Dag Jolijn, Gegenereerd! En ik heb gezien dat nr 13136 wm_lh_g_temp_sup_plan_tempo ertussen staat! (output linux) :)
Groetjes, Caroline -----Oorspronkelijk bericht----- Van: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens freesurfer-requ...@nmr.mgh.harvard.edu Verzonden: dinsdag 17 mei 2016 22:50 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Freesurfer Digest, Vol 147, Issue 29 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: 3T flag (Moeller, Sebastian) 2. Re: FreeSurfer Validation and Longitudinal Analysis of WM Hyperintensities (Navena Rebecca Lingum) 3. Re: ERROR: cannot unpack mosiacs without ASCII header (Douglas N Greve) 4. Re: wm parcellation (Douglas N Greve) 5. Re: Same coordinates for all labels (Douglas N Greve) 6. Re: segfault using brainstem module from dev version (Martin Reuter) 7. WM Hyperintensities (Martin Reuter) 8. errors in wm and pial boundaries (Corinna Bauer) 9. Re: errors in wm and pial boundaries (Bruce Fischl) 10. Question on Yeo 2015 cognitive atlas (Josh Gray) 11. Postdoctoral Position in Infant MRI Analysis at UNC-Chapel Hill (gangli) 12. Freesurfer (Limachia, Gaurang (NIH/NINDS) [F]) ---------------------------------------------------------------------- Message: 1 Date: Tue, 17 May 2016 16:01:19 +0000 From: "Moeller, Sebastian" <sebastian.moell...@rwth-aachen.de> Subject: Re: [Freesurfer] 3T flag To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <daac6e30-68d8-4c96-a658-1cd19d6a7...@rwth-aachen.de> Content-Type: text/plain; charset="utf-8" Hi Kasper, > On May 17, 2016, at 17:44 , Kasper Jessen <kaspe...@cnsr.dk> wrote: > > Thanks for the answers :-) > > Sebastian: What do you mean with "A somewhat wrong, but intuitive rationale > is with array coils the loops are smaller and hence the coil sensitivity > profiles as well and these modulate the intensity inhomogeneity. But again > that is probably wrong?" > > What is it that is probably wrong? I would be amazed if that rationale was a truthful description of the full physical basis for the changes in inhomogeneities; and to be on the safe side (I never even discussed this with a physicist) I declare that it is incomplete and hence ?wrong?. The last thing I want is to spread half-baked information as ground truth? Best Regards Sebastian > > Best regards, > Kasper > > 2016-05-17 14:48 GMT+02:00 Moeller, Sebastian > <sebastian.moell...@rwth-aachen.de>: > Hi Kasper, > > > > On May 17, 2016, at 10:05 , Kasper Jessen <kaspe...@cnsr.dk> wrote: > > > > I would like to know the following: > > > > a) what is the differences between the 3T Atlas (schwartz atlas) and the > > standard atlas? > > b) what does the 3T-specific NU intensity correction parameters do > > differently than the standard? > > If I recall correctly this is based on > http://www.sciencedirect.com/science/article/pii/S1053811909006703: > Improvement of brain segmentation accuracy by optimizing > non-uniformity correction using N3 > > Type Journal Article > Author Weili Zheng > Author Michael W. L. Chee > Author Vitali Zagorodnov > URL http://www.sciencedirect.com/science/article/pii/S1053811909006703 > Volume 48 > Issue 1 > Pages 73-83 > Publication NeuroImage > ISSN 1053-8119 > Date October 15, 2009 > Journal Abbr NeuroImage > > So most likely it reduces the N# smoothing distance from the default > 200 to 50 > > Here is the relevant part from recon-all (v5.3): > if ($DoNuIntensityCor3T) then > # params from Zheng, Chee, Zagorodnov 2009 NeuroImage paper > # "Improvement of brain segmentation accuracy by optimizing > # non-uniformity correction using N3" > set NuIterations = 1; > set cmd = ($cmd --proto-iters 1000 --distance 50) > endif > > A somewhat wrong, but intuitive rationale is with array coils the loops are > smaller and hence the coil sensitivity profiles as well and these modulate > the intensity inhomogeneity. But again that is probably wrong? > > Best Regards > Sebastian > > > > > Best > > Kasper > > > > 2016-05-10 8:09 GMT+02:00 Kasper Jessen <kaspe...@cnsr.dk>: > > Dear FreeSurfer group, > > > > Our subject sample has been obtained on a 3 Tesla MR scanner. For this > > reason we used the -3T flag to enable the 3T-specific NU intensity > > correction parameters and usage of the special 3T atlas for Talairach > > alignment. > > > > However, where can i find the documentation for the above? > > > > Best regards, > > Kasper > > > > > > > > > > > > -- > > Kasper Jessen, > > MD, PhD student > > Center for neuropsychiatric Schizophrenia Research (CNSR) Mental > > Health Centre Glostrup Nordre Ringvej 29-67 > > 2600 Glostrup > > Tlf.: 24430136 > > E-mail: kaspe...