Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

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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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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