Freesurfer March 2024

freesurfer@nmr.mgh.harvard.edu

58 participants
61 discussions

[FreeSurfer] Lesion detection at different thresholds
by Krystal Xiwing Yau 18 Apr '24

18 Apr '24

External Email - Use Caution Dear FS experts, I am testing out which threshold works the best for the image. As I tested 0.3 and 0.9, the lesion masks do show the difference but the measurement is the same. Please see below for your information: [cid:abc00aac-cc49-4ef4-9cca-50c4bf72188b] Fig 1. Lesion.mgz with a threshold of 0.3 applied to FLAIR image [cid:7e206b3b-741a-497a-aec8-5bef569267b7] Fig 2. Lesions.mgz with a threshold of 0.7 applied to FLAIR image Do the volume of lesions supposedly different with threshold adjustments? The following code is what I used for running samseg: run_samseg --input $FREESURFER_HOME/${i}.nii $FREESURFER_HOME/${i}_flair_reg.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --threshold 0.7 --output $SUBJECTS_DIR/${i}_samsegOutput_thold0.7/ --save-posteriors --threads 8 Thank you for your attention. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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PetSurfer: Can kinetic modeling be applied to PET data with single frame?
by WONG Wan Wa 11 Apr '24

11 Apr '24

External Email - Use Caution Hi experts, As stated in the subject, can kinetic modeling be applied to PET data with only one frame? Or we just stop at ROI analysis without kinetic modeling? Best, Angel

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Easyreg > cortical parcels missing after SynthSeg with --parc option ?
by r04458005＠ntu.edu.tw 08 Apr '24

08 Apr '24

External Email - Use Caution Hello Freesurfer Developpers, I attempted to run mri_easyreg (Freesurfer 7.4) between two images. After I ran mri-easyreg adding these images (--ref_seg --flo_reg), I get again the > no cortical parcels. The following is the command I used and the error code. What did I do wong? Any hints? Thanks in advance for your help. Best, Edward mri_easyreg --ref /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0 mm_T1_scalp_trip.nii --flo /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only/pre_042_0000 .nii.gz --ref_seg /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0 mm_T1_scalp_trip_synthseg.nii --flo_seg /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042 /pre_042_0000_synthseg.nii.gz --ref_reg /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042 /pre_042_ref_reg.nii.gz --flo_reg /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042 /pre_042_flo_reg.nii.gz --fwd_field /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042 /pre_042_FWF.nii.gz --bak_field /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042 /pre_042_BWF.nii.gz 2024-03-31 15:50:23.731218: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2024-03-31 15:50:23.752531: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2024-03-31 15:50:23.752807: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations. To enable the following instructions: AVX2 AVX_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags. 2024-03-31 15:50:24.041622: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT using 1 thread Segmentation of reference image already exists; reading from disk Error: No cortical labels found; does the segmentation include cortical parcels?

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Re: [Freesurfer] Freesurfer Waitlist
by Bess Lam 30 Mar '24

30 Mar '24

1 0

mri_volsynth fails but exits with 0 exit status
by Aaron Tanenbaum 29 Mar '24

29 Mar '24

External Email - Use Caution I am currently running FreeSurfer 7.4. I wrote a script using the program mri_volsynth. I noticed for the first time the program was trying to write files where it did not have write permissions. It outputted a few error messages but gave a 0 exit status. It would be nice to have it exit with a nonzero exit status.

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Extracting significant regions - Longitudinal two stage model
by Liliana Wu 29 Mar '24

29 Mar '24

External Email - Use Caution Hi, I ran a longitudinal two stage model analysis in 83 participants comparing two groups. After applying cluster correction, I am seeing several significant regions, and I was wondering if there is a way to extract each significant cluster from each participant. I appreciate any help! Thank you, Liliana

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autorecon1 issue
by Saifullah Tumrani 29 Mar '24

29 Mar '24

External Email - Use Caution I am using freesurfer to preprocess my t1w 3d Mris using autorecon1 which includes first 5 preprocessing techniques till skullstripping it worked well for 4 different datasets including ixi one from open neuro SRBPS but when i am using it for another dataset which has alsmost same configuration it’s talairach transformation fails for some samples and brain matter is removed in the final brainmask.mgz file moreover i applied autorecon-all for this dataset and even the process stopped for some showing error talaraich failed and for some samples the whole pipeline was executed without any error but in manual inspection i found brain matter removed by freesurfer kindly help me solving this problem. I later found bad skull stripping fix at this link FsTutorial/SkullStripFix_freeview - Free Surfer Wiki <https://secure-web.cisco.com/1W6bcIn5Fy404rUlulLdvgZBsqq1rLSJmG1UU4wSK-ttJn…> using some commands but i am facing errors using these command recon-all -skullstrip -wsthresh -clean-bm -no-wsgcaatlas -subjid skullstrip1_before kindly look into this if you have also experience same issues or have any insight on this. A response will be appriciated. Thanks

