Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

Fwd: -dura_thresh
by Octavian Lie 27 Mar '17

27 Mar '17

Can anybody comment on the new dura_thresh flag? See below, Many thanks, Octavian. ---------- Forwarded message ---------- From: Octavian Lie <octavian.lie(a)gmail.com> Date: Sat, Mar 11, 2017 at 9:28 AM Subject: -dura_thresh To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Dear All, In FS6.0.0, this flag is added to manually adjust watershed threshold instead of its automatic calculation. I went back to the original paper by Segonne et al, and I could identify the prefllooding height h and the post watershed threshold t. I assume the flag refers to the latter. Since the threshold varies between subjects, where is it specified in the log file of a recon-all run? Also, could you indicate a (narrow) range one could start with if trying to manually adjust a run, based on your experience? Also, what is the watershed direction based on t (higher t values lead to more aggressive dura removal, or the other way around? Thank you very much, Octavian

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Does FreeSurfer detect black holes in T1WI
by Timothy M 25 Mar '17

25 Mar '17

Hello, I cannot seem to find any documentation regarding detection of "black holes" on T1WI (e.g., in patients with multiple sclerosis). Does FreeSurfer provide this functionality? If so, is there any documentation on the subject? Thank you, Timothy

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intensity normalization and GM exclusion
by Meaghan Perdue 24 Mar '17

24 Mar '17

Hello, I attended the September 2016 Freesurfer training course, and I am seeking help to resolve a consistent issue with white and pial surface extraction that seems to be rooted in poor intensity normalization. Our lab is working with a pediatric dataset acquired on a 3T scanner and recon-all was run in Freesurfer v5.3. Throughout the dataset, we have found that the surfaces are cutting off white matter and excluding a significant amount of gray matter, particularly in the lateral temporal lobes. I have attached several images to illustrate the problem. As you can see in the images, the pial surface in the lateral temporal lobes hugs close to the white/gray boundary and excludes gray matter. We have used the -3T flag when running recon-all for all subjects, and we have manually changed the smoothing distance in mi_nu_correct to 30 for several subjects in an attempt to improve this, but we did not get a better result. We are hesitant to address this problem using control points because it would require adding many control points across many slices in nearly all the subjects, and we would like to avoid the reliability/replicability issues of so much manual editing. (Not to mention the time required to do such heavy editing). Is there any way to address this automatically through the recon pipeline? Many thanks, Meaghan Perdue

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error with mris_make_face_parcellation
by Almarshad F. 24 Mar '17

24 Mar '17

Hi freesurfer's experts; I was trying to use mris_make_face_parcellation lh.surf $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot to generate uniform-sized parcellation .. but i get the following error *** Error in `mris_make_face_parcellation': double free or corruption (out): 0x0000000003fec560 *** ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f96d00ef7e5] /lib/x86_64-linux-gnu/libc.so.6(+0x7fe0a)[0x7f96d00f7e0a] /lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f96d00fb98c] mris_make_face_parcellation[0x41065b] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f96d0098830] mris_make_face_parcellation[0x40b529] i also attached the log file kidest regards, fatima

3 10

Defect Holes different between scans in same subject
by Brad Matushewski 24 Mar '17

24 Mar '17

We have a study where subjects are scanned one, and a second time 6 months later. I am looking for changes between the two time point and often times there is a large difference in the "number of defect holes prior to fixing" within the same subject. Can anyone comment on the significance of this? Given the same brain being scanned 6 months later, how / why is there such a difference? [Logo] Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP. Laboratory for Brain & Heart Health School of Kinesiology Western University Room 402, Arthur & Sonia Labatt Health Sciences Building London, ON, Canada, N6A 5B9 Tel: (519) 661-2111 x 89066 Fax: (519) 850-2447

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use mris_make_face_parcellation
by Almarshad F. 24 Mar '17

24 Mar '17

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Longitudinal: obtain rigid registration matrix from cross to long subject
by Matthieu Vanhoutte 24 Mar '17

24 Mar '17

Dear Freesurfer's experts, I would like to obtain the rigid registration matrix of the transformation between cross and long subject. Where could I find this (.dat or .lta file) ? Best regards, Matthieu

2 2

Freesurfer for PET images
by shi yao wang 24 Mar '17

24 Mar '17

Dear FS experts: We have a few PET images for brain. Just wondering if FS can be used to measure brain volume? Do I have to have T1 MRI as reference? thanks Lawrence

2 1

question about "mean curvatura"
by 李慧 23 Mar '17

23 Mar '17

Dear FreeSurfer Group, Sorry for interrupting. I am Hui Li, a researcher fron Beijing, China, interesting in sMRI of mind disorder. Recently, I am working on some data about schizophrenia. I compared the patients and healthy controls, and found that the main difference between these two groups is the index of "meancurv". So I searched online for the papers described "meancurv" of using FreeSurfer package, however, most of the papers reported an index---gyrificaiton, some of the gyrificaiton was calculated from "absoult mean curvatura", for example articles from Dr. Luders (A curvature-based approach to estimate local gyrification on the cortical surface, NeuroImage, 2006, 29, 1224). Then I looked for how to calculate "meancurv" in FreeSurfer, I found that "The curvature in general is measured as 1/r, where r is the radius of an inscribed circle. Since mean curvature is the average of the two principal curvatures it has the units of 1/mm. The Gaussian curvature is the product of them, so it is 1/mm^2". I am confused about these two concepts of "mean curvatura", could you help me to understand the "mean curvatura" in FreeSurfer? What is the biological meaning of this index, does it share the same anatomical meaning with Dr. Luders'? Could I use "mean curvatura" from FreeSurfer represent Gyrification Index? Thanks all of you so much. Hui Li

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Smooth overlay in command line
by Dorian P. 23 Mar '17

23 Mar '17

Is it possible to set the smooth overlay option (i.e. no of iterations) from command line instead of freeview? I am taking some screenshots that would look nicer with a smoothed overlay. Dorian

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