Freesurfer March 2023

freesurfer@nmr.mgh.harvard.edu

104 participants
154 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.

4 11

SAMSEG choice of the input
by Giulio Siracusano 10 Sep '23

10 Sep '23

External Email - Use Caution Dear Experts, I'm trying to understand what is the best input choice for running SAMSEG --recon in order to have the closest results as possible when compared against ASEG after executing (separately) an instance of recon-all all (and the raw input files in NIFTI format). I'm very well aware that ASEG and SAMSEG are different methods. I'm using the aseg.stats file as a results of the recon-all all command (here renamed as aseg.recon-all.stats for an easier identification). These stats should be my reference. Currently I've run the samseg command using the following input variants: 1) raw input file (brain MP-RAGE sequence) converted into a mgz archive (Raw.mgz). samseg --t1w ./Raw.mgz --s 002_S_0685_DIRECT --recon --refmode t1w The corresponding results are attached into (samseg.direct.stats) 2) This time I've used the file T1.mgz which is one of the intermediate results generated after running recon-all -autorecon 1. Specifically, this is the output of (mri_normalize <https://secure-web.cisco.com/1JV3nYNrViePm1qpOtzuMUtCndnVtCut-gp7OyXxNuXIOk…> -g 1 -mprage nu.mgz T1.mgz). samseg --t1w ./T1W/T1.mgz --s 002_S_0685_DIRECT_T1W --recon --refmode t1w The corresponding samseg.stats file is attached and called (samseg.direct.t1.stats). 3) this time I've used the file brainmask.mgz which is the last intermediate result generated after running recon-all -autorecon 1. Specifically, this is the output of mri_watershed <https://secure-web.cisco.com/1DjG5BDGTEbHYOWKmd4lc63SOmX8IrmziV9_NRWhpCskwO…>. samseg --t1w ./brainmask.mgz --s 002_S_0685_DIRECT_BRAIN --recon --refmode t1w The corresponding samseg.stats file is attached and called (samseg.brain.stats). I've noticed that the SAMSEG stats file (samseg.brain.stats) as obtained when using the brainmask.mgz as input file is the closest with the ASEG statistics (aseg.recon-all.stats). I also observe that the unknown volume is the lowest (# Measure Unknown, 5329.102436, mm^3) when using brainmask.mgz as input for SAMSEG, whereas is higher (Measure Unknown, 325302.894793, mm^3) when using T1.mgz as input file and is the highest (Measure Unknown, 946924.354060, mm^3) for the raw input. I know that for running recon-all we use the raw input files (for example, in NIFTI format), but I wanted to know what is the best possible configuration for SAMSEG in terms of input file in order to have the closest match between SAMSEG and ASEG statistics. Could it be possible to use the intermediate result T1.mgz or brainmask.mgz as input file for running samseg command? Is it a technically correct procedure? Do we need to use only the raw data as input for running samseg --recon command? Hope this is clear Regards GS

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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.

2 6

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

2 4

-gcareg dropped from -autorecon2-volonly
by Christopher Markiewicz 06 Apr '23

06 Apr '23

External Email - Use Caution Hi all, This is a duplicate of a bug report on GitHub (https://secure-web.cisco.com/1C5EnDIMtZh6wk0SJMqe8l166ycKmSdnL5atT3CIHDPAY1…) `DoGCAReg` was removed from `-autorecon2-volonly` in commit 4b9af5fc8c559e944400b885ef89f3682f94e0da, but this seems unrelated to the commit message. It's still in `-autorecon2`. Is there a reason it shouldn't be present, or was this a mistake? This issue affects versions 7.3.0+. Apologies for doubling up if you saw it; my impression is the mailing list is more actively monitored. Best, Chris

2 5

FLAIRpial bug
by Silvia De Francesco 04 Apr '23

04 Apr '23

External Email - Use Caution Dear developers, We encountered the bug related to the analysis with FLAIR in recon-all (recon-all -s ${subj} -i T1.nii.gz -FLAIR FLAIR.nii.gz -FLAIRpial -all). We obtain a worse segmentation with FLAIR than only with T1. We use FreeSurfer v. 7.3.2 We also tried to run the analysis placing the line PlaceMMPialSurf --mm_min_inside 50 --mm_max_inside 200 --mm_min_outside 10 --mm_max_outside 50 in the global-expert-options.txt file in the $SUBJECTS_DIR and run recon-all -s ${subj} -FLAIRpial -autorecon3, the output seems better but the pial is ever worst than with only T1. What does the values of mm_min_inside mm_max_inside mm_min_outside mm_max_outside mean? Some suggestions to solve this problem? Thank you Silvia

1 1

Which motion correction parameters are used in FSFAST?
by Andy Kim 03 Apr '23

03 Apr '23

External Email - Use Caution Dear FreeSurfer Developer, Hi. Thanks to FreeSurfer, I could perform surface-based activation analysis with FSFAST. Now I want to do surface-based functional connectivity analysis. For the sake of consistency, I want to use the same nuisance regressors as used in FSFAST. Unfortunately I'm stuck in motion correction parameters. According to https://secure-web.cisco.com/10LyHLSQ2Psfux7V-2TqU0TpTUpRE9gROQ8dm_KryluL_Q…, motion correction parameters are stored in mcprextreg. Since there are 6 columns, I guess they are 3 translations and 3 rotations. On the other hand, none of them are in mcAll, X.mat. What are the 18 motion correction parameters in X.mat? and which motion correction parameters are used as nuisance regressors in FSFAST? Thanks in advance. Kind regards, Andy (Junghyun) Kim

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Finding non-contiguous labels within an annotation
by Colleen Hughes 03 Apr '23

03 Apr '23

External Email - Use Caution Hello, I have an fsaverage5 parcellation/annotation based on Schaefer 200 (attached). The parcel boundaries are supposed to be adjusted iteratively resulting in 200 contiguous parcels with new boundaries. In this person, it is clear from plotting in freeview that 1 vertex from a visual parcel migrated to be surrounded by the SOM (blue) and VAN (violet) network on the lateral side (same hemisphere). This doesn’t happen in all subjects, so I’d like to write a function to find this and similar parcels that are not contiguous in a more automated fashion. So far, I’ve used the matlab read_annotation.m function to count vertices per parcel but that’s not quite right because it treats all vertices with the same label as the same thing. Not sure if there is a way to identify neighboring vertices so I can see if any have the same label (contiguous) or not. I investigated mri_surfcluster but I’m not sure how to make it treat the annotation as the input. Perhaps there is a way to project the values (1-200) associated with each label to their vertices. And then mri_surfcluster requires contiguity so it may identify if there is a mismatch between the expected # of parcels and observed # of clusters. I am using freesurfer 7.3.2, Matlab 2020a, M1 iMac. Any thoughts on how to identify non-contiguous vertices within a parcellation? Thank you, Colleen -- Colleen Hughes, PhD Postdoctoral Researcher Laboratory of Brain and Cognition Montreal Neurological Institute-Hospital McGill University

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Freesurfer March 2023