Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

Re: [Freesurfer] surface area of a patch in fsaverage_sym white and pial surface
by Douglas N Greve 06 Sep '12

06 Sep '12

Yes, it is probably best to do it with those as those have the averages across the subjects used to create the atlas. If you just use the area of the cluster on the pial, it will be somewhat smaller. doug On 09/06/2012 01:53 PM, Ritobrato Datta wrote: > Hi Doug, > > I need to dump the surface area of a patch in fsaverage_sym lh. > > But I need to dump the value for fsaverage_sym pial surface, white surface and inflated surface. > > I noticed that in the folder freesurfer/subjects/fsaverage_sym/surf/ > > there is > > ?h.white.avg.area.mgh > > ?h.pial.avg.area.mgh > > What are these ? > > Can I just apply my patch/mask/label on ?h.white.avg.area.mgh and ?h.pial.avg.area.mgh to get the corresponding scalars ? > > Please let me know. > > We are finishing up this paper and need these values as soon as possible. > > Any help will be very much appreciated. > > Thanks a lot > > Rito > > > -- 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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creating a gca file from .mgz files
by Jeff Thompson 06 Sep '12

06 Sep '12

>From the gcaFormat freesurfer wiki page I know that: The .gca file is composed of three volumes, which can be extracted like this:mri_convert atlas.gca -nth 0 means.mgz mri_convert atlas.gca -nth 1 labels.mgz mri_convert atlas.gca -nth 2 priors.mgzwhere:means --> the mean intensity of the most likely labellabels --> indices of the most likely label at each voxel (indices refer to '#No.' column of $FREESURFER_HOME/FreeSurferColorLUT.txt)priors --> the probability that that label occurs at that voxel Is it possible to go the other way? I want to create the labels.mgz file and the others manually, and turn that into the .gca file with mri_convert. Can this be done? Thank you, Jeff Thompson

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question about painting SPM results onto Freesurfer
by keepmoon 06 Sep '12

06 Sep '12

Hello everyone, I just read the information about "paintig SPM results onto Freesurfer" ( http://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting) It shows how to painting SPM results from statistic step (ex. spmT.img) to surface space. I tested the procedure and it worked. But I don't understand what is displayed on Freesurfer surface. Are all the significant differences from SPM statistic results are displayed on this surface? or some part of t values are displayed (which part)? As cortical thickness displayed on surface, each thickness value is painted on each vertex. But here t-value image from SPM is volume image, how to paint it on surface? Someone could give a little detailed explaination?? Thanks in advance Karry

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Fw: Re: Re: mri_surf2surf error
by zzy7758＠mail.ustc.edu.cn 06 Sep '12

06 Sep '12

Hi Bruce My command line is cd $SUBJECTS_DIR/subjid/surf mri_surf2surf \ --s con_52 \ #It is my Processed freesurfer date --trgsubject fsaverage \ --hemi lh \ --sval lh.thickness \ --tval lh.thickness.fsaverage.mgh \ --reshape #or reshape-factor 7 Zhu > -----Original E-mail----- > From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> > Sent Time: 2012-9-6 20:15:35 > To: zzy7758(a)mail.ustc.edu.cn > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_surf2surf error > > Hi Zhu > > what is your command line? > > Bruce > > > On Thu, 6 Sep 2012, zzy7758(a)mail.ustc.edu.cn wrote: > > > Hi Freesurfers, > > > > I'm trying to extracting thickness value for a ROI which is created by afni.I follow the workflows of "Cortical Thickness of a Volume-defined ROI". The ROI mask and T1 volume file are all talairach transformed. > > When I map the thickness data to the fsaverage subject with mri_surf2surf,an error occured: > > "dimension inconsistency in source data > > Number of surface vertices =154984 > > Number of value vertices =163842"(23406*1*7) > > So I use reshape-factor 7 flag ,but it does not work, how can I fix this? > > Any advise would be appreciated! > > > > best > > Zhu > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > 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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contrast matrix
by Meng Li 06 Sep '12

06 Sep '12

Hi Freesurfer experts, When I perform the statistical analysis, I am very confused with the following questions: My experimental design includes 3 discrete factors: diagnosis with two levels (A, B); genotype with two levels (G, T); gender (F, M), and two covariates. So I can get 8 classes: AGF, AGM, ATF,ATM, BGF, BGM, BTF, BTM. 1) I want to perform 2 (diagnosis)* 2(genotype) interaction analysis with regressing out the effect of gender and two covariates, but I don't know the rules for setting the contrasts for the interaction. The contrast matrix I used is: 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 is it correct? If it is correct, how to explain the results, for example, what does the positive (or negative) clusters stand for? Or the clusters showed in the t-test statistical map are the regions that have the significant interaction? 2) When I perform the main effect of dignosis, is the following matrix I used correct? 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 (I think it regressed out the effect of genotype and gender, that is it takes the genotype as a covariable) Or I should create another fsgd file, that has 4 classes: AF, AM, BF, BM. And I can use the matrix (0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0) to perform the main effect of diagnosis. which one is right? Any help will be very appreciated. Best wishes, Meng

