Freesurfer June 2023

freesurfer@nmr.mgh.harvard.edu

75 participants
107 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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Re: [Freesurfer] MANCOVA + Posthoc Testing Design Matrix Setup
by Cristina A. F. Román 15 Oct '23

15 Oct '23

External Email - Use Caution Hello, I am looking to run a MANCOVA to examine cortical gray matter differences across three groups (accounting for several covariates), and I was hoping to get input on whether I am setting up my design matrix correctly. Groups: 3 Covariates: Age (demeaned), disease duration (DD; demeaned), sex Simplified Example: Group EV1(Grp1) EV2(Grp2) EV3(Grp3) EV4(age) EV5(DD) EV6(sex) 1 1 0 0 0.25 0.75 -1 1 1 0 0 0.25 0.25 -1 1 0 1 0 -0.75 -0.25 1 1 0 1 0 0.5 -0.75 1 1 0 0 1 -0.5 0.5 1 1 0 0 1 0.25 0.25 -1 Questions: 1. Is this an appropriate way to do a three-group comparison with covariates? Or, is it better to just run three separate t-tests (including covariates)? 2. Regarding post-hoc testing, would I just do three separate t-tests? This issue here, I imagine, is that the individual t-test results may not reflect the original MANCOVA results (e.g., post-hoc testing reveals a new significant area that was not significant in the MANCOVA). 3. One other option is to run the initial MANCOVA within a statistical program (i.e., using global cortical gray matter volumes) and then follow up with postdoc testing within FSL (i.e., t-tests). Would this make sense? Thanks in advance for your time and help, Cristina

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Question about mri_nu_correct.mni
by ruifeng14＠gmail.com 15 Oct '23

15 Oct '23

External Email - Use Caution Hi all, I am running Freesurfer 7.3.2 on T1 images (LPI orientation) with 176*256*256 FOV, 1mm isotropic resolution. I saw that the Ants N4 bias correction is done after the FOV is expanded to 256*256*256, not on the original image. Shouldn't the zeros in the expanded image affect the bias correction? Thanks. Best, Ruifeng

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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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Calculate cortical thickness of a volumetric ROI
by Carlos Alcocer 20 Jul '23

20 Jul '23

External Email - Use Caution Hello, I am trying to calculate the cortical thickness of a volumetric ROI that I created that I have in subject space for every subject in my dataset. I was using https://secure-web.cisco.com/1Z5OP8XDp2iTZo4YMybrzCFH9SwKBzyQx9vsSEFhl_f6qf… as a guide. Since, I already have the volumes in subject space. I did a modified pipeline and only did the following for each subject: 1. mri_vol2surf --mov /path/to/ROI5.nii --regheader --projfrac-max 0 1 0.1 --interp nearest --hemi lh --out lh.ROI5.mgh 2. mri_segstats --seg $SUBJECTS_DIR/subjid/surf/lh.ROI5.mgh --in lh.thickness --sum segstats-ROI5.txt Does this make sense? Also, separately, is the volume that is also computed in this method accurate? I noticed that the volume is always equal to the number of voxels, which I assume a voxel is equal to 1mm^3? However, when looking at aseg.stats these volumes have different values from their number of voxels. Thank you, Carlos

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Asymmetry analysis
by Carlos Alcocer 20 Jul '23

20 Jul '23

External Email - Use Caution Hello, I am trying to do an asymmetry analysis using steps detailed in https://secure-web.cisco.com/1E9BKFPFixB_mpRwvgfFNlEN0qYfJdo8MVLo6aeqDf-afy… However, step 1.3 starts with running: mris_apply_reg --src lh.map.mgh --trg lh.map.lh.fsaverage_sym.mgh --streg $SUBJECTS_DIR/subject/surf/lh.fsaverage_sym.sphere.reg $FREESURFER_HOME/subjects/fsaverage_sym/surf/lh.sphere.reg What is this lh.map.mgh file? and where can I find it/how can i make it? Thank you, Carlos

2 3

Extracting cortical thickness values for each subject using labels
by Akansha Mahesh Naraindas 20 Jul '23

20 Jul '23

External Email - Use Caution Hi I have made custom labels to use as ROIs, I was wondering if there was any way to get thickness values at each vertex for a participant but just within the areas covered by specific label files, So from the lh.thickness.fwhm0.fsaverage.mgh file, would I be able to extract thickness values from this file, but just within the region covered by aparc-rh-046.label ? Do you know of a way to do this? Thanks Akansha

3 3

Fwd: error in recon all
by alanood alsaleh 20 Jul '23

20 Jul '23

External Email - Use Caution Hello Freesurfer developer I tried to run a recon all commands for 36 subjects, and 30 finished without any issues. However, 6 of them were terminated with the ERROR (Talairach failed!). Can you please help me to sort this problem out? Please find the attachments (I attached the recon all script I used and the log file that I got for the subject with an error ). Regards Alanood

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Variation in volume when recon-all is run 1416 times on the same subject
by 神保岳大 20 Jul '23

20 Jul '23

External Email - Use Caution Dear FreeSurfer team, We were interested in the reproducibility of multiple runs of recon-all and repeated recon-all 1416 times on the same subject. We then checked the left and right brain results for the volume obtained from the Aseg process. The right brain showed exactly the same volume, while the left brain showed a small variation. We thought that the variation in volume between the left and right brains would be the same. But why is this not the case in reality? The volume_attemps1416.csv is attached. For example, the Left-Lateral-Ventricle in this file has variation, but the Right-Lateral-Ventricle has no variation, as shown below. *Left-Lateral-Ventricle*12377.8 12375.9 12375.9 12380 12376.4 ... *Right-Lateral-Ventricle*7514.7 7514.7 7514.7 7514.7 7514.7 ... 1) FreeSufer vesion: 7.2.0 2) Platform: Red Hat Enterprise Linux 8.6 3) uname -a: Linux fn01sv01 4.18.0-372.36.1.el8_6.x86_64 #1 SMP Thu Nov 17 16:37:07 EST 2022 x86_64 x86_64 x86_64 GNU/Linux 4) volume_attemps1416.csv: Summarized results of 1416 aseg.stats. ───────────────────────────────── Takehiro Jimbo, Ph.D. TEL: 050-5308-1575 Email: info(a)jras.co.jp URL: https://secure-web.cisco.com/1v12MsuoCVOvbnqcvpETpiPtEYjXBUvx9IxdD0D4EvElKE… ─────────────────────────────────

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Freesurfer June 2023