Freesurfer

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19 participants
30088 discussions

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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Which Volume is the one in Qdec measures?
by amirhossein manzouri 17 Mar '14

17 Mar '14

Hi All, Would please let me know about the origin of volume in the measures menu of Qdec, so I can interpret the results from group comparisons. Is it Gray Matter volume? Best regards, Amirhossein Manzouri

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