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Re: [Freesurfer] mri_watershed and other errors.
by Darren Gitelman 06 Sep '12

06 Sep '12

OK. So do you have any other suggestions? Is there some minor difference between my version and yours that would explain this behavior. Other settings to try? Darren On Wed, Sep 5, 2012 at 4:28 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > our internal development version. > On Wed, 5 Sep 2012, Darren Gitelman > wrote: > > > Bruce > > I used the following > > version: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522 > > > > Is that the same as the one you are using or are you referring to an > > internal development version? > > > > I will try Nick's suggestion as well. > > > > Darren > > > > On Wed, Sep 5, 2012 at 4:05 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > > > > wrote: > > I'm running it now with the current dev version and it's passed > > the skull > > stripping stage and it seems to have worked fine... > > > > On Wed, > > 5 Sep 2012, Nick Schmansky wrote: > > > > > Darren, > > > > > > I forgot to mention that you'll need to add > > > > > > -clean-bm > > > > > > after the -no-wsgcaatlas flag, otherwise the prior > > brainmask.mgz will be > > > retained and the new one will be saved as brainmask.auto.mgz. > > > > > > Nick > > > > > > > > > On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote: > > >> Nick, List: > > >> > > >> > > >> > > >> Still no luck with this data. See attached as an example. > > >> > > >> > > >> > > >> To get to this point I had run: > > >> > > >> > > >> > > >> recon-all -all > > >> > > >> > > >> > > >> This ran to the error: mri_watershed Error: GLOBAL region of the > > >> brain empty ! > > >> > > >> > > >> > > >> Then I followed your recommendation below > > >> > > >> > > >> > > >> recon-all -s <subjid> -skullstrip -no-wsgcaatlas, which had no > > errors > > >> and then > > >> > > >> recon-all -s <subjid> -autorecon2 -autorecon3 > > >> > > >> > > >> > > >> This produced the result attached. > > >> > > >> > > >> > > >> I then deleted this directory and re-imported all the dicom data > > for > > >> this subject. Looked at the images, which look fine. > > >> > > >> Then I ran recon-all -s <subjid> -autorecon1 > > >> > > >> > > >> > > >> This fails with the mri_watershed error. > > >> > > >> > > >> > > >> Then I ran recon-all -s <subjid> -skullstrip -no-wsgcaatlas. > > >> > > >> > > >> > > >> This runs without error but when I look at the brainmask.mgz it > > looks > > >> just like the attached image. > > >> > > >> > > >> > > >> Is there some way to set the thresholds differently? The T1 image > > >> looks fine to me although perhaps the intensity is slightly less > > than > > >> usual, but it doesn't seem particularly noisy. > > >> > > >> > > >> > > >> Darren > > >> > > >> > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer(a)nmr.mgh.harvard.edu > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > 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. > > > > > > > > > > -- > > Darren Gitelman, MD > > Northwestern University > > 710 N. Lake Shore Dr. > > Abbott 11th Floor > > Chicago, IL 60611 > > Ph: (312) 908-8614 > > Fax: (312) 908-5073 > > > > > > > > > -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073

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Frontiers Special Topic: Networks Underpinning Language Repetition
by Seán Froudist Walsh 06 Sep '12

06 Sep '12

Sent on behalf of Marcelo L. Berthier and Matthew A. Lambon Ralph Dear colleagues As host editors of an innovative open access journal, Frontiers in Human Neuroscience, we are currently organizing a Special Topic centered around “Dissecting the function of networks underpinning language repetition”. We would be thrilled if you submitted an article to this Special Topic. A Frontiers’ Special Topic features the latest advances and challenges in hot research areas and attempts to unify the best researchers. It is a collection of at least ten articles, which may be comprised of any one of Frontiers’ article types. The proposed structure of this Special Topic is provided below and we would be happy to hear your suggestions. Hosting Journal: Frontiers in Human Neuroscience Topic Title: Dissecting the function of networks underpinning language repetition Host Editor(s): Marcelo L. Berthier, Matthew A. Lambon Ralph Topic description In the 19th century ground-breaking observations on aphasia by Broca and Wernicke suggested that language function depends on the activity of the cerebral cortex. At the same time, Wernicke and Lichtheim also elaborated the first large-scale network model of language which incorporated long-range and short-range (transcortical connections) white matter pathways in language processing. The arcuate fasciculus (dorsal stream) was traditionally viewed as the major language pathway for repetition, but scientists also envisioned that white matter tracts travelling through the insular cortex (ventral stream) and transcortical connections may take part in language processing. Modern cognitive neuroscience has provided tools, including neuroimaging, which allow the in vivo examination of short- and long-distance white matter pathways binding cortical areas essential for language. However, the state of the art on the neural correlates of language repetition reveals contradictory findings, with some researchers defending the role of the dorsal and ventral streams, whereas others argue that only cortical hubs (Sylvian parieto-temporal cortex [Spt]) are crucially relevant. An integrative approach would conceive that the interaction between these structures is essential for verbal repetition. For instance, different sectors of the cerebral cortex (e.g., Spt, inferior frontal gyrus/anterior insula) act as hubs dedicated to short-term storage of verbal information or articulatory planning and these areas in turn interact through forward and backward white matter projections. Importantly, white matter pathways should not be considered mere cable-like connections as changes in their microstructural properties correlate with focal cortical activity during language processing tasks. Despite considerable progress, many outstanding questions await response. Therefore, this topic welcomes contributors addressing the following questions (1) how white matter pathways instantiate dialogues between different cortical language areas; (2) what are the specific roles of different white matter pathways in language functions in normal and pathological conditions; (3) what are the language consequences of discrete damage to branches of the dorsal and ventral streams; 4) what are the consequences (e.g., release from inhibition) of damage to the left white matter pathways in contralateral ones and viceversa; (5) how these pathways are reorganised after brain injury; (5) can the involvement/sparing of white matter pathways be used in outcome prediction and treatment response; and (5) can the microstructure of white matter pathways be remodelled with intensive rehabilitation training or biological approaches. It is anticipated that the articles in this Research Topic will enhance the understanding of the neural organization of language repetition providing clues on therapeutic interventions of brain damaged individuals. Submission of original data is desirable, but we also encourage mini-reviews and perspective papers which offer provocative and insightful interpretations of the recent literature in the field. Abstract Submission Deadline: November 1, 2012 Researchers can participate by submitting a max. 1 page abstract/outline of work related to the focus of the research topic, through the Frontiers submission system, on or before the abstract submission deadline. Authors will be notified by the host editors whether their abstract has been accepted or rejected. Article Submission Deadline: May 1, 2013 You may find submit abstracts and find more information by clicking on this link: http://www.frontiersin.org/Human_Neuroscience/researchtopics/Dissecting_the… We look forward to hearing from you Sincerely yours, Marcelo L. Berthier Matthew A. Lambon Ralph

