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Coordinate of orig.mgz
by Kim, Gwang-Won 27 Oct '20

27 Oct '20

Dear expert, I obtained “sig.mgh” from resting fMRI data using Freesurfer. Then, I opened the file using tksurfer. I selected vertex 156439 out of 163842 in the file “sig.mgh”. In the terminal, there were several coordinates as followings: Selected vertex 156439 out of 163842 Current -36.76 -22.70 -10.66 orig -59.96 -33.44 8.59 pial 0.00 0.00 0.00 I have a question for orig “-59.96 -33.44 8.59”. The coordinate (x=59.96 y=-33.44 z=8.59) is in the ~/freesurfer/7.1.1/subjects/fsaverage/mri/orig.mgz, right? Thanks, Gwangwon

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Re: [Freesurfer] [EXTERNAL] Freesurfer Digest, Vol 200, Issue 36
by Basavaraju, Rakshathi 27 Oct '20

27 Oct '20

External Email - Use Caution Re:"Re: [Freesurfer] Creating ROI from sig.mgh" Dear Douglas, Do you recommend running mri_glmfit-sim on each individual subject? I have a significant cluster in sig.mgh derived out of a contrast involving many subjects in vertex-based lgi analysis. Now I want an ROI out of the significant cluster (p<0.001 uncorrected) and extract lGI values from this created ROI from each subject. Dr. Rakshathi Basavaraju (MD Psychiatry) Postdoctoral Research Scientist Taub Institute for Research on Alzheimer's Disease and the Aging Brain Columbia University Medical Centre 622 West, 168th Street, New York - 10032 E-Mail: rb3419(a)cumc.columbia.edu<mailto:rb3419@cumc.columbia.edu> https://indiaalliance.org/fellow/rakshathi-basavaraju ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Tuesday, October 20, 2020 2:32 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [EXTERNAL] Freesurfer Digest, Vol 200, Issue 36 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Problem of the Mapping Label to the Subject (Douglas N. Greve) 2. Re: Creating ROI from sig.mgh (Douglas N. Greve) 3. Re: Problem of the Mapping Label to the Subject (Wang, Ruopeng) 4. Re: Problem of the Mapping Label to the Subject (???) 5. fwhm values for gyrification index analysis (vittal korann) 6. Tracula error: run list is longer than subject list (Shanika Jayakody) 7. Re: Exited with errors, segmentation fault (Hoopes, Andrew) 8. mkanalysis-sess and mkcontrast-sess scripts for FIR analysis (Fang, Angela,Ph.D.) 9. Re: surf pial_lgi not created in version 7.1.0 (Kathy L. Pearson) 10. Re: Tracula error: run list is longer than subject list (Yendiki, Anastasia) 11. replace the vertex_label_index in .annot file ( 1248742467 ) 12. why can't I receive a reply from others in my mailbox? ( 1248742467 ) 13. Statistic Difference Region on the Fsaverage Turned into No Statistic Difference after Mapping onto the Subjects (???) 14. Problem with dcmunpack on freesurfer (Praveen Raghunathan) 15. Error during skullstripping: numerical result out of range (Hye Min Shin) 16. Re: Problem with dcmunpack on freesurfer (fsbuild) ---------------------------------------------------------------------- Message: 1 Date: Mon, 19 Oct 2020 12:22:50 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Problem of the Mapping Label to the Subject To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <16e556fb-a4e8-01b4-87fe-15d672cd645a(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" There is no QDEC in 7.X, we have abandoned it. On 10/19/2020 11:09 AM, ??? wrote: > > ????????External Email - Use Caution > > Thanks for your help, I have tried FS 7.1.1, while there is no Qdec > command when I tried FS 7.1.1 in the terminal window. How should I > start the Qdec in the 7.1.1 version. > > Best wishes > Mengjun Li > > > > -----????----- > *???:*"Wang, Ruopeng" <RWANG4(a)MGH.HARVARD.EDU> > *????:*2020-10-19 21:07:45 (???) > *???:* "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> > *??:* > *??:* Re: [Freesurfer] Problem of the Mapping Label to the Subject > > I think this is a bug in freeview from FS 6.0.0 that has been > fixed in 7.x. Would it be possible for you to try FS 7.1.1? A > quick workaround you may try first is to change the offset for the > inflated surface to 0 0 0 in freeview 6.0.0. > > Best, > Ruopeng > >> On Oct 19, 2020, at 2:38 AM, ??? <mengjun(a)csu.edu.cn >> <mailto:mengjun@csu.edu.cn>> wrote: >> >> ????????External Email - Use Caution >> >> >> >> >> >> Dear FreeSurfer Developers: >> >> My name is Mengjun Li, I am a MD in the Second Xiangya >> Hospital, Central South University. I compared the cortex, >> area, volume in the mild traumatic brain injury patients with >> health control by the FreeSurFer and found the problem when >> mapping label to the single subjects. >> >> There is statistic difference in the area and volume >> between?the mild traumatic brain injury patients and the >> health control, I defined the?statistic difference region as >> a label on the fsaverage and mapped this label to subjects by >> the Qdec. Although the label defined on the fsaverage was >> mapped onto all subjects successfully,the label in the >> subjects did not match well with the inflated cortex of the >> subjects. At the same time, the volume and area value of the >> label have been extracted in every subject and I found that >> there is no statistic difference between the mild traumatic >> brain injury patients and health control. I have checked the >> segmentation of every subjects and it was a good job done by >> FreeSurFer. Attached figures illustrated the label mapping >> results. >> >> Figure 1: the label defined on the fsaverage >> Figure 2: the lateral view of the label in the subjects >> Figure 3: the inferior view of the label in the subjects >> >> FreeSurfer >> version:?freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c >> Platform: macOS High Sierra >> >> I am sending this email for help since I am not sure how to >> fix this problem. Looking forward to hearing your reply! >> Thank you very much! >> >> Best wishes >> Mengjun Li >> Second Xiangya Hospital >> Central South University. >> >> >> >> >> >> <Figure 1.png><Figure 2.png><Figure >> 3.png>_______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e…