@cnsr.dk eller kasper.jes...@regionh.dk > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@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@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Kasper Jessen, > MD, PhD student > Center for neuropsychiatric Schizophrenia Research (CNSR) Mental > Health Centre Glostrup Nordre Ringvej 29-67 > 2600 Glostrup > Tlf.: 24430136 > E-mail: kaspe...@cnsr.dk eller kasper.jes...@regionh.dk > _______________________________________________ > Freesurfer mailing list > Freesurfer@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. ------------------------------ Message: 2 Date: Tue, 17 May 2016 16:37:18 +0000 From: Navena Rebecca Lingum <nlin...@uwo.ca> Subject: Re: [Freesurfer] FreeSurfer Validation and Longitudinal Analysis of WM Hyperintensities To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <8950ad6c-3fce-4aa1-ac22-67feb8adb...@uwo.ca> Content-Type: text/plain; charset="windows-1252" Dear Martin, Thank you kindly for your prompt response. I am actually having difficulties with the delineation of White Matter Hyperintensities at a single time point. I apologize if my question is redundant and perhaps an answer to it is already mentioned elsewhere. As it stands, I am finding it difficult to understand the exact ?pipeline? of commands necessary to perform this segmentation and accurate delineation of WMH. I have ran the recon -all command on my T1w images, but I suspect a proper segmentation of WMH would require a T2w Flair (which I have). How do I go about combining the preprocessing data produced by FreeSurfer with my T2w images to produce a WMH mask/volume/stats? Any help on the matter is much appreciated! Kindly, Navena Lingum On May 16, 2016, at 4:24 PM, Martin Reuter <mreu...@nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu>> wrote: Hi Navena, There is currently no dedicated stream for longitudinal WM abnormalities (in the sense of joint estimation and modeling). You can, however, make use of the longitudinal stream and it's increase reliability - e.g it is working in the same space across time, which should help get more reliable estimates. Best, Martin On 05/16/2016 01:47 PM, Navena Rebecca Lingum wrote: Dear FreeSurfer experts, My colleagues and I would like to use FreeSurfer to perform a longitudinal analysis of white matter hyperintensities. Is there an additional add-on for the software to perform this analysis or can this analysis be performed using the recon-all command? Navena Lingum _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160517/72b8059f/attachment-0001.html ------------------------------ Message: 3 Date: Tue, 17 May 2016 12:48:07 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] ERROR: cannot unpack mosiacs without ASCII header To: freesurfer@nmr.mgh.harvard.edu Message-ID: <573b4b47.2020...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Please remember to include previous correspondence otherwise we can't keep track of the problem! Eg, I don't have the previous email to see what the error was. Is it possible that the disk filled up? On 05/17/2016 09:49 AM, Aloi, Joseph wrote: > Hi Doug, > > Yes, you are correct- data I have previously processed without any > problems is no longer being processed. > > My version of freesurfer is 5.3.0; I only downloaded it a few weeks > ago so I have not changed my freesurfer version recently. > > Thanks! > > Joseph Aloi > Graduate Student, MD/PhD Scholars Program Department of Pharmacology > and Experimental Neuroscience University of Nebraska Medical Center > > Neurobehavioral Research Assistant, Center For Neurobehavioral > Research Boys Town National Research Hospital > > > > The information in this e-mail may be privileged and confidential, > intended only for the use of the addressee(s) above. Any unauthorized > use or disclosure of this information is prohibited. If you have > received this e-mail by mistake, please delete it and immediately > contact the sender. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ------------------------------ Message: 4 Date: Tue, 17 May 2016 13:03:39 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] wm parcellation To: freesurfer@nmr.mgh.harvard.edu Message-ID: <573b4eeb.70...