Freesurfer December 2023

freesurfer@nmr.mgh.harvard.edu

52 participants
65 discussions

xhemi
by Joost Janssen 06 Mar '24

06 Mar '24

External Email - Use Caution Dear Doug, The objective is to have _regional_ laterality index for thickness for aparc mapped to the left hemisphere. The following commands work without error but are they correct for meeting my objective? Thanks. surfreg --s $subject --t fsaverage_sym --lh --no-annot surfreg --s $subject --t fsaverage_sym --lh --no-annot --xhemi mri_convert $subject/surf/lh.thickness $subject/surf/lh.thickness.mgh mri_convert $subject/surf/rh.thickness $subject/surf/rh.thickness.mgh mris_apply_reg --src $subject/surf/lh.thickness.mgh --trg $subject/surf/lh.thickness.lh.fsaverage_sym.mgh --streg $subject/surf/lh.fsaverage_sym.sphere.reg fsaverage_sym/surf/lh.sphere.reg mris_apply_reg --src $subject/surf/rh.thickness.mgh --trg $subject/surf/rh.thickness.lh.fsaverage_sym.mgh --streg $subject/xhemi/surf/lh.fsaverage_sym.sphere.reg fsaverage_sym/surf/lh.sphere.reg fscalc $subject/surf/lh.thickness.lh.fsaverage_sym.mgh pctdiff0 $subject/surf/rh.thickness.lh.fsaverage_sym.mgh div 200 -o $subject/surf/li.thickness.lh.fsaverage_sym.mgh mri_segstats --annot fsaverage lh aparc --i $subject/surf/li.thickness.lh.fsaverage_sym.mgh --sum $subject/stats/li.thickness.aparc.stats -joost

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recon all with optiBET brain mask
by BALBONI Irene 27 Feb '24

27 Feb '24

External Email - Use Caution Hello, I would like to run recon all on a batch of subjects using 2 inputs (mprage and mp2rage). I would also like to run recon all using as brain mask not the standard brain mask generated by recon-all itself but a previously created optiBET. Would you have any suggestion on how to proceed? I tried simply replacing the brainmask file with the optiBET but it did not work. Just for context all my participants (150) have been already segmented using recon-all but we noticed during quality control that we still have skull stripping and pial surface errors for the majority of them and that is why we would like to implement the optiBET mask. Thanks for your help, Irene Balboni PhD student She/Her Institute de plurilinguisme<https://secure-web.cisco.com/1pftPU5_0h0FupMF_jZDy_UxBYrJAQ-AW89umP7RzP_duH…> | Université de Fribourg & Brain and Language Lab<http://secure-web.cisco.com/1GVUYNYViIIVEm2bvje-SiFox0WAIrWlf7gC0y8Dy1Yk6xj…> | Université de Genève c/o Campus Biotech Chemin des Mines 9 – 1202 Université de Genève, CH +41(0)223790141 Twitter<https://secure-web.cisco.com/17WKW8eFYGf6kC7ikhhz87_g3_OExqqtlPMTRdUfjaGR0u…> | ResearchGate<https://secure-web.cisco.com/17QR3OuPCdu6j4aAtW1iy0qnt2WV8MA0yHG3gonUNgbpno…> | Linkedin<https://secure-web.cisco.com/10d7bSA4mUh4az6x-hBwYc5c1373f-jWI1YMV5SjB-YHxE…>

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Manual/reproduce conform
by Dipterix Wang 23 Feb '24

23 Feb '24

External Email - Use Caution Dear FreeSurer Wizards, I'm trying to run the recon-all command on one of my template brains such that the resulting Norig and Torig are identical. I understand that fs always conforms the MRI to 256^3 before segmentation. I wonder if there is any way that I can resample the original MRI to achieve the same Norig and Torig? More specifically, currently the Torig (vox to tkrRAS) is [,1] [,2] [,3] [,4] [1,] -1 0 0 128 [2,] 0 0 1 -128 [3,] 0 -1 0 128 [4,] 0 0 0 1 If I resample the input image such that Norig (vox to scanRAS) equals this matrix, can I expect that "conform" does not change the orientation? Alternatively, is there any method I can use to "predict" or reproduce the Torig from the original MRI outside of FreeSurfer? Thanks, - Dipterix

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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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Create a Binarized ROI for Surface
by Na, Xiaoxu 07 Feb '24

