Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

Re: [Freesurfer] Questions about surface coordanates
by Islem Rekik 30 Aug '16

30 Aug '16

Hi all, I have a similar problem using Paraview: When I visualize the surface lh.pial and the anatomical image brainmask.mgz using FreeView they nicely overlap; however, after I convert lh.pial to lh.pial.vtk and brainmask*.mgz* to brainmask*.mha* and visualize them using Paraview, they are in different spaces. Do I need to apply a transformation matrix to lh.pial using the command line mri_surf2surf so the VTK surface will overlap with the image when using Paraview? I find this quite confusing. Thanks! Kindly, Islem On Tue, Aug 30, 2016 at 9:21 AM, Douglas Greve <greve(a)nmr.mgh.harvard.edu> wrote: > tksurfer always uses the ?h.orig coordinates. Also keep in mind that the > vertex index is 0-based whereas matlab is 1-based. When you click on a > point, you should see something like the following print out > selected vertex 123491 out of 163842 > current -39.11 15.65 11.26 > orig -55.67 -10.37 19.95 > pial 0.00 0.00 0.00 > white -55.76 -10.29 19.93 > > > > > On 8/30/16 5:12 AM, Dongnandi wrote: > > Dear Experts, > > I tried to extract vertex coordinates information from > ‘fsaverage/surf/lh.pial’ file using matlab function ‘read_surf’, but I > found that the coordinates returned by the function are different from what > I saw in tksurfer, here are the screenshots: > > The vertex index starts from 0 in tksurfer, so I select the second > elements in matlab. Why is the result different from what has been shown in > tksurfer(also different in freeview)? Which one should I report? > > Is there any way to transform the surface coordinates to the MNI152 space? > > > > Thank you very much! > > Dong > > > > > _______________________________________________ > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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. > > -- Dr. Islem Rekik; MSc, PhD IDEA Lab, UNC-Chapel Hill Biomedical Research Imaging Center Chapel Hill, NC 27599

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rfMRI and T2w image
by Dev vasu 30 Aug '16

30 Aug '16

Dear Sir, In order to run my structural analysis pipeline , i require T2w images, but unfortunately we have not performed T2w scans , my colleague suggests we can use rfMRI instead T2w images Could you please let me know if i can use rfMRI image instead of T2w image?. Thanks Vasudev

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volume, surface area, and thickness
by Woo-Suk Tae 30 Aug '16

30 Aug '16

Dear FreeSurfer experts and developers I am confronted with some technical question of a reviewer. I am not sure about "volume = thickness-by-surface area" and the review's opinion (attached below) about volume, surface area, and thickness was correct. Any comments from FreeSurfer's experts would help me. Sincerely yours Woo-Suk Tae Seoul, Korea I added the reviewer's comments. --------------------- 1. Volume/thickness: The authors cite many papers that show volume and thickness differences in MDD. The unresolved part here, however, is the RELATION between cortical thickness and cortical volume: There is no doubt, that both measures are found affected in MDD. This is, because cortical thickess multiplied by the surface area of a gyrus results in its volume, so volumse = thickness-by-surface area. Surface area values themselves are technically more noisy and usually thus less sensitive (due to the problem of false attributions to an area). So, volume is influenced by thickness and surface and is the less specific measure. If a volume effect is detected in a study, it is unclear, if it is driven by thickness, or surface area, or both. In this respect, the study of Schmaal et al. is telling, as it analyzed BOTH measures, finding only thickness effects of MDD, and (practically) no surface area changes except for adolescent MDD. In the adolescent MDD samples gross surface area differences were detected. This means, that the question of "superiority" is rather a question of "specificity": (Cortical) volume findings in adult MDD are mostly driven by thickness differences and are in on way independent from thickness differences. In this respect, the authors should follow the basic geometric principles of morphometry and point out the relatedness of the two. They can simply check this in their FreeSurfer variables (e. g. for total grey matter volume). Not reporting surface area is leaving an interpretational gap as surface area differences could in addition drive volume differences. The authors may want to decide not to present surface area results, but then they should discuss this as limitation to disentangle the origin of volumetric (cortical) effects. This seems important as methylation effects and FKBP5 interact with early life time stress, so effects on surface area as seen in adolescent MDD highlight that surface area effects could play in. ---------------------------------------------------------------------------------------- Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Medical Research Center Anam Hospital, Korea University Medical Center, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6831 email: woosuk.tae(a)gmail.com, woostae(a)gmail.com <woostae(a)naver.com> ----------------------------------------------------------------------------------------

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Re: [Freesurfer] questions about split region from the 7 and 17 networks, from huasheng liu
by Thomas Yeo 29 Aug '16

29 Aug '16

Hi Huasheng, Here you go: https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_Sp… I am also cc-ing the freesurfer list. --Thomas On Tue, Aug 30, 2016 at 11:05 AM, liuhas_20040125 <liuhas_20040125(a)163.com> wrote: > Dear professor Yeo : > > > > My name is Huasheng Liu, I'm from central south university, china. > > I read the emails you wrote to Yu-chieh Chen in freesurfer's mail-archive, > > (from: > https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41288.html) > > and you provided a link to files you extracted individual regions from the 7 > and 17 networks: > > > > " I have previously extracted individual regions from the 7 and 17 > networks. You can download them here > (https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_JNeurophysiol11_SplitLabels.z…)" > > > > > > It seems the link has broken, and i can't get zip file, can you kindly > give me a copy? > > > > > > Thank you very much for read this email and sorry for occupied your time. > > > > Best wishes! > Huasheng Liu > > > > 2016-08-30 > ________________________________ > liuhas_20040125