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Add --a2009s to your command line. Note that the colors will not differ between the ctx and wm labels. On 05/17/2016 07:28 AM, Caroline Beelen wrote: > > Dear FS team, > > Thank you for your answers before (email: WmParc). We now realize that > we?ve formulated our question wrong, since our problem is mainly in > creating the wmparc.a2009s.mgz file. We ran the following command: > > mri_aparc2aseg --s <subjid> --labelwm --hypo-as-wm --rip-unknown > --ribbon --o mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz > (<subjid> was replaced by our subject and the ribbon command was set > to ?noribbon? because we otherwise received the message the that the > ribbon command was unknown.) > > > If we run this command, we can extract grey matter labels with > fslmaths (e.g. 11136 for the left planum temporale), but not the white > matter labels we are looking for (this is 13136 for the left planum > temporale). > > The problem seems to be in the labelling of the white matter. > > Many thanks. > > Jolijn & Caroline > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ------------------------------ Message: 5 Date: Tue, 17 May 2016 13:04:01 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Same coordinates for all labels To: freesurfer@nmr.mgh.harvard.edu Message-ID: <573b4f01.8010...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Set the threshold to be something non-zero (eg, ---thmin .00000001) On 05/17/2016 10:47 AM, Nabin Koirala wrote: > Dear FS team, > > I am trying to find the centroid using mri_surfcluster using the > following command but I am getting the same coordinate for all labels. > I couldn't quiet understand what's wrong. Your suggestion would be > really appreciated. > > NOTE: The coordinates differs for hemisphere. > > mri_surfcluster --in ./S/surf/rh.thickness --clabel > ./S/centroid/rh.frontalpole.label --sum ./S/centroid/sum.rh.6.label > --centroid --thmin 0 --hemi rh --subject S > > Thank you. > > Regards, > Nabin > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ------------------------------ Message: 6 Date: Tue, 17 May 2016 13:27:08 -0400 From: Martin Reuter <mreu...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] segfault using brainstem module from dev version To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <573b546c.8040...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" Hi Vincent, I tried it on my machine and it works. No segfault and the registration looks good. Is your dev version older? I don't specifically remember fixing anything recently, but it may be best to download a more recent robust_register binary? It could also be that something else is incompatible on your system (e.g. different centos versions etc). Best, Martin On 05/13/2016 10:29 AM, Vincent Beliveau wrote: > > Hi Martin, > > I assume you want the actual inputs, not the command, sorry about that > ;) I've attached the tmp folder created by the brainstem module. > > Best, > > Vincent. > > On 13.05.2016 16:21, Vincent Beliveau wrote: > >> Hi Martin, >> >> Thanks for the help. From the brainstem-structures.log, >> mri_robust_register is called by the brainstem module as follow: >> >> /data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/ >> bin//mri_robust_register >> --mov imageDump.mgz --dst >> /indirect/data1/vbeliveau/atlas/proc/MR/recon_final/f5249_GD/tmp/BS_T >> 1based//BS-DE-binaryMask_autoCropped.mgz >> -lta trash.lta --mapmovhdr imageDump_coregistered.mgz --sat 50 >> >> Best, >> >> Vincent >> >> On 13.05.2016 16:13, Martin Reuter wrote: >> >> Hi Eugenio and Vincent, >> >> I cannot remember when I say robust_register crash the last time. >> It should never happen. So it could also be that the inputs are >> already corrupted. Can you send the inputs to that command so >> that I can try to replicate and see if this is still a bug or >> what is going on? >> >> Thanks, Martin >> >> >> On 05/13/2016 09:54 AM, Eugenio Iglesias wrote: >> >> It seems that mri_robust_register crashed. Martin, any ideas? >> The algorithm worked because the rough registration from the >> previous step was apparently enough to yield a decent >> segmentation. >> Maybe we should consider stopping the whole process if >> mri_robust_register dies... >> Juan Eugenio Iglesias >> Postdoctoral researcher BCBL >> www.jeiglesias.com >> www.bcbl.eu >> >> Legal disclaimer/Aviso legal/Lege-oharra: >> www.bcbl.eu/legal-disclaimer >> >> >> ------------------------------------------------------------------------ >> *From: *"Vincent Beliveau" <vincent.beliv...