Freesurfer October 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
95 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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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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PETSurfer
by Emma Tinney 07 Dec '23

07 Dec '23

External Email - Use Caution Hi I am reaching out to ask some questions about PetSurfer. I am working with an open access dataset (ADNIDOD<https://secure-web.cisco.com/1CEWzN2wc2OketK1X9ZfAONKbe4S8QwQqJbEzc-uLebpb5…>) to analyze neurobiological differences in veterans with a history of TBI. I am hoping to use the PET data (there are the raw dicoms and preprocessed PET data) to segment the choroid plexus using a specific segmentation software.<https://secure-web.cisco.com/1UhF7rhtSZAlDXzE9N3KqTGlmagy96emXFw2bQ51_0Eb0I…> I have already done the segmentation on the T1 images, but am hoping to apply the masks to the preprocessed PET images. I was looking at using the “mri_gtmpvc” command to segment the choroid plexus using the mask I already created but was hoping for some guidance. There are also several options of preprocessed PET data I can chose from, including “co-registered averaged standardized image and voxel” including “co-registered averaged standardized image and voxel with unform resolution” and “co-registered averaged” or “co-registered dynamic”. If anyone are willing to help or can connect me to someone how might have time to reply or quickly chat, that would be great. I appreciate the support and am looking forward to using PetSurfer.

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Importing atlas with mris_register: "hips not supported"
by Jasmine Cakmak 09 Nov '23

09 Nov '23

External Email - Use Caution Hello, Any help with this issue is greatly appreciated. I am trying to import the Neuromorphometrics atlas into Freesurfer as a part of my segmentation analysis. I have run recon-all on my template subject (IXI550) and the subject to register (PSCI15_003), and taken the atlas.nii and used mri_vol2surf and mris_seg2annot, all without errors. Now I am trying to register IXI550 and PSCI15_003 to each other so that I am then able to run mris_apply_reg. I am receiving the error "hips not supported," both on Ubuntu 22.04.2 LTS and my M1 mac. Is there a way to resolve this error (found below), or a different way for me to apply the atlas to the recon-all of my subjects? I am using freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275. mris_register PSCI15_003/surf/lh.sphere IXI550/surf/lh.sphere reg_PSCI15003_IXI550.dat cwd /mnt/d/Jasmine2023/Neuromorph cmdline mris_register PSCI15_003/surf/lh.sphere IXI550/surf/lh.sphere reg_PSCI15003_IXI550.dat 0 inflated.H 1 sulc 2 smoothwm (computed) 7.3.2 7.3.2 reading surface from PSCI15_003/surf/lh.sphere... reading template parameterization from IXI550/surf/lh.sphere... error: hips is not supported error: hips is not supported MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=unkno, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 -------------------- tol=5.0e-01, sigma=0.0, host=unkno, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization 1 Reading lh.sulc curvature mean = 0.000, std = 3.574 Segmentation fault Thank you so much in advance for any help. Jasmine

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Group analysis question
by Nicolette Barber 09 Nov '23

09 Nov '23

External Email - Use Caution Hello, I am working on a project using FreeSurfer, and I am trying to set up a whole brain group analysis. However, I am not sure how to set up the FSDG files, etc., as my dependent variable is not a cortical measurement. My dependent variable is a neuropsychological battery, culture, and brain measurement are my independent, and my covariate is ICV. I have been trying to figure this out for a while now. Is there a way to change the dependent variable for mriglm_fit? And if so, how would I set this up? I am using version 6. Thank you, Nicolette

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dt_recon question
by Mirsol Choi 09 Nov '23

09 Nov '23

External Email - Use Caution Hi there, I am currently going through the dt_recon tutorial on your website and I just have a quick question regarding the recon-all and dt_recon commands on freesurfer. For me to process dt_recon, my understanding is that I must process recon-all first. But where my confusion lies is: - do I perform recon-all on the actual dwi.nii.gz image, then dt_recon with the same dti files (including the bval and bvec of the same dwi.nii.gz file) OR - should I have two separate sets of data, one T1 and one DTI, and perform recon-all on T1 images and take DWI images from the same subject to perform dt_recon? My understanding was that the second bullet is the right way to go since the dt_recon uses the outputs from T1 recon-all to register properly. Please let me know which one is correct, and if I am missing something. Thank you so much for your help, I really appreciate your time. M

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SynthSEG continued developments
by Dawn Matthews 09 Nov '23

09 Nov '23

External Email - Use Caution Thank you for all of the work of the FreeSurfer team in continuing to make advances to the Freesurfer suite of tools. I wondered if you could comment on (a) any work or plans to include hippocampal subfield, brainstem subfield, or corpus callosum subfield segmentations, and (b) the robustness of SynthSEG to defacing/refacing software as compared to Freesurfer? Thanks very much.

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PETsurfer kinetic modeling
by Dawn Matthews 09 Nov '23

09 Nov '23

External Email - Use Caution Congratulations to the FreeSurfer team in the continued progress made in the FS tool set. I wondered if you could comment on whether it is feasible to create a custom reference region (other than specifying, for example, cerebellar cortex or another predefined FS mask) for PETsurfer kinetic modeling (e.g. a cerebellum subfield) or whether there perhaps is an existing cerebellar subfield atlas that can be run with PETSurfer (e.g. crus2)? In addition, can you please confirm whether the Logan model can be run using a reference region (i.e. without requiring arterial input)? Thanks very much and kind regards.

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Freesurfer October 2023