2 1

Part brain is missing
by Chen Yang 29 Mar '24

29 Mar '24

External Email - Use Caution Dear FreeSurfer Developers, I am trying to do the processing for structural MRI data. I found that part of brain is missing in one data (see Fig.1). Then I tried to change the watershed parameter, but it didnt work at all (no matter which number I use), the brainmask looks the same as before. So I did the manual editing, cloned voxel from T1.mgz to brainmask.mgz. Then I run the -autorecon-pial, but it froze in this step - fix topology. I checked 'wm.mgz', it contained a lot skull and a lot of WM are missing (see Fig.2). I also tried to manually edit the brainmask.mgz and wm.mgz, then run '-autorecon-wm' but it also froze in -fix topology. I put other might relevant information in the end. I've searched in the mail archive but didn't find similar errors. I am not sure if I did anything wrong. Does anyone have any thoughts on how to trouble-shoot this problem? Also, Ive attached the recon-all.log in case it's of any use. Thanks in advance! Best regards, Chen Other might relevant Information: 1) Coil element is wrong. 'HE2,4;NE2'. 2) I got an error message when I wad doing the recon-all first time: watershed error: indices out of bounds. Then I added the command line 'mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz $mir/nu.mgz' based on this page <https://secure-web.cisco.com/1uRXBiwoaszcFJpp3kKMMx2gS1DnuVTXjdvnMG63iVHxJH…>. Then I got another error message in recon-all: mri_em_register: could not open brainmask.mgz so I added some cp to nu.mgz. It worked but the part of brain is missing, as I mentioned in the beginning (Fig.1). 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Platform: Linux 5.10.0-28-amd64 3) uname -a: Linux ramones 5.10.0-28 -amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux 4) recon-all.log: see attached -- Chen Yang PhD Student Independent Research Group 'Milestones of Early Childhood Development' Max Planck Institute for Human Cognitive and Brain Sciences Email:yangc@cbs.mpg.de

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Fw: Discrepancy between mris_preproc and mri_surf2surf results when mapping individual's measures to fsaverage space
by tyzhang＠ibp.ac.cn 29 Mar '24

29 Mar '24

External Email - Use Caution Dear FreeSurfer Experts, Sorry, I think I've found the answer. It's because Jacobian correction was performed for mris_preproc, right? Tongyu Zhang -----原始邮件----- 发件人:tyzhang@ibp.ac.cn 发送时间:2024-03-20 16:31:23 (星期三) 收件人: freesurfer(a)nmr.mgh.harvard.edu 抄送: 主题: Discrepancy between mris_preproc and mri_surf2surf results when mapping individual's measures to fsaverage space Dear FreeSurfer Experts, I'm currently working on mapping cortical morphometric measurements from each individual in the HCP dataset to the fsaverage space. I have noticed that both the mris_preproc and mri_surf2surf commands can achieve this function. However, I found that the vertex-level measurements for cortical thickness, sulcal depth, and curvatures are consistent between these two commands, but the results for surface area and gray matter volume are totally different. I am puzzled by this inconsistency and speculate that perhaps these two commands are calculated on different surfaces? I don't understand why the two commands get different results since the inputs are the same. My command are as follows: (Different surface area values will be obtained in lh.area.fsaverage.mgh and lh.area.fsaverage.gii files) mris_preproc --s id --meas area --target fsaverage --hemi lh –out /Results/CorticalFeatures/id/lh.area.fsaverage.mgh mri_surf2surf --srcsubject id --trgsubject fsaverage --hemi lh --sval /HCP/id/surf/lh.area --tval /Results/CorticalFeatures/id/lh.area.fsaverage.gii Thank you so much! Tongyu Zhang

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Discrepancy between mris_preproc and mri_surf2surf results when mapping individual's measures to fsaverage space
by tyzhang＠ibp.ac.cn 29 Mar '24

29 Mar '24

External Email - Use Caution Dear FreeSurfer Experts, I'm currently working on mapping cortical morphometric measurements from each individual in the HCP dataset to the fsaverage space. I have noticed that both the mris_preproc and mri_surf2surf commands can achieve this function. However, I found that the vertex-level measurements for cortical thickness, sulcal depth, and curvatures are consistent between these two commands, but the results for surface area and gray matter volume are totally different. I am puzzled by this inconsistency and speculate that perhaps these two commands are calculated on different surfaces? I don't understand why the two commands get different results since the inputs are the same. My command are as follows: (Different surface area values will be obtained in lh.area.fsaverage.mgh and lh.area.fsaverage.gii files) mris_preproc --s id --meas area --target fsaverage --hemi lh –out /Results/CorticalFeatures/id/lh.area.fsaverage.mgh mri_surf2surf --srcsubject id --trgsubject fsaverage --hemi lh --sval /HCP/id/surf/lh.area --tval /Results/CorticalFeatures/id/lh.area.fsaverage.gii Thank you so much! Tongyu Zhang

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Freesurfer March 2024