Freesurfer February 2023

freesurfer@nmr.mgh.harvard.edu

85 participants
122 discussions

Unit of the Numbers in cache.th40.neg.y.ocn.dat
by Na, Xiaoxu 17 Feb '24

17 Feb '24

External Email - Use Caution Dear Freesurfer Experts, As I'd like to extract the average value of each subject in the cluster after running group analysis, may I know the unit of these numbers? Since the one I'm running is surface area, and the cluster is 444mm^2, all the numbers in the file cache.th40.neg.y.ocn.dat is in the range of [0.55 1.05], may I know if this is correct and if so, how the unit is for those? Thanks a lot! ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx 1 -4.8321 40067 444.11 -58.1 -16.6 -23.9 0.0002 0 0.0004 670 -2784.11 Regards, Xiaoxu ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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How is cache.th40.pos.sig.voxel.mgh computed, exactly?
by Mark Ebden 04 Aug '23

04 Aug '23

External Email - Use Caution Hi, I was wondering if anyone knows how the numbers in cache.th40.pos.sig.voxel.mgh are computed, or where I'd look to learn this. There is a one-liner in the documentation<https://secure-web.cisco.com/1R2vQZUhHj-zAreoIH8kMlOuUPh5jYx8TyPmfmDzbM1Dl-…> but I'd like the mathematical details of the correction etc. so I can determine what the final numbers (from 0 to 1) represent. I've noticed from browsing the plot in FreeView that significant areas have values close to 1, which is puzzling. Thanks if you could point me in the right direction. Kind regards, Mark Mar [cid:b7c6e65e-f85e-4206-aaa0-1ec00aa2fde2] Mark Ebden, D.Phil (Pronouns: He/Him) Research Analyst The Hospital for Sick Children 555 University Ave, Toronto ON M5G 1X8 P 416.888.0841 [cid:3b077a75-32bb-46ed-b1d2-b74379e6a8d1]<https://secure-web.cisco.com/17-WtJwO2uIWyZ7umzDRCiH0I5Q1NZ-tfYcx_zx9tznEDb…> ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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Tracula statistics outputs for version 7.2
by King-Wai Chu 18 Jul '23

18 Jul '23

External Email - Use Caution Hi, Upon further examination of pathstats.byvoxel.txt and pathstats.overall.txt, I have 2 more questions. Since my previous 3 questions still have not been answered, I'm including them here so that they are all in one place. The 2 new questions are 4) and 5), my previous 3 questions are appended after. 4) I have noticed that the averages of AD, RD, MD and FA in pathstats.byvoxel.txt are exactly the same as the *_Avg_Center in pathstats.overall.txt. According to the tutorial, *_Avg_Center in pathstats.overall.txt is the "average over highest-probability path only" and the AD, RD, MD and FA in pathstats.byvoxel.txt is the value at the "position on the maximum a posteriori path". Does it mean that "highest-probability path only" and "position on the maximum a posteriori path" are the same or one of them should be changed to the other one? 5) Are the averages of AD_Avg, RD_Avg, MD_Avg and FA_Avg in pathstats.byvoxel.txt suppose to match *_Avg(average over the entire support of the path distribution) in pathstats.overall.txt? When I removed the duplicate points in pathstats.byvoxel.txt, the averages of AD_Avg, RD_Avg, MD_Avg and FA_Avg come very close to the value of *_Avg in pathstats.overall.txt I don't think I can calculate the averages by including the duplicate points in 4) but removing them in 5). Either including them in both or not at all. Questions from my previous email. 1) There are duplicate points in pathstats.byvoxel.txt, is it normal? I didn't try it on all 42 tractcs. For the few I've looked at, they all have duplicate points. I used the default setting in the config file to run trac-all. 2) When I do along-tract statistical analysis, sig.mgh and z.mgh are 1D files. When embed the sig.mgh and z.mgh statistical maps from the analysis into the template .trk (*.display.trk, which is 3D), it seems to me that sig.mgh and z.mgh don't have enough information to give *.display.trk the voxel values for the *.overlay.trk. There is no one-to-one voxel corresponding between sig.mgh and *.display.trk. What am I missing? Or what's the embedding process do? 3) When I convert .trk(*.overlay.trk, for example) to nii.gz or ascii using dmri_trk2trk or mri_convert the voxel values of the .trk file don't get converted into the .nii.gz or ascii file, only the x,y,z coordinates are converted. Is there a way to get the voxels values of the .trk file when converting to .nii.gz or ascii format? Thanks, King-Wai -- King-Wai Chu, Ph.D. Program Analyst Mental Illness Research, Education and Clinical Center (MIRECC, VISN3) James J. Peters Dept. of Veterans Administration Medical Center (OOMH) 130 W. Kingsbridge Road Bronx, NY 10468

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different results for gtmpvc with different tracers
by Federica Di Antonio 09 Jun '23