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Best mesh generation from hippocampus aseg segmentation
by Gonzalo Rojas Costa 27 Oct '20

27 Oct '20

External Email - Use Caution Hi: Which is the best library or software to create the hippocampus mesh from aseg segmentation? Sincerely Gonzalo Rojas Costa

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recon2-wm: does not start from -filled
by Wei Koo 27 Oct '20

27 Oct '20

External Email - Use Caution Hello FreeSurfer Developers, I am trying to recompute the surfaces after wm edits using this command line : recon-all -autorecon2-wm -hires -s subject_id , but when I do run that command, it starts at mri_normalization and not mri_filled which then gives me wm.mgz without the manual edits I've made. FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0 (also tried with freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0)

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mri_surf2vol method one
by Yixin Ma 27 Oct '20

27 Oct '20

External Email - Use Caution Hi Freesurfer experts, I'm trying to write the normals of the GM/WM meshes to the entire ribbon. We usually do it by: 1) Generate normal files from rh.white and lh.white mris_convert rh.white rh.white.gii mris_convert -n rh.white rh.white.normals.asc 2) Use matlab 'read_normals' function to read the normals and write individual directions xyz as a paint format file. g = gifti([path 'Analysis/' exam '/' subject '/surf/rh.white.gii']); norm = read_normals(g,[path 'Analysis/' exam '/' subject '/surf/rh.white.normals.asc']); write_wfile([path 'Analysis/' exam '/' subject '/surf/rh_normx.w' ],norm(:,1)); write_wfile([path 'Analysis/' exam '/' subject '/surf/rh_normy.w' ],norm(:,2)); write_wfile([path 'Analysis/' exam '/' subject '/surf/rh_normz.w' ],norm(:,3)); 3) Use mri_surf2vol method two to paint the normals into the ribbon. But the problem is that method two gives me lots of holes in the ribbon. I'm wondering if it's possible to use mri_surf2vol method one to paint the normals into the ribbon because method one does not leave holes in the ribbon. However, it seems like the overlay does not accept paint file format (rh_normx.w). The overlay in method one accepts rh.thickness as an input, as shown in the example on the website. I'm wondering how to convert the painting files to have the same format as rh.thickness? Thank you in advance, Yixin