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mri_surf2surf error
by zzy7758＠mail.ustc.edu.cn 06 Sep '12

06 Sep '12

Hi Freesurfers, I'm trying to extracting thickness value for a ROI which is created by afni.I follow the workflows of "Cortical Thickness of a Volume-defined ROI". The ROI mask and T1 volume file are all talairach transformed. When I map the thickness data to the fsaverage subject with mri_surf2surf,an error occured: "dimension inconsistency in source data Number of surface vertices =154984 Number of value vertices =163842"(23406*1*7) So I use reshape-factor 7 flag ,but it does not work, how can I fix this? Any advise would be appreciated! best Zhu

2 1

Covary for a categorical variable in mri_glmfit
by Jeff Sadino 05 Sep '12

05 Sep '12

Hello, I am trying to covary for Gender in mri_glmfit, but I am having errors pop up. I tried to follow Doug's suggesting in this post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12272.html but after modifying my Xg.dat file and rerunning mri_glmfit, it says: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.53319e+07 I can run it using the --illcond flag, but then I get a bunch of: *** CEPHES ERROR: fdtrc domain error *** Can anyone please give advice on how to covary for Gender in mri_glmfit (or qdec)? As always, thank you for all of your great help!! Jeff Sadino

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Re: [Freesurfer] mri_watershed and other errors.
by Darren Gitelman 05 Sep '12

05 Sep '12

Bruce I used the following version: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522 Is that the same as the one you are using or are you referring to an internal development version? I will try Nick's suggestion as well. Darren On Wed, Sep 5, 2012 at 4:05 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > I'm running it now with the current dev version and it's passed the skull > stripping stage and it seems to have worked fine... > > On Wed, > 5 Sep 2012, Nick Schmansky wrote: > > > Darren, > > > > I forgot to mention that you'll need to add > > > > -clean-bm > > > > after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be > > retained and the new one will be saved as brainmask.auto.mgz. > > > > Nick > > > > > > On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote: > >> Nick, List: > >> > >> > >> > >> Still no luck with this data. See attached as an example. > >> > >> > >> > >> To get to this point I had run: > >> > >> > >> > >> recon-all -all > >> > >> > >> > >> This ran to the error: mri_watershed Error: GLOBAL region of the > >> brain empty ! > >> > >> > >> > >> Then I followed your recommendation below > >> > >> > >> > >> recon-all -s <subjid> -skullstrip -no-wsgcaatlas, which had no errors > >> and then > >> > >> recon-all -s <subjid> -autorecon2 -autorecon3 > >> > >> > >> > >> This produced the result attached. > >> > >> > >> > >> I then deleted this directory and re-imported all the dicom data for > >> this subject. Looked at the images, which look fine. > >> > >> Then I ran recon-all -s <subjid> -autorecon1 > >> > >> > >> > >> This fails with the mri_watershed error. > >> > >> > >> > >> Then I ran recon-all -s <subjid> -skullstrip -no-wsgcaatlas. > >> > >> > >> > >> This runs without error but when I look at the brainmask.mgz it looks > >> just like the attached image. > >> > >> > >> > >> Is there some way to set the thresholds differently? The T1 image > >> looks fine to me although perhaps the intensity is slightly less than > >> usual, but it doesn't seem particularly noisy. > >> > >> > >> > >> Darren > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > 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. > > -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073

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