Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

hypothalamus?
by Ella 18 Mar '14

18 Mar '14

Hi all, I'm looking to create a mask for the hypothalamus on individual subjects. I've had a good look at the literature, and at the moment, am I right in thinking the automatic segmentation in Freesurfer doesn't currently include the hypothalamus? thanks in advance Ella

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Problem about Surface-based Registration
by yufeng huang 18 Mar '14

18 Mar '14

I followed the process of creating a registration template from scratch(GW)( https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) to do the surface-based registration. My question are as followed: 1 I want to know if I need to use the mri_cvs_registrater to replace mri_register. 2 I check the result and find it produce the lh.sphere.reg.newtemplate1 and rh.sphere.reg.newtemplate1 in each subjects's surf folder. I want to know how to check the result by using the new file. 3 Should I need to re-run recon-all after the mri_register for every subjects? Thanks very much for your help!

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tkmedit edit voxel tcl script
by Joerg Pfannmoeller 18 Mar '14

18 Mar '14

Hello, if I have selected a voxel in a volume with tkmedit with a tcl script, how can I set the voxel value to 0. Sincerely yours pfannmoe

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Fw: Re: view time course in freeview
by charujing123 17 Mar '14

17 Mar '14

Hi doug and other FS experts, Thanks very much doug. rh.ttest.thickness.10.mgh is created from the mris_preproc to merge all the subjects' thickness into one file. Then group t-test can be done. I try tksurfer -t rh.ttest.thickness.10.mgh, but the command window echoes its usage. Just as you told me freeview has a new version to see time course for this file. I wonder where I can download it. Thanks doug, All the best. Rujing Zha 2014-03-13 charujing123 发件人：Douglas Greve <greve(a)nmr.mgh.harvard.edu> 发送时间：2014-03-12 22:57 主题：Re: [Freesurfer] view time course in freeview 收件人："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： But what is in rh.ttest.thickness.10.mgh? Is it a stack of all your subjects (the file you passed with --y to mri_glmfit)? If so, then add "-t rh.ttest.thickness.10.mgh" to your tksurfer command line. Ruopeng just added something to freeview to do it, but you'd have to get a new version doug On 3/11/14 9:46 PM, charujing123 wrote: Hi doug, sig.mgh is my result for two group t-test on pial thickness of whole brain. So I want to see the time course of thickness of rh.ttest.thickness.10.mgh vertex by vertex. Thanks. All the best. Rujing Zha 2014-03-12 charujing123 发件人：Douglas N Greve <greve(a)nmr.mgh.harvard.edu> 发送时间：2014-03-12 00:16 主题：Re: [Freesurfer] view time course in freeview 收件人："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： the time course of what? On 03/11/2014 07:18 AM, charujing123 wrote: > Hi FS experts, > For the sig.mgh, can I see the time course vertex by vertex in freeview? > Thanks. > All the best. > Rujing Zha > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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 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/ _______________________________________________ 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

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mris_preproc, mri_surf2surf and lme_mass_vw
by Eric Cunningham 17 Mar '14

17 Mar '14

Hello Freesurfer experts, The lme_mass_vw script runs for a long time and outputs info into the matlab terminal. Most look like this: Location #####: Algorithm did not converge. Initial and final likelihoods: ###, ### Running this script, for almost every line, the initial and final likelihoods are "Inf". Is this indicative of a problem? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Getting these results made me wonder if the Y-input was built properly. Using mris_preproc and mri_surf2surf to smooth, we tested 10mm smoothing and no smoothing in addition to the 30mm smoothing we had been doing originally. The results: smoothed to 30 ~ almost every likelihood = Inf, Inf smoothed to 10 ~ some (1 in 5? 10?) likelihood = Inf not smoothed ~ no instances of likelihood = Inf, Inf Thanks, -Eric

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Consistent Dura issues
by Jonathan Holt 17 Mar '14

17 Mar '14

Hi all, I’m working with a particularly stubborn data set whose defining characteristic is dura along the posterior of the brain. It’s become so consistent that I’m hoping to find a way to perhaps tweak recon-all so as to take care of the issue in a more automated manner and save many many man hours of manual work. Is this possible? jon

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Re: [Freesurfer] Displaying ROI's from Destrieux atlas (aparc.a2009s)
by Douglas N Greve 17 Mar '14

17 Mar '14

Hi Laura, please make sure to post to the list. Thanks! This is possible. Run mri_annotation2label to break the annotation up into labels, then use mris_label2annot to recombine only the ones you want back into an annotation doug On 03/17/2014 03:55 PM, Laura Taylor wrote: > Sorry, I will try to explain better. > > I have used the average thickness (ThickAvg) stats from the > rh/lh.aparc.a2009s.stats file in my data analysis comparing cortical > thickness in different patient groups. > > For my results, I have say 10 areas from the rh/lh.aparc.a2009s.stats > that are thicker in one patient group than in another. I would like > to visually display these specific areas of cortex that are thicker in > one group than another on a whole/half brain. > > I can load the annotation file in freeview with all of the 74 regions > per hemisphere in different colors, but I'd like to make it so that my > 10 regions of interest are say red and the rest of the brain (64 other > regions) are, e.g. grey. > > Is this possible? > > Thank you, > > Laura > > > On Mon, Mar 17, 2014 at 12:24 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > I'm not sure what you mean, can you elaborate? > doug > On 03/17/2014 03:02 PM, Laura Taylor wrote: > > Hi there, > > > > I am looking to somehow display a handful of cortical areas from the > > Destrieux atlas (aparc.a2009s). Is there a way to do this? > > > > Thanks, > > > > Laura > > > > > > > > > > _______________________________________________ > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > > -- 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: 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/

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Segmentation fault:11 with mris_anatomical_stats
by Rupa Sabbineni 17 Mar '14

17 Mar '14

Good morning! I was trying to run the mris_anatomical_stats command and for some subjects I keep getting Segmentation fault:11 error. Some of the posts in the archive suggested that I run the recon-all command since it usually means that subjects surfaces are out of sync SO I RERAN RECON_ALL(which created the stats). Then I reran the mris_anatomical_stats command and got the segmentation fault again. The command im using is mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh A little background on the new.label. We got the label by doing a regression in qdec at FDR 0.05 which created cluster and peak cluster label. Can anyone please provide me some insight on how to trouble shoot this problem? Thank you! Rupa

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Displaying ROI's from Destrieux atlas (aparc.a2009s)
by Laura Taylor 17 Mar '14

17 Mar '14

Hi there, I am looking to somehow display a handful of cortical areas from the Destrieux atlas (aparc.a2009s). Is there a way to do this? Thanks, Laura

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[Label] Extract coordinate of Corpus Callossum
by Thomas PAUL 17 Mar '14

17 Mar '14

Dear FreeSurfer experts, I've been using FreeSurfer for 2 months now, and I have a question on how to proceed to do the following thing: My goal is to obtain the CRS coordinates of the corpus callossum. Here is what I was thinking to do, based on what I read: 1. Annotation to segmentation: mri_annotation2label --seg --hemi ?? --subject bert volume_annot.mgh => I need to provide an hemisphere, which one should I use, should I do this for both ? 2. Binarize the volume, keeping the label we want: mri_binarize --i volume_annot.mgh --match 86 --o corpusCallossum.mgh => I use the number 86 based on the LUT table... 3. Execute: mri_surfcluster --in corpusCallossum.mgh --thmin 0.5 --subject bert --hemi ?? --o outputfile.mgh Am I on the right path? I am not sure on how to use the outputfile.mgh after. Did I miss any arguments in the command line? Thank you in advance for your help Thomas Paul.

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