Freesurfer April 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
229 discussions

Re: [Freesurfer] Intermediate stages of cortical inflation
by Xuelong Zhao 14 Apr '14

14 Apr '14

Addendum to the previous post: Can I use lh.orig as the input surface instead of lh.inflated? Also, I ran the command you suggested (I changed -w flag to 10 and used lh.orig as the input surface): mris_sphere -w 10 lh.orig lh.sphere_test However, when I viewed the output of the intermediate forms, all of them were nearly spherical, only lh.sphere_test0010 deviated slightly from the sphere. Even so, it seems its very hard to capture the unfolding process from the cortex to the sphere. Should I be using some other flags? For instance, if I used -w 1 instead, would this help? Thanks. From: andrewzhao(a)live.com.au To: fischl(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intermediate stages of cortical inflation Date: Fri, 11 Apr 2014 16:20:33 +1000 Great, will give this a try. Thanks for clarifying the command flags. Is it also possible to specify the scale using the flag - scale 1? > Date: Fri, 11 Apr 2014 01:38:01 -0400 > From: fischl(a)nmr.mgh.harvard.edu > To: andrewzhao(a)live.com.au > CC: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] Intermediate stages of cortical inflation > > sorry, it shouldn't say "patch", but "file". We will fix that. I wouldn't > run it with -n. Without it, it will run until it asymptotes. I would try: > > mris_sphere -w 20 lh.inflated lh.sphere > > cheers > Bruce > > > cheers > Bruce > > > On Fri, 11 > Apr 2014, Xuelong Zhao wrote: > > > Thanks for pointing this binary out- I didn't realize the user could access it outside > > of recon-all. > > I've had a look at the fswiki for mris_sphere and it doesn't seem to be complete. I > > used it in the following format but not sure if this is correct: > > > > mris_sphere -n 160 -w 20 -scale 1 lh.orig lh.sphere_test > > > > I want to check that the above command converts lh.org to a sphere in 160 iterations, > > writes out every 20th iteration and ensures the area is preserved? > > > > Also, on the fswiki site: > > > > * > > > > mris_sphere [options] <surface file> <patch file name> <output patch> > > > > > > I'm not certain if <output patch> is synonymous with output surface? Also, what is the > > purpose of a <patch file name>? Thanks. > > > > > > > Date: Thu, 10 Apr 2014 11:30:15 -0400 > > > From: fischl(a)nmr.mgh.harvard.edu > > > To: xuelongzhao(a)hotmail.com > > > CC: freesurfer(a)nmr.mgh.harvard.edu; greve(a)nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] Intermediate stages of cortical inflation > > > > > > yes, many of our binaries take the -w <n> flag to write out a snapshot of > > > the minimization every nth step, including mris_sphere > > > > > > cheers > > > Bruce > > > > > > > > > On Thu, 10 Apr 2014, Xuelong Zhao wrote: > > > > > > > Is it also possible to track the inflation all the way to the sphere? I was hoping > > that > > > > I could take snapshots of equi-area intermediate forms as the cortex is unfolded > > onto > > > > the sphere instead of stopping at the inflated cortex. Thanks. > > > > > > > > > > > > > > > > > Date: Wed, 9 Apr 2014 08:31:46 -0400 > > > > > From: fischl(a)nmr.mgh.harvard.edu > > > > > To: freesurfer(a)nmr.mgh.harvard.edu > > > > > CC: greve(a)nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] Intermediate stages of cortical inflation > > > > > > > > > > you can use -w 1 to write out every step in the inflation process and > > > > > choose what you want. If you want it to preserve surface area during > > > > > inflation (as opposed to just at the end), also include -scale 1 > > > > > > > > > > cheers > > > > > Bruce > > > > > > > > > > > > > > > On Wed, 9 Apr 2014, Xuelong Zhao wrote: > > > > > > > > > > > Hi, > > > > > > > > > > > > I would like to ask whether it is possible to display different levels of > > > > > > cortical inflation? > > > > > > > > > > > > I have been using the command: mris_inflate > > > > > > > > > > > > but the -dist and -n flags do not seem to make that much difference. Also, > > > > > > if I use fsaverage lh.orig as the input file and using the default options > > > > > > for mris_Inflate I don't seem to be able to recover the lh.inflated surface. > > > > > > > > > > > > Are there any alternative commands to control the level of inflation? > > > > > > Thanks. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > 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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Calculation to create pc1fit metrics
by Rees, Elin 12 Apr '14

12 Apr '14

Dear FreeSurfer Experts, I am wanting to create my own pc1fit metrics of change for each atlas region for each subject in order to calculate regional effect sizes. All documents describe this as the percent change with respect to the value at tp1, evaluated from the linear fit?. What does the linear fit refer to exactly and how can I compute this on my raw thickness data extracted with aparcstats2table? Many thanks, Elin

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QDEC repeated measures.
by Walton, Matt 11 Apr '14

11 Apr '14

I am wondering if there a way to account for repeated measures when running a QDEC analysis. I have 60 scans taken from 39 subjects (ranging between 1 scan per subject to 5 scans per subject). Over all I am trying to corrlelate freesurfer measures of thickness and volume with scores from a language test. I am also corrected for age and gender. Is there anyway you can think of to correct for the extra scans? Thanks, Matt

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Mapping a subject to common space
by Jonathan Holt 11 Apr '14

11 Apr '14

Hello all, I’m using mri_surf2surf to try to resample a subject to fsaverage, so far I have mri_surf2surf --hemi lh --srcsubject [SUBJECT] --cortex --trgsubject fsaverage however I’m pretty certain that I need both —sval and —trgfmt, but this is the confusing bit as I’m not sure what I should be passing to sval and what format is standard for output… please advise if I’m missing any other flags for surf2surf jon

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test- please disregard
by sabin khadka 11 Apr '14

11 Apr '14

Sorry all. Just a test e-mail.