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Reproducibility of freesurfer analyses across different version of linux
by Knut J Bjuland 29 Aug '16

29 Aug '16

Dear FreeSurfer experts,I found this paper about named “Reproducibility of neuroimaging analyses across operating systems” (Glatard et al., 2015). There were differences in cortical morphometry like cortical thicknes between images proscced in the same version of freesurfer with different version of Linux or glibc for Freesurfer, and according to the paper, it was caused by how different version of glibc handles small single precssion floating numbers. I have therefore some questions. Are there plans for freesurfer to use double floating numbers in steps that may be affected by numerical stability? Or can this problem be solved by using staticall linking glibc into Freesurfer? Best regards Knut Jørgen BjulandPhD candidateNTNU

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Results different between mean-centered and raw covariates -- glm_fit
by Corinna Bauer 29 Aug '16

29 Aug '16

Hello all, I am wondering why results would change completely for between group volume analysis when using demeaned/mean-centered ICV compared to using ICV as a covariate in mri_glmfit? See the figures below. Does demeaning the covariate inherently change the results comapred to the raw covariate values? Thanks Corinna

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wm.mgz enclosed in pial/white surface
by Fire Tech 29 Aug '16

29 Aug '16

2 1

How to transfer the VTK cortical surface to the diffusion space?
by Islem Rekik 29 Aug '16

29 Aug '16

Hi there! Since this is my first time using FreeSurfer, I found it quite challenging to get the handle on the different coordinate systems used. My goal is to generate vtk files where the vtk cortical surface and the vtk fiber tracts are in the same space (for one individual subject). Basically, I used recon-all to generate the cortical surfaces and trac-all to generate dtifit_FA.mgz and dtifit_V1.mgz for tractography in the original diffusion space. I used the transformation matrices generated in dmri/xmfs to transfer the cortical surface into the diffusion space, but not of them seem to work. What I find quite confusing is that when I visualize the surface lh.pial and the anatomical image brainmask.mgz using FreeView they nicely overlap; however, after I convert lh.pial to lh.pial.vtk and brainmask.mgz to brainmask.mha and visualize them using Paraview, they are in different spaces. To do so, I used the command line mri_surf2surf so the surface will overlay with brainmask.mha image when using Paraview, but none of the transformation matrices seems to warp the surface onto the anatomical (structural FreeSurfer) space. I also tried to warp it to the diffusion space and the anatomical original space, but it never overlapped with the images nested in these respective spaces. It is always floating somewhere else! I would like to know which transformation I need to: 1. apply to have the VTK surface overlap with the brainmask.mha image in the anatomical space and, 2. apply another transformation to transfer the VTK surface to the diffusion space where I perform tractography. Also, does TRACULA perfom whole brain tractography? I really appreciate your help! Kindly, Islem

1 0

Hippo campal subfield segmentation
by Boris Marendic 27 Aug '16

27 Aug '16

Hello, I am new to using FreeSurfer, and need a little help. I have downloaded and installed FS 2 days ago (from https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall ). To verify the installation I proceeded with all steps on the first page, and everything worked fine. Then I decided to try the hippo campal segmentation, and I tried the scripts on the following page: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation?hi ghlight=%28hippo%29 . Running the first script recon-all -s bert -all -hippo-subfields resulted in a 20+ hour run of FS which completed successfully. Then I started the kvlQuantifyHippocampalSubfieldSegmentations.sh to analyze the bert results, and it died on me. I looked into the errors and into the script itself using an editor, and I found out that the script wants to descend (or "cd") into some folders named "left" and "right". However, running the "recon-all" script on the test subject bert (from above) did not generate "left" and "right" folders at all. I looked through the archived messages and did not find an answer to my issue. Can you help me out here? Is this a known bug and are there updated scripts that I should maybe download? The output of the kvlQuantifyHippocampalSubfieldSegmentations.sh script is provided below Thank you in advance Boris Marendic ---------------------------------------------------------------------------- ----------------------------- OUTPUT OF THE SCRIPT kvlQuantifyHippocampalSubfieldSegmentations.sh > kvlQuantifyHippocampalSubfieldSegmentations.sh /home/freesurfer/subjects resultsDirectory /home/freesurfer/subjects cd /home/freesurfer/subjects numberOfSubjects: 12 resultsDirectory /home/freesurfer/subjects startIndex: 1 endIndex: 12 Sides to evaluate: left right Current subject: bert/ cd bert/ Quantifying subject bert/ left Doing left side cd left /home/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: cd : left: No such file or directory failed to do cd left

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Hippocampal Subfields for T2-FLAIR images
by Hari Guragain 27 Aug '16

27 Aug '16

Dear Freesurfer community, I am trying to get the segmentation of hippocampal subfields by using the development version of the freesurfer. I have few normals with T2-FLAIR images along with T1 whose subfield volume needs to be calculated. I am wondering if the algorithm that calculate the hippocampal subfields can handle the T2-FLAIR? According to the wiki ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) it can handle the T2 but didn't say anything about the T2-FLAIR. It would be great if someone clarify this. Thank you, Hari Guragain

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