@nru.dk> >> *To: *"Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> >> *Sent: *Friday, May 13, 2016 2:40:11 PM >> *Subject: *[Freesurfer] segfault using brainstem module from >> dev version >> >> Hi list (and Eugenio), >> >> I've ran the brainstem module from the dev version on some >> data processed with FS v5.3. The module created some great >> segmentations of brainstem but when taking a closer look at >> the log file, there is 2 seg faults which occur when calls to >> mri_robust_register are made, with the following output (full >> log attached, see line 319 and 371): >> >> >> /data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register: >> line 3: 36835 Segmentation fault mri_robust_register.bin "$@" >> >> /data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register >> --mov imageDump.mgz --dst >> >> /indirect/data1/vbeliveau/atlas/proc/MR/recon_final/f5249_GD/tmp/BS_T1based//BS-DE-binaryMask_autoCropped.mgz >> -lta trash.lta --mapmovhdr imageDump_coregistered.mgz --sat >> 50: Segmentation fault >> mv: cannot stat ?imageDump_coregistered.mgz?: No such file or >> directory >> >> I'm curious about how is this affecting the overall process, >> as otherwise everything appears to be working smoothly. >> >> Best, >> >> Vincent. >> >> -- >> Vincent Beliveau, MSc >> Neurobiology Research Unit >> Juliane Maries Vej 28, 3rd floor >> Rigshospitalet, building 6931 >> DK-2100 Copenhagen, Denmark >> >> phone: +45 3545 6718 >> e-mail: vincent.beliv...@nru.dk >> <mailto:vincent.beliv...@nru.dk> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@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. >> >> >> -- >> Martin Reuter, PhD >> Assistant Professor of Radiology, Harvard Medical School >> Assistant Professor of Neurology, Harvard Medical School >> A.A.Martinos Center for Biomedical Imaging >> Massachusetts General Hospital >> Research Affiliate, CSAIL, MIT >> Phone: +1-617-724-5652 >> Web :http://reuter.mit.edu >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@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. >> >> -- >> Vincent Beliveau, MSc >> Neurobiology Research Unit >> Juliane Maries Vej 28, 3rd floor >> Rigshospitalet, building 6931 >> DK-2100 Copenhagen, Denmark >> >> phone: +45 3545 6718 >> e-mail: vincent.beliv...@nru.dk <mailto:vincent.beliv...@nru.dk> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@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. > > -- > Vincent Beliveau, MSc > Neurobiology Research Unit > Juliane Maries Vej 28, 3rd floor > Rigshospitalet, building 6931 > DK-2100 Copenhagen, Denmark > > phone: +45 3545 6718 > e-mail: vincent.beliv...@nru.dk <mailto:vincent.beliv...@nru.dk> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160517/4cf303e0/attachment-0001.html ------------------------------ Message: 7 Date: Tue, 17 May 2016 13:32:44 -0400 From: Martin Reuter <mreu...@nmr.mgh.harvard.edu> Subject: [Freesurfer] WM Hyperintensities To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <573b55bc.70...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" Hi Navena, I am the wrong person to answer questions about the WM lesion stream. I think the one that is available in FreeSurfer is only based on T1 images, but a prototype of a better stream exists, that can incorporate different modalities. Best, Martin P.S. Changed the subject, to reflect that this is not a longitudinal question any more. On 05/17/2016 12:37 PM, Navena Rebecca Lingum wrote: > Dear Martin, > > Thank you kindly for your prompt response. > > I am actually having difficulties with the delineation of White Matter > Hyperintensities at a single time point. I apologize if my question is > redundant and perhaps an answer to it is already mentioned elsewhere. > > As it stands, I am finding it difficult to understand the exact > ?pipeline? of commands necessary to perform this segmentation and > accurate delineation of WMH. I have ran the recon -all command on my > T1w images, but I suspect a proper segmentation of WMH would require a > T2w Flair (which I have). How do I go about combining the > preprocessing data produced by FreeSurfer with my T2w images to > produce a WMH