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test- please disregard
by sabin khadka 11 Apr '14

11 Apr '14

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vertex-wise surface area values?
by sabin khadka 11 Apr '14

11 Apr '14

Hi all, I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject <subject dir> area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. Thanks for the help. -Sabin

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vertex wise surface area values?
by sabin khadka 11 Apr '14

11 Apr '14

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Re: [Freesurfer] wm and pial edits - what to correct and what not?
by Markus Gschwind 11 Apr '14

11 Apr '14

Dear Bruce, Thanks for your detailed answer! > it's tough to tell for sure on just a single slice, particularly if it is > the intensity normalized one that removes a lot of the contrast if it is > (as you suspect) doing the wrong thing. What does the orig look like? We > try pretty hard to avoid including deep, highly myelinated gray matter > inside the white matter surface, but of course if the contrast is low > enough we can fail. If you scroll backwards and forward a few slices does > or look in a different orientation does it look different/better? Sometimes > the surface is curving sharply and this kind of thing will show up on a > single slice, but actually isn't a significant inaccuracy. Yes, when scrolling throug the slides it really appears consistent across several slides (actually the attached screenshots showed Freeview in coronal, sagittal and axial perspective of the same region). Here is the orig attached together with the wm, pial and white. So how should I treat it? > As for the dura, that certainly looks like a problem for thickness > estimates. Have you tried using the graph cuts skull stripping? That is > more aggressive than mri_watershed. You can also play with the watershed > parameters to try to get more dura removed. Finally, if you have a T2-space > FLAIR scan we can use that to properly reposition the surfaces (or less > ideally, a T2-space scan without a FLAIR inversion). No, unfortunately there are no other images at disposition. How would one go with the graph cuts ? I found "mri_gcut [-110| -mult <filename> |-T <value>] in_filename out_filename", but how is it run within recon-all in order to repair (FS version 5.3)? Thank you so much! Markus 2014-04-07 14:47 GMT+02:00 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > Hi Markus > > it's tough to tell for sure on just a single slice, particularly if it is > the intensity normalized one that removes a lot of the contrast if it is > (as you suspect) doing the wrong thing. What does the orig look like? We > try pretty hard to avoid including deep, highly myelinated gray matter > inside the white matter surface, but of course if the contrast is low > enough we can fail. If you scroll backwards and forward a few slices does > or look in a different orientation does it look different/better? Sometimes > the surface is curving sharply and this kind of thing will show up on a > single slice, but actually isn't a significant inaccuracy. > > > As for the dura, that certainly looks like a problem for thickness > estimates. Have you tried using the graph cuts skull stripping? That is > more aggressive than mri_watershed. You can also play with the watershed > parameters to try to get more dura removed. Finally, if you have a T2-space > FLAIR scan we can use that to properly reposition the surfaces (or less > ideally, a T2-space scan without a FLAIR inversion). > > cheers > Bruce > > > > On Mon, 7 Apr 2014, Markus Gschwind wrote: > > Dear all, >> I would like to show some very frequent and typical cases of segmentation >> problems in my bunch of data of normal subjects (after recon-all), of >> which >> I couldn't find a description in the wiki(http://surfer.nmr.mgh. >> harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWith >> Data/FreeviewEditingaRecon). >> >> I am therefore not sure if these types of error are serious and will >> affect >> later results like thickness, curvature, GWR, etc. >> >> Here are the examples (c.f. attached screenshots from Freeview) >> >> 1) In the primary sensory-motor cortex it frequently happens that the >> "?h.white" line lies several mm within the wm border (c.f. yellow arrow), >> I >> did not observe this behavior in other places. >> >>Would I need to edit that? >> >> 2) Sometimes the "?h.pial" line includes also dura or parts of the skull >> (green arrow). >> >>Is it necessary to edit that as well? >> >> 3) Another question concerns the yellow parts of the wm which sometimes >> are >> much larger than the ventricles and also include both caudate nuclei (not >> shown). >> >>Is this a problem? >> >> Thanks in advance!! >> >> Markus >> >> > >

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Problems running Monte Carlo Simulations
by Gautam Tammewar 11 Apr '14

11 Apr '14

Hi all, I'm trying to run Monte Carlo simulations on cortical thickness data I got using mri_glmfit, but I'm running into some errors. 1) I used the command mri_glmfit-sim --glmdir lh.thickness.fwhm20.diagnosis_scanner.dods.glmdir/ --cache 2.0 pos The error I receive says "cannot find /usr/local/freesurfer_x86_64-5.1.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm40/pos/th20/mc-z.csd" I'm wondering why the script is looking in the directory "fwhm40" when the data is smoothed using FWHM 20. The directories available under fsaverage/lh/cortex go from fwhm01 to fwhm30. 2) Also, for another test I'm running, I created my own average subjects (instead of using fsaverage). Is there a way to generate the files that are created under /average/mult-comp-cor for this average subject so that I don't have to use the "--sim" flag to run simulations? Thanks, GT

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Freesurfer April 2014