Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Regenerating Pial Surfaces
by Matthew Clem 13 Aug '14

13 Aug '14

Hi FreeSurfers, I have gone through correcting pial surfaces for one subject, and ran the script to regenerate the surfaces: recon-all -autorecon-pial -subjid 1 After running without error, it appears the pial surfaces have not changed at all. Does FS overwrite the previous lh.pial and rh.pial files, or are new files created with the regenerated surfaces? I have searched the machine and have not found any new files, unless they are hidden somewhere I am unaware of. Thanks, Matt ________________________________ UT Southwestern Medical Center The future of medicine, today.

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occipital lobe WM errors
by Walton, Matt 13 Aug '14

13 Aug '14

Hello Freesurfer team, I've used freesurfer to segment (recon-all) approximately 30 different subjects from a study. I've noticed that a large number of these subjects have a misclassification of the white and pial boundaries in the occipital lobe (such that grey matter is being classified as white matter). I believe this problem is originating from my scanner and original data. I'm acquiring a T1W BRAVO sequence on a GE Discovery 750w 3T scanner, using a 32 channel phased array head coil. For many subjects, this acquistion gives intensity inhomogeneity in the occipital lobe. I've begun using a GE based correction technique (PURE) on the images, and it appears to improve the intensity in the occipital lobe, but Freesurfer is still frequently misclassifying. I'm wondering what would be the best way to edit the data. I've often tried to edit the wm.vol, but this doesn't seem to fix anything. For the most part, the wm.vol is correct to begin with, but the wm cutting line isn't segmenting with the wm.vol. I've also tried to add control points but this doesn't seem to improve anything either. I've attached an image which I hope will further explain my problems. Thanks for any help

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quick pointer: tool to extract gray/white contrast vectors from [lr]h.w-g.pct.mgh
by Krieger, Donald N. 13 Aug '14

13 Aug '14

What is the tool to extract the contrast vectors from surf/[ lr]h.w-g.pct.mgh ? Thanks, Don

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Qcache for different fsaverage
by Vy Dinh 13 Aug '14

13 Aug '14

Dear developers, I just have a brief technical question about using qcache for multiple fsaverages. If I wanted to write my subjects to a new fsaverages, I know that one can use the command Recon-all -qcache -target fsaverage2 -s subid However, does this overwrite the current normalized data to reflect the new fsaverages, or write new data? Are there any special steps that I need to take with respect this change when conducting group comparisons in qdec? Thank you, Vy -- Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health

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Re: [Freesurfer] proportion of surface area of significant region
by Lars M. Rimol 13 Aug '14

13 Aug '14

Thanks, Doug! So I tried this method using fsaverage/surf/lh.white.avg.area.mgh. The results seem to be reasonably consistent with the ones I get when eyeballing the p-maps overlayed on fsaverage in tksurfer. Would you agree that's a reasonable "sanity check"? When I compare the results to just counting vertices, there doesn't seem to be a huge difference between proportion of #vertices and proportion of surface area. So either there isn't a lot of variance in the sizes of the faces, or the variance is evenly distributed. Finally, if I want to convert from an individual map or the cohort mean map to mm² units, can I do it by scaling the ico area vertex values by the ratio between native and ico total area? So: (vertex value from mean cohort map * total area for cohort mean map) / total area for fsaverage/surf/lh.white.avg.area.mgh, where total area would be the sum of all vertex values? Thank you! LMR ------------------------------------------------------------------------------------------------------- You don't want to get the surface area from the faces of fsaverage. Instead use the values in fsaverage/surf/lh.white.avg.area.mgh (this is the average of the group used to create fsaverage), or, probably better, get an average area map for your cohort doug On 07/30/2014 08:38 AM, Lars M. Rimol wrote: > Hi Bruce, > > I would like to be able to tell what proportion of a region of > interest (ROI), as defined in atlas space by e.g. Desikan-Killiany, > that shows a significant effect (based on a p-map). For now I overlay > the p-map on the inflated surface of fsaverage in tksurfer and eyeball > the proportion. > > Given a p-map, if I find the FDR threshold and identify the vertices > within a given ROI that have a p-value greater than the threshold, > then I can find the proportion of the ROI that is suprathreshold. > E.g., I find 1986 suprathreshold vertices in "bankssts" out of 2137, > so 93% of vertices in bankssts show a significant effect. > > My question is: Does that tell me anything about what proportion of > the ROI's surface area is affected in atlas space? Obviously, if the > faces were uniform, there would be a 1 to 1 relationship between > #vertices and area. In the original tesselation of any dataset the > size of the faces is uniform, but that changes with topology fix and > deformation. I assume that is true also for fsaverage? (so I can't > assume [#sig vertices] / [# tot vertices] == the proportion of the > ROI's area that is significant in atlas space) > > I can find the surface area of the suprathreshold region for my sample > (or any subset thereof) by looking at a mean area map. But I'm unsure > how to do that for fsaverage itself? Is there information on regional > surface area directly available? Or would using getFaceArea.m or > getFacesArea.m or similar functions be a solution? > > > Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway

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Cortical Segmentation reliability in Mid-Line structures
by amirhossein manzouri 13 Aug '14

13 Aug '14

Dear All, I wonder if you have experienced or there is any report on cortical segmentation reliability in the mid-line structures of the brain, so one should take them into consideration in running group differences with Qdec? Best regards, Amirhossein Manzouri

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V1 and V2 labels valid with clinical populations?
by krista kelly 13 Aug '14

13 Aug '14

Does anyone know of any support (i.e. articles/data) suggesting that the V1 and V2 labels automatically created in the Freesurfer pipeline, especially when looking at surface area/gyrification, are valid to use with clinical populations? In particular, visually deprived populations? Thanks! Krista

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mri_em_register intervention?
by Makaretz, Sara Johanna 12 Aug '14

12 Aug '14

I am having trouble getting a usable brainmask for one of my subjects - a screenshot of the initial brainmask.mgz is attached as image_1. The talairach transformation looks fine, so I tried running recon-all -multistrip with raised watershed heights to no avail - see image_2. Does this mean the problem is with the mri_em_register step / lta output? How can I check this, and what can I try changing? Thank you!

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Flip ROI in fsaverage / mris_left_right_register
by Bastian Cheng 12 Aug '14

12 Aug '14

Dear Freesurfers, I am trying to flip an overlay (.mgh) to the contralateral hemisphere. The overlay is in fsaverage-space. I am using it only for visualization (and not doing any statistics). I noticed that there was a program that could achieve this: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_left_rig… ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_re… However it is not online anymore. Would this still be the right way to do it? Best regards, Bastian

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Mac OS X update
by carolina.mr 12 Aug '14

12 Aug '14

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