mask/volume/stats? > > Any help on the matter is much appreciated! > > Kindly, > Navena Lingum > >> On May 16, 2016, at 4:24 PM, Martin Reuter >> <mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>> wrote: >> >> Hi Navena, >> >> There is currently no dedicated stream for longitudinal WM >> abnormalities (in the sense of joint estimation and modeling). You >> can, however, make use of the longitudinal stream and it's increase >> reliability - e.g it is working in the same space across time, which >> should help get more reliable estimates. >> >> Best, Martin >> >> On 05/16/2016 01:47 PM, Navena Rebecca Lingum wrote: >>> Dear FreeSurfer experts, >>> >>> My colleagues and I would like to use FreeSurfer to perform a >>> longitudinal analysis of white matter hyperintensities. Is there an >>> additional add-on for the software to perform this analysis or can >>> this analysis be performed using the recon-all command? >>> >>> Navena Lingum >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@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@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160517/10f6d018/attachment-0001.html ------------------------------ Message: 8 Date: Tue, 17 May 2016 13:49:50 -0400 From: Corinna Bauer <corinna...@gmail.com> Subject: [Freesurfer] errors in wm and pial boundaries To: Mailing Freesurfer List <freesurfer@nmr.mgh.harvard.edu> Message-ID: <cajosp4k15-ikhhpun+yzsqfkmkexlfbucxpowyg+4psmf0v...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello all, We are analyzing data from our collaborators and are running into some difficulties with the accuracy of the pial and wm boundaries. The wm.mgz appears to follow the actual WM, independent of the wm surface boundary. Attached is an example showing two types of problems. 1. the WM surface is inaccurate regardless of the number of control points used. 2. The pial surface is inaccurate, missing a bunch of the sulcal and gyral patterns of the left parietal lobe (see area around cursor). For completeness, I have also included the wm.mgz at the same slice. I should mention that these problems has been occurring in multiple subjects. Any suggestions?? Thanks Corinna -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160517/22c5e39b/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2016-05-17 13:48:29.png Type: image/png Size: 28718 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160517/22c5e39b/attachment-0002.png -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2016-05-17 13:47:24.png Type: image/png Size: 45793 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160517/22c5e39b/attachment-0003.png ------------------------------ Message: 9 Date: Tue, 17 May 2016 15:46:04 -0400 (EDT) From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] errors in wm and pial boundaries To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <alpine.lrh.2.20.1605171545350.30...@door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Corinna it's hard to tell what's going on from a single slice. If you upload the subject and tell us the specific coordinates that you see problems in we will take a look cheers Bruce On Tue, 17 May 2016, Corinna Bauer wrote: > Hello all,We are analyzing data from our collaborators and are running > into some difficulties with the accuracy of the pial and wm > boundaries. The wm.mgz appears to follow the actual WM, independent of > the wm surface boundary. Attached is an example showing two types of problems. > 1. the WM surface is inaccurate regardless of the number of control > points used. > 2. The pial surface is inaccurate, missing a bunch of the sulcal and > gyral patterns of the left parietal lobe (see area around cursor). > > For completeness, I have also included the wm.mgz at the same slice.? > > I should mention that these problems has been occurring in multiple > subjects. > > Any suggestions?? > > Thanks > > Corinna > > ------------------------------ Message: 10 Date: Tue, 17 May 2016 15:53:18 -0400 From: Josh Gray <jgray7...@gmail.com> Subject: [Freesurfer] Question on Yeo 2015 cognitive atlas To: freesurfer@nmr.mgh.harvard.edu Message-ID: <caenb_sdiftm3dhr8biv+a59pks9simfkrqzzosekypvjfxl...