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There is no view-label option after loading the .annot file
by 1248742467 27 Oct '20

27 Oct '20

External Email - Use Caution Hello, Fs my freesurfer version is 6,  I see others have the view button after load .annot file, But my version does not have this option.  Do I need to update the version? And I have installed fs6, can I install fs 7.1 on the same machine? What's more, After loading the .annot file in freeview, can I reset its name, index, color through view-label? Looking forward to your reply

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mri_nu_correct error: flar --uchar not recignized
by erbilnurhan 27 Oct '20

27 Oct '20

External Email - Use Caution Hello FreeSurfer Developers, I'm trying to compute volumetric data from MPRAGE images by using recon-all as decribed athttps://surfer.nmr.mgh.harvard.edu/fswiki/recon-all I've got the following message: mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 ERROR: flag --uchar not recognized Does anyone have any thoughts on how to trouble-shoot this problem? Also, I've attached the recon-all.log in case it's of any use. FreeSurfer version: freesurfer-darwin-macOS-7.1.1 (freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0) macOS high Sierra 10.13.6, x86_64 XQuartz 2.7.11 (xorg-server 1.18.4) recon-all.log: see attached Sincerely, Nurhan Erbil

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How is Total cortical gray matter volume calculated?
by Ian Hardingham 27 Oct '20

27 Oct '20

External Email - Use Caution Hi Freesurfers, Is "total cortical gray matter volume" from aseg.stats calculated based on the recon-all Surfaces? Or using a different method? I ask because I have been trying to calculate the grey matter volume based on the area between the surfaces, and I have been getting different results. Thanks, Ian

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Issue with extracted thickness value from significant cluster or peak vertex
by Julian Macoveanu 27 Oct '20

27 Oct '20

External Email - Use Caution Hi, I am using FS 7.1.0. After running the surface thickness GLM analysis I get one cluster after correction for multiple comparison showing a significant group difference. I want to make a plot illustrating this group difference. However, when using the mean values from: cache.th30.abs.y.ocn.dat, I don’t see the expected group difference in these values. Question 1) Are the subjects cluster mean values in y.ocn.dat adjusted for the covariates I used in the fsgd file? E.g. age, sex and TIV? Question 2) I inserted these mean cluster values from y.ocn.dat in SPSS and tried verify the statistics both with and without adjustment for covariates and did not get the expected significant group region which I expected in either case. Why is this? Question 3) I moved on to extract the thickness values from peak vertex in my significant cluster. For this I used mris_convert which I just wanted to be confirmed that is correct: mris_convert -c lh.thickness.fwhm15.fsaverage.mgh $freesurferdir/fsaverage/surf/lh.orig output.asc After extracting the thickness value for all subjects from the peak vertex as reported by the sig.cluster.summary , I still have the same issue as before, I find no group expected group difference. Interestingly, the significant cluster I found is part of the superior_frontal region in aparc2009. When I extract these values it almost shows significant group differences in the entire region, in line with the surface GLM findings. Thanks, Julian

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lh.white edits
by Wei Koo 27 Oct '20

27 Oct '20

External Email - Use Caution Hello FreeSurfer Developers, I am trying to make edits to the white matter segmentation. I have tried making edits to wm.mgz and repeating recon2-wm but I was wondering if there is a way to make direct edits to lh.white? I've searched the lists and did not seem to find anything regarding editing the surface directly.

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