Freesurfer

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30099 discussions

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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Re: [Freesurfer] caudate and putamen to surface
by gong jinnan 11 Apr '14

11 Apr '14

Hi Prof. Greve, Thanks for your reply. Sorry, perhaps I have made some mistake in my data analysis. I just want to show tractography results of basal ganglia in surface space using FSL. Could transform fit_paths.nii.gz to surface be a brief way? In order to do mdi_vol2surf (transform volume ROIs in T1 space to surface) I should have register.dat. Is that a correct way to get it using "bbregister --s SubID --mov T1.nii --init-fsl --reg register.dat " Sincerely, Jinnan

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Installing only Freeview
by Janosch Linkersdörfer 11 Apr '14

11 Apr '14

Hi all, is there a way, to install only freeview not the whole Freesurfer package (on Mac OS X). Or, alternatively, can somebody please tell me what I can safely remove after installing the whole package to be able to still run Freeview, but save the maximum of hard disk space? I do all processing on a remote computing server, but my VNC connection does not allow to display freeview, so I use sshfs to mount the server locally on my MacBook and use the local Freeview to inspect or correct files. Thanks, Janosch

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Tumor Segmentation in FreeSurfer
by Mohammed Goryawala 11 Apr '14

11 Apr '14

Hello FreeSurfer Experts, On review of stats file in FreeSurfer a tumor volume is reported. How is tumor segmentation achieved by FreeSurfer? Thank you Mohammed Goryawala, PhD

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Subcutaneous fat and intensity normalisation
by N. Medic 11 Apr '14

11 Apr '14

Dear FreeSurfers, I have a question concerning pctsurfcon and subcutaneous fat. The first step in the Freesurfer processing pipeline is intensity normalisation, which assumes that high intensity signal is due to white matter and uses this as a reference point. However this happens prior to skull stripping and therefore slices contain subcutaneous fat, which also has a high signal intensity. When processing images from obese subjects might the large amount of subcutaneous fat affect intensity normalisation thereby affecting measures like pctsurfcon further down the line? Or does freesurfer distinguish between subcutaneous fat and white matter? Thanks Nenad

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Re: [Freesurfer] Intermediate stages of cortical inflation
by Bruce Fischl 11 Apr '14

11 Apr '14

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. > > > >

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longitudinal template generation with manual registration
by Andreas Werner 10 Apr '14

10 Apr '14

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Vertexwise surface area value?
by sabin khadka 10 Apr '14

10 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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Large areas of white matter ignored, even with control points
by Andrea Grant 10 Apr '14

10 Apr '14

Hello, I'm working with T1 weighted scans obtained at 7T and have a problem with a subject. I preprocess the images to deal with the B1 inhomogeneity (normalize to PD and mask noisy pixels), and have successfully segmented about 20 scans. I often need to use control points, but they normally work just as I expect. However, I have one subject where large areas of the brain are completely excluded from the segmentation (basically the entire occipital lobe). I added control points and re-ran, to no effect. I'm attaching a screenshot of the brainmask with surfaces, my control points, and the white matter mask. Clearly, the skull stripping wasn't very successful (I adjusted the watershed threshold manually, but at one value I got the current result and at a single integer lower I lost half the brain). I have successfully segmented other subjects with equally poor skull strips, though, so I don't believe this has any bearing on the current issue. Is editing the white matter mask the only way to fix this? If so, do I need to carefully fill in on every slice, or can I just brush in here and there to sort of "goose" the white matter into that region? I can do the slice by slice fix, but if there's a way to avoid the several hours it will take me, I would love to know! Thanks, Andrea ----- Andrea Grant Visual Neuroimaging Technologist Center for Magnetic Resonance Research, University of Minnesota 2021 6th St. SE, Minneapolis, MN 55455, 612-626-4948 gran0260(a)umn.edu umn.edu/~gran0260 <http://umn.edu/%7Egran0260>

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