effects by regressing out cortical > thickness, but no basis for this correction method has been > provided. Any insight would be appreciated. > > n.b. to obtain the pet uptake values I used mri_segstats --seg > mri/aparc+aseg.mgz --sum pet.segstats.dat --i $petanat --ctab > rois.txt > > Thank you, > Corinna > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Missing white matter
by Knut J Bjuland 30 Jun '11

30 Jun '11

Hi I have mri picture where there is a large area where white matter is marked as grey. I might also add that this patient has enlarged ventricle and less white matter. I can not send the files on the list, I can however send the files if I get an addresses to send them too. What I ca I say howevere is that in this particulare areas are there none white matter from the cortex to the collusum. Cheers Knut J

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long_mris_slopes
by Seán Froudist Walsh 30 Jun '11

30 Jun '11

Dear FreeSurfers, I am looking for a little help comparing longitudinal data. I have three timepoints on each patient and have been able to get individual spc-thickness maps using the long_mris_slopes command where my table included all three time points. I would however like to compare different timepoints with each other: tp3-tp2 and tp2-tp1. I was hoping it would be as simple as specifying a new qdec table including (for example) only tp3 and tp2, and giving new output names using the following command long_mris_slopes --qdec ./qdec/long.qdec.tableTP23.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --out-avg=long23.thickness-avg.mgh --out-rate=long23.thickness-rate.mgh --out-pc1=long23.thickness-pc1.mgh --out-spc=long23.thickness-spc.mgh --out-stack=long23.thickness-stack.mgh --out-label=long23.cortex --time scan --qcache fsaverage but I get the following error: mris_calc: Sorry, but I seem to have encountered an error. While making backup of internal data arrays, it seems that some of the backups already exist. I'm not really sure what the internal data arrays are, and would greatly appreciate any help. Many thanks in advance and all the best, Seán

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Cortical Thickness
by leonardo kay 30 Jun '11

30 Jun '11

Hi Freesurfer experts. Do anyone know how to measure the cortical thickness of an specific brain area? I have been using mris_anatomical_stats but it only outputs the brain cortical thickness of the requested hemisphere. Best regards. -- Leo Kay.

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Over-smoothing of pial surface
by Yagna Pathak 29 Jun '11

29 Jun '11

Hi, I am trying to extract the pial surface for one of my subjects using freesurfer. Unfortunately, the last couple times that I ran recon-all, it generated a surface that was overly smoothed. I suspect this is due to a poor contrast in my MRI images. I tried to edit them via matlab and run them again. First, I got a talairach transform error and when I re-ran it with the -notal-check flag, I got a global region empty error. I was wondering if there is a way to enhance the mri images in freesurfer to obtain better contrast for a more accurate pial surface. Please let me know what is the best way to tackle this problem. I do not think it's the version of freesurfer, because the pial surface was created fine for some of the other subjects. Thank you, YP

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SupraTentorial Volume question
by Righart, Ruthger Dr. 29 Jun '11

29 Jun '11

Dear Freesurfer experts, I posted one week ago a question about the SupraTentorial Volume that is indicated in the aseg.stats but unfortunately did not receive any suggestions as yet. 1. SupraTentorial Vol. is defined as Cortex + CorticalWhiteMatter + SubCortGray (http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats) but when I sum up these columns myself from the aseg.stats I do not arrive at the exact value of SupraTentorial Vol that is indicated in the same aseg.stats. For some of my subjects this value is higher, for some it is lower. What could be the reason for these differences? Is CSF and ventricle volume already subtracted from the SupraTentorial Volume? 2. Is it possible to exclude lesions from the volume-based measures by incorporating a self-defined lesion mask for each subject? Any help or suggestions is very much appreciated! Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany ruthger.righart(a)med.uni-muenchen.de

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