07 Feb '24

External Email - Use Caution Dear Freesurfer Expert, We would like to extract mean Cth values for each subject within a own-creaded ROI (surface defined), using freeview (for instance). Is it possible to create a ROI (i.e. spherical surface) surrounding a particular vertex of an sig.mgh file? (and then extract its mean Cth values for each subject)? I think this is not a new question, and it was posted somehow on https://secure-web.cisco.com/15jmZMEaxCepVMfyQImwGR_dFusKbz7ObR8zcE3AMwMwg6…, and https://secure-web.cisco.com/1nS4AASSkp9fTCLDzqspNVvBf35PGarlPS708pOXtzpIMD…, but I'm still encountering questions. These commands did run, but together they didn't create a binarized mask with 1 for the sphere around the coordinates, and 0 for the other voxels. Would you recommend what I should change? Thank you so much! $mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/lh.thickness --pdf sphere --sphere-center -7.4 67.22 60.27 --radius 5 --o delta.sm00.mgh $mris_fwhm \ --smooth-only \ --subject fsaverage \ --hemi lh \ --i delta.sm00.mgh \ --niters 10 \ --o delta.sm10.mgh $mri_binarize --i delta.sm10.mgh --min 10e-5 --o delta.sm10.bin.mgh 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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mri_watershed and improvements of skullstripping
by Michelangelo Fabbrizzi 01 Feb '24

01 Feb '24

External Email - Use Caution Dear Freesurfer experts, I am new to FS, and I would have couple of questions. I used in sequence: A- recon-all -i sub-01_T1w.nii.gz -s sub-01_recon -autorecon1 B- recon-all -skullstrip -wsthresh 5 -clean-bm -s sub-01_recon C- recon-all -skullstrip -clean-bm -gcut -subjid sub-01_recon The brainmask.mgz obtained is good (no skull, brain is okay), however if I now use mri_watershed to obtain the bem surfaces, it looks the brainmask.mgz is not used and it is created a new one called ws.mgz that still contain some piece of skull that generate wrong BEM surfaces; even using -h 5 the result is not optimal: mri_watershed -h 5 -useSRAS -surf /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/sub-01_recon /Users/michelangelo/Test_skullstripping/sub-01_recon/mri/T1.mgz /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/ws.mgz I am wondering: - how can I force the mri_watershed command to use the brainmask.mgz already created after step C above, instead of creating a new one? - is it possible to use the -gcut command also for mri_watershed? Thanks, appreciated, Miche

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Infant_recon_all generated surface does not align well with the provided aseg file
by Yanbin Niu 11 Jan '24

11 Jan '24

External Email - Use Caution Hi Freesurfers, I'm currently working on running infant_recon_all with our edited aseg.nii.gz for newborn data. However, we've encountered an issue where the generated surface does not align well with the provided aseg file. I have attached some screenshots as an example, in which a fold that infant_recon_all is failing to fully recognize. This problem seems consistent across the brain and subjects. I'm reaching out to inquire if anyone has experience with this issue and if there are specific parameters that we can adjust to address this issue. Here is the command we've been using: infant_recon_all --s sub-1041 --age 1 --inputfile ${SUBJECTS_DIR}/sub-1041/mprage.nii.gz --segfile ${SUBJECTS_DIR}/sub-1041/aseg.nii --masked ${SUBJECTS_DIR}/sub-1041/brain_mask.nii.gz Thank you, Yanbin Niu

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Use of infantFS and FS in the interval 2 - 4.5 years of age
by Michelangelo Fabbrizzi 11 Jan '24

11 Jan '24

External Email - Use Caution Dear FS experts, I see it is recommended to use infantFS below 2 years of age, whereas FS has been used for 4.5 years and above. I was wondering what could be used in the interval 2 - 4.5 years of age: which are benefits and drawbacks of both? Thanks, appreciated, Mic

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FS 6.0 outputs for use with 7.2 Tracula
by Alexopoulos, Dimitrios 07 Jan '24

07 Jan '24

External Email - Use Caution Can the tracula version in FS 7.x be used with surface outputs generated with FS 6.0? Our segmentations/surfaces generated with 6.0 look good but we'd like to generate the 42 WM pathways incorporated in FS 7x. Is this possible? I was under the impression the aparc+aseg segmentation is what is used by Tracula. Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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mri_error_no_clear_message
by Fargol Rezayaraghi 02 Jan '24

02 Jan '24

External Email - Use Caution Hi FreeSurfer Team, I hope this email finds you well. I'm trying to use a T1 image to get the aparc+aseg and wmparc nifti files. I was using this command: recon-all -s Subject1 -i T1.nii - all -notal -check ( I used recon-all -s Subject1 -i T1.nii - all first, and after getting Talairach error, I added -nota -check at the end). I'm getting following messages without clear error number: recon-all -s Subject1 exited with ERRORS at Thu Dec 14 21:18:02 EST 2023 For more details, see the log file /home/developer/Desktop/freesurfer/7.2.0/subjects/Subject1/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1cQznhKx0XPPZTJqsioLqCSeP_2I8A9nJBXfsYwGFwxBXmD… The version of the freesurfer: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b My platform is ubuntu 18_04_06 on Oracle VM VirtualBox I've attached the log file. -- Kind Regards, *Fargol R. Araghi (Rezayaraghi)* Ph.D. Candidate, University of Washington Department of Mechanical Engineering http://secure-web.cisco.com/1etf29AnmyfO7JDA1iwX4HvYcM0WXmMMFv-FG5QUpvlXzXt… <https://secure-web.cisco.com/1OE6aYFeTkmWM7FGsUCe4yHngfS6aQZieqg2uFkxfDu0qu…>

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Freesurfer December 2023