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello, I am interested in applying the Yeo 2015 cognitive atlas to structural data. Basically, I want to quantify networks C1-12 in my structural data by exporting the voxel size of each network for each subject into an text file (so I would have left and right hemisphere voxel totals for networks C1-12 for each subject). It is analogous to what is routinely done with the desikan and destrieux atlas. I know you can change the threshold of the networks, but I suspect 1e-5 is fine (i.e., what is depicted on the website). Is there a quick way to do this? Thank you, Josh Gray -- Graduate Student Psychology Dept. - Clinical Program Experimental & Clinical Psychopharmacology Laboratory University of Georgia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160517/152a9cb0/attachment-0001.html ------------------------------ Message: 11 Date: Tue, 17 May 2016 16:09:28 -0400 From: gangli <lig...@gmail.com> Subject: [Freesurfer] Postdoctoral Position in Infant MRI Analysis at UNC-Chapel Hill To: freesurfer@nmr.mgh.harvard.edu Message-ID: <caaxmhz+z4ylnpqfncznujhp4lx2s2hekxdxsa_ju-mjsrfg...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Postdoctoral research associate positions are available in the Department of Radiology and Biomedical Research Imaging Center (BRIC) at the University of North Carolina at Chapel Hill (UNC-Chapel Hill). Our current focuses are to better understand the dynamic and critical early brain development in both health and disease, via multimodal neuroimaging analysis. The successful candidate will support our efforts either in advancing neuroimaging analysis technologies or in neuroscience applications. We are seeking highly motivated individuals who have extensive research experience in neuroimaging analysis (e.g., structural, diffusion or functional MRI) and demonstrated academic excellence, including publications in first-class journals and conferences. The candidate should have a Ph.D. (or equivalent) in Neuroscience, Computer Science, Applied Mathematics/Statistics, Electrical Engineering, Biomedical Engineering, or related fields. Good command of programming tools including Matlab, C++, Linux, and scripting are necessary to carry out the research work in this group. The successful candidate will be part of a diverse group including neuroscientists, radiologists, psychologists, physicists, biostatistician, and computer scientists, and will build upon the group's extensive foundation on neuroimaging analysis. If interested, please email resume to Dr. Gang Li (gang...@med.unc.edu <https://outlook.unc.edu/owa/redir.aspx?SURL=r-ilRGXKGkv6jOyzGz3FjAPbDG9VNfM_5tB5-93QunnYyKIaCSXTCG0AYQBpAGwAdABvADoAZwBhAG4AZwBfAGwAaQBAAG0AZQBkAC4AdQBuAGMALgBlAGQAdQA.&URL=mailto%3agang_li%40med.unc.edu> ). For more information, please visit: http://www.unc.edu/~gangl/contact.html <https://outlook.unc.edu/owa/redir.aspx?SURL=HcVZFV_dUot9RdWseT8XGNDO-UYKJHN6Rq4hbDpT_MTYyKIaCSXTCGgAdAB0AHAAOgAvAC8AdwB3AHcALgB1AG4AYwAuAGUAZAB1AC8AfgBnAGEAbgBnAGwALwBjAG8AbgB0AGEAYwB0AC4AaAB0AG0AbAA.&URL=http%3a%2f%2fwww.unc.edu%2f%7egangl%2fcontact.html> . -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160517/7faf3ee0/attachment-0001.html ------------------------------ Message: 12 Date: Tue, 17 May 2016 20:49:50 +0000 From: "Limachia, Gaurang (NIH/NINDS) [F]" <gaurang.limac...@nih.gov> Subject: [Freesurfer] Freesurfer To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <d360fc2d.10d0%gaurang.limac...@nih.gov> Content-Type: text/plain; charset="euc-kr" I made the necessary changes to the white matter, and when I ran recon all the changes with the voxels showed up, but there was no change to the contour lines. In order to change the gray matter volume, I can?t find the changes I already made on the white matter (the picture with green control points). If I am able to see the changes I made to the white matter, I can utilize the control points to modify the segmentation. Also will this impact the gray matter volume as well as per your previous response to my question. Thanks, Gaurang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160517/fe68ea89/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2016-05-16 at 5.22.19 PM.png Type: image/png Size: 463296 bytes Desc: Screen Shot 2016-05-16 at 5.22.19 PM.png Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160517/fe68ea89/attachment.png ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 147, Issue 29 *******************************************
wmparc.a2009s.stats
Description: wmparc.a2009s.stats
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