09 Jun '23

External Email - Use Caution Dear experts, I hope this email finds you well. I run the pvc correction with mri_gtmpvc for subjects data obtained with two different PET tracers. In gtm.stats.dat, for every subject and every region, the number of voxels evaluated for amyloid tracer is approximately twice the volume evaluated for the second tracer. I'd expect that the volume of a region for the same subject doesn't change with the tracer. Do you think this error can result from previous errors in the analysis? Or is it in some way plausible? Thank you for your patience, Federica

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PETsurfer: PVC without psf of the scanner
by Federica Di Antonio 08 May '23

08 May '23

External Email - Use Caution Dear experts, Few weeks ago i wrote to this mailing list but I didn't receive any answer, so I'll try again: mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask 1 .01 --mgx .01 --o gtmpvc.output If I put psf to 0, there is no PVC, and the same happens if I don’t put that flag at all.t all Is able mri_gtmpvc to evaluate the fwhm without receiving it from the user? I apologize for the repetition, Thanks for your patience, Federica

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How to find topological defects
by KennethSPrice 13 Mar '23

13 Mar '23

External Email - Use Caution Hello Freesurfers, I've found the tutorial for editing wm.mgz (https://secure-web.cisco.com/1_VE6Du8jnccjig75E4hpWkJh1_YR3uP_xPzMfYusO6K01…) I'm curious if there is a way to find the topological defects easily? Is there a text file in the stats folder, for example, which locates the coordinates of topological defects? Thanks, Ken Sent with [Proton Mail](https://secure-web.cisco.com/1KF2a2rKWu_5CevMXrlKZAUb4EzG3VQGOQnGyxhP… secure email.

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Error using chol
by Caspar M. Schwiedrzik 13 Mar '23

13 Mar '23

External Email - Use Caution Hi! I am running into an issue with fast_selxavg3b. I am attempting a first level PPI analysis. The command is mkanalysis-sess -fsd bold -native -delay -2/2 -notask -TR 2 -polyfit 6 -analysis [xxx] -funcstem [xxx] -runlistfile mooneyppi.list -nuisreg motion.dat 6 -tpef tpef_dvars.dat -acfbins 5 -acffwhm 0 -mask [xxx] -force -nuisreg juice.dat 1 -nuisreg fixation.dat 1 -taskreg ppi.dat 4 I get the following error: GLS Residual Pass run 1 t= 0.0 Error using chol Matrix must be positive definite. Error in fast_selxavg3b (line 942) Wseg = inv(chol(toeplitz(acfrun))'); Before that, I am getting several warnings of this kind: > In fast_selxavg3b (line 895) Warning: Matrix is singular, close to singular or badly scaled. Results may be inaccurate. A few of them, but not run 1, have RCOND = NaN. This is with versions 7.2 and 5.3. I found one previous conversation on the mailing list regarding this error in the context of a resting state analysis, but no conclusion. Any advice would be appreciated. Thanks! Caspar

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white and pial surfaces of the hippocampus
by Khazar Ahmadi 13 Mar '23

13 Mar '23

External Email - Use Caution Dear FS experts, Id like to delineate WM and pial surfaces in the hippocampus and subsequently bin GM layers of it (like the approach that is commonly used for laminar analyses in V1 or other sensory cortices). I think the current output of recon-all does not contain WM/pial surfaces in subcortical regions. Have tried running the FS hippocampal module. It generates subfields (in .mgz format) and volume estimates but I cannot find any surface-based output. Is there a way to obtain pial and WM surfaces in this region? I have another question regarding surface-based representation of the subfields. Based on the paper by Sämann et al., 2020 (see the link below; Figure 6), I think it is possible to have surface-based visualization of the subfields using ENIGMA, but I could not find additional documentation on that. Any ideas on how to obtain surface-based segmentation of the hippocampus would be greatly appreciated. Thanks a lot, and best wishes, Khazar https://secure-web.cisco.com/162vGALDRGyKKidOcJ8MJ6vwNqV2G11ikgdRoQJk8awcbY… -- Khazar Ahmadi, PhD Postdoctoral Researcher, Institute of Cognitive Neuroscience, Department of Neuropsychology, Ruhr University Bochum, Bochum,Germany

2 1

VirtualBox pass code
by Jennifer Kilmer 07 Mar '23

07 Mar '23

External Email - Use Caution Hello, Is it possible to have the virtual box passcode sent to me? Thank you in advance! Jennifer

1 1

MRI image quality metrics
by MANSON ERIC NAAB 06 Mar '23

06 Mar '23

External Email - Use Caution Dear FreeSurfer experts, Please, I need your assistance and guidance on calculating the contrast-to-noise ratio (CNR) and signal-to-noise-ratio (SNR) of White matter, Gray matter, and CSF of the brain after recon-all. Thank you

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Freesurfer February 2023