Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

hippo sf segmentation 6.0 dev
by Vaz pandolfo, Renata 30 Aug '16

30 Aug '16

Dear Eugenio, I have a couple of questions regarding the hippocampus subfields segmentation on the dev FS 6.0 which I hope you could help me with. We are comparing the volumes of hippocampal subregions of patients and controls, and we would like to be as consistent as possible with the input so that the output reflects only the differences we expect to see. The problem is that we have a large number of controls but not all of them have the same sequences (T1, T2 or FLAIR) as the patients. So our questions are: If the T1s from some subjects have a 1x1x1 resolution and others have 0.8x0.8x0.8 isotropic resolution, do we have to create two groups of controls and patients for each sequence? In other words, does the resolution of the T1 affect the freesurfer segmentation in a way that we can't compare 1x1x1 with 0.8 x 0.8 x 0.8? Also, we would like to use T2s or FLAIRs as additional inputs to improve the results. Which sequence is preferably recommended? In our case, most controls and patients have the same FLAIR sequence, so to keep it consistent we would probably use FLAIR if that's worth it. Finally, we also have different T2s: some isotropic, some anisotropic and partial cooverage of the brain, and some anisotropic that are aligned to the hippocampus (resolution: 1x1x3, best resolution on coronal slices). Considering that they are just additional inputs, do they have to be consistent as well? In other words, should we *only* compare patients and controls that had the same T2 sequence as additional input and same T1 sequence as main input, or can we "mix and match" the additional inputs? Thank you in advance for your help, Renata

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Brainstem nucleus
by Alshikho, Mohamad J. 30 Aug '16

30 Aug '16

Hi Iglesias, Kindly, we would like to know if there are any methods in Freesurfer that can help to segment that brain stem nucleus. I mean output the nucleus automatically as a small masks, so these small masks can be used in other analyses (e.g. fMRI) I am thinking of creating masks for these nucleus depending on an atlas. I open the T1 image in Fslview and I create the mask for the nucleus of interest. But this is so hard, not accurate and time consuming. The reason for my question. We highly appreciate any suggestion! Best, Mohamad

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Re: [Freesurfer] rfMRI and T2w image
by Dev vasu 30 Aug '16

30 Aug '16

Dear sir, I was checking for your reply about my question in Freesurfer Forum but unfortunately i could not your answer although ":Freesurfer Digest, Vol 150, Issue 43 " Today's topics section indicates that you have replied to my question. Following is my question : 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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mri_glmfit-sim permutation testing running after 3 days!
by Ajay Kurani 30 Aug '16

30 Aug '16

Hi Freesurfer Experts, I am trying to use freesurfer's mri_glmfit-sim tool to run permutation testing on cortical thickness data (as recommended by Doug in my previous post: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.html ) Most of the tutorials I found were not related to permutation testing so the subsequent steps may be incorrect. Please let me know where I go wrong... 1) I first ran QDec to generate a folder for the analysis which would create the subsequent fsgd and y files needed my mri_glmfit-sim. I am running both left and right hemisphere cortical thickness analysis with 10mm smoothing. The following is for just the left hemisphere. Note I am doing a 3 group comparison, but for this 2 group ttest I manually centered the data based on the 3 group mean for age and education. 2) I ran the following command: /mri_glmfit-sim --glmdir ./HCvsPAT_lh_thickness_10mm/ --sim perm 10000 2 perm.abs.2 --sim-sign abs --bg 16 Prior to running the command above, from the y.fsdg file I deleted the fwhm estimate of 13mm since this was not correctly estimated (ACF with long tails). I assumed that by removing this estimate, it would force the permutation test to calculate based on the data but when looking at the log output I see the following which says fwhm 0: cmdline mri_glmfit.bin --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Avg-Intercept-thickness.mtx --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-Male-Female-Intercept-thickness.mtx --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-PD-MCI-Intercept-thickness.mtx --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-X-Gender-Group-Intercept-thickness.mtx --sim perm 625 2 ./HCvsPAT_lh_thickness_10mm//csd/perm.abs.2.j013 --y /home/akurani/Documents/PPMI/FS_Final/qdec/HCvsPAT_lh_thickness_10mm/y.mgh --mask ./HCvsPAT_lh_thickness_10mm//mask.mgh --sim-sign abs --fwhm 0 --fsgd ./HCvsPAT_lh_thickness_10mm//y.fsgd dods --surf fsaverage lh white --sim-done ./HCvsPAT_lh_thickness_10mm//csd/poll/done.perm.abs.2.j013 3)I started this a few days ago on a 16 core machine and it is still running in the terminal. I have 150 subjects in the analysis and specified 10000 iterations. In the terminal I assumed when I reach Poll 10000 it would be complete but currently I am at : Poll 13341 job 1 Thu Aug 25 12:03:51 CDT 2016 Questions: a) I am curious, is this going to run 10,000 simulations X 150 patients or does the Poll number not have anything to do with the number of iterations it is on? b) Did I run this procedure correctly? Was I incorrect in deleting the fwhm estimate from y.fsgd file generated by Qdec even though we know the estimate is incorrect since smoothness assumed a gaussian distribution as opposed to gaussian with heavy tails c) I noticed in the logfile the following warning: INFO: gd2mtx_method is dods Computing normalized matrix Normalized matrix condition is 5.65727 Matrix condition is 935.597 Found 136777 voxels in mask Reshaping mriglm->mask... search space = 89675.729228 ERROR: design matrix is not orthogonal, cannot be used with permutation. If this something you really want to do, run with --perm-force Poll 2 job 1 Tue Aug 23 22:58:18 CDT 2016 I am not sure if this means my simulation is incorrect? Thanks, Ajay

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

30 Aug '16

It is a software that visualizes VTK files and also "mha" images: http://www.paraview.org/ [image: Inline image 1] Thanks! I really appreciate your help! Islem On Tue, Aug 30, 2016 at 10:28 AM, Douglas Greve <greve(a)nmr.mgh.harvard.edu> wrote: > What is paraview? I would contact the developers. > > On 8/30/16 10:24 AM, Islem Rekik wrote: > > 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.e >> du/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 > > _______________________________________________ > 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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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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