Freesurfer April 2023

freesurfer@nmr.mgh.harvard.edu

80 participants
105 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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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.

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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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09 May '23

External Email - Use Caution I registered a subject to mni space using the mri_cvs_register command with the --mni flag. However, the output files do not include a new aparc.a2009s+aseg.mgz. I wanted this atlas overlayed on the mni registered subject so I could extract one of the labels. Is this possible? Thanks, Carlos

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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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freeview rh and lh overlay_mask files both showing in the lh hemisphere
by Jewelia Karina Yao 05 May '23

05 May '23

External Email - Use Caution Hi FreeSurfer Developers, I'm trying to use freeview to load the rh and lh inflated surfaces together with overlays and overlay masks. I'm able to this separately and successfully for each hemisphere, but when I try to load the hemispheres together, both of the overlay_mask files show up on the left hemisphere and not the right hemisphere. The following is the command I'm using: freeview -f ${SUBJECTS_DIR}/${SUBJECT}/surf/rh.inflated:curvature_method=binary:overlay=rh.phase.mgz:overlay_custom=1.57,153,0,0,2.20,255,0,0,2.83,255,255,0,3.46,0,255,255,4.08,0,0,255,4.71,0,0,102:overlay_threshold=1.57,4.71:overlay_color='clearlower','clearhigher',colorscale:overlay_mask=${SUBJECTS_DIR}/${SUBJECT}/label/rh.ve_20pct.thresh.label \ -f ${SUBJECTS_DIR}/${SUBJECT}/surf/lh.inflated:curvature_method=binary:overlay=lh.phase.mgz:overlay_custom=1.57,153,0,0,2.20,255,0,0,2.83,255,255,0,3.46,0,255,255,4.08,0,0,255,4.71,0,0,102:overlay_threshold=1.57,4.71:overlay_color='clearlower','clearhigher',colorscale:overlay_mask=${SUBJECTS_DIR}/${SUBJECT}/label/lh.ve_20pct.thresh.label I've tried running this with 7.1.1 and 7.2.0 on Mac 10.15.7 and Linux w/Ubuntu 22.04 but still run into the same issue. Let me know if there's something I'm missing or if there's a better way to troubleshoot. Thanks! Jewelia

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contrast-FSGD question
by Fred d'Oleire Uquillas 03 May '23

03 May '23

External Email - Use Caution Dear Fs support, If I have the following FSGD with 4 classes and 3 variables, and I'd like to run an interaction of ROIa x ROIb controlling for the third covariate (eTIV), would I use the following contrast? [0 0 0 0 0.25 -0.25 -0.25 0.25 0.25 -0.25 -0.25 0.25 0 0 0 0] For the interaction of ROIa x ROIb x class + eTIV. Thank you so much in advance for your help! All the best, Fred

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Re: [Freesurfer] dcmunpack behavior with scouts
by Douglas N. Greve 02 May '23

02 May '23

External Email - Use Caution I've attached a new version of dcmunpack. Try running this with -keep-scouts and without -keep-scouts Let me know if this runs successfully in both situations (I'm using you as my tester:) On 4/18/2023 10:51 AM, Proulx, Jean Sebastien wrote: > > Sorry for the late follow-up. > > Yes, that is what I’m doing. With dcmunpack -auto-runseq I convert > everything, then use the log/series-info.dat to do further renaming to > BIDS—at least that is what I am trying to, but this is another topic. > > Thanks for the help and > > Have a very good day! > > Sébastien >

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Freesurfer April 2023