Freesurfer September 2023

freesurfer@nmr.mgh.harvard.edu

71 participants
88 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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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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Longitudinal multimodal processing
by gabriel robert 04 Nov '23

04 Nov '23

External Email - Use Caution Dear experts in longitudinal neuroimaging We carefully read the papers about possible biases introduced by treating timepoints images differently (Reuter and Fischl NI 2011, for example) to estimate unbiased anatomical and functional changes of brain development in healthy individuals. We took good note that treating each time point independently would remove asymmetry biases at the cost of reduced power. In our project, we would like to analyze about 800 scans both 3DT1, diffusion (FA preprocessed with fsl TBSS) and functional task BOLD at 3 time points (14 years-old, 19 years-old and 23 years-old). Each time point scans are preprocessed individually and normalized to a specific group-based template at the corresponding time point (not a within-subject midpoint symmetric space) and to the standard MNI space. Our question: We'd like to use a home-made study-specific multimodal atlas to resample ROI BOLD mean contrasts and fractional anisotropy at each time point but this atlas is *based on the last time point only (23 years-old).* Does this situation fall into the 'asymmetry-induced bias in longitudinal processing' ? Our feeling is most probably yes but given the sample size this is likely to be marginal compared to the effect size and results would still be interpretable... ? Many thanks for time, interest and insight, Best wishes Gabriel

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[FreeSurfer] regeneration of aseg.stats from manually edited aseg.mgz
by Krystal Xiwing Yau 02 Nov '23

02 Nov '23

External Email - Use Caution Dear FreeSurfer experts, I edited some images that under-segmented the brain by coloring the missing brain regions. When I used the edited aseg.mgz to regenerate aseg.stats, the new statistics did not show the increase of the volumes that I edited. Please see the following command lines that I have run on Linux: mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject Sub-180 May I know what step(s) I have missed before generating the aseg.stats? Please kindly advise. Thank you very much! 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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Tkregister2 GUI not responding fully
by Viktorija Pratuseviciute 02 Nov '23

02 Nov '23

External Email - Use Caution Hello, We are trying to process a scan with a failed talairach. We have been able to visualize the misalignment and attempted to use the following command (tkregister2 --s PI163 –fstal) to manual adjust the talairach.xfm based on the tutorial (https://secure-web.cisco.com/1acx6rTd53-Vz7knc_wTrpqifC8PTuiKKanQydzd8QVOyX…) The tkregister2 GUI opens up, however only certain functions work: I can switch between target and moveable, I can also double click on sliding scales to switch coronal, saggital and horizontal views, however I am not able to move any of the sliders including the rotate or translate brain and hence unable to fix the talairach. Is there a way to fix this issue? Or an alternative way to fix the bad talairach output? We are using freesurfer/7.3.1 and have attempted the command on our server command line on both mac and windows with same results. Many thanks, Viki

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lta_convert issue with ants Registration Matrix
by Yazdan Rezaee Jouryabi 18 Oct '23

18 Oct '23

External Email - Use Caution Dear all, Hi for checking registration i used fsl applyxfm on an Image(1)(Called Image.nii ) with specific Registration Matrice (Which we suppose to receive when we apply registration Methods) and Generate the "fsl_resampled.nii.gz" (Note: Image Orientations were LAS and in one other Experiment with also the same problem PSR) for our case i will attach the "fsl.mat" (Desired Matrix) using, fsl, freesurfer, and ants i got the correct results (let's call them "fslregistered.mat" and "freesurfer.mat" the converted lta to fsl-liked Matrix) Everything is OK till now But the converted lta-like and fsl-like matrix for ANTs (Which are called ants.lta, and ants.mat) using the lines below: - ConvertTransformFile 3 ./ANTS/ants_0GenericAffine.mat ./ANTS/ants.txt - lta_convert --initk ./ANTS/ants.txt --outlta ./ANTS/ants.lta --src ./Image.nii --trg ./fsl_resampled.nii.gz --ltavox2vox - lta_convert --inlta ./ANTS/ants.lta --outfsl ./ANTS/ants.mat --src ./Image.nii --trg ./fsl_resampled.nii.gz As All Results Images (Registered Image of all Methods) are aligned perfectly i think that there might be some issues with lta_convert Best Regards Yazdan Rezaee J *P.S. *" I've checked the one similar mail on this topic and the conclusion on that was about (sform, qform) incompatibility but the affine matrices of S-form and q-form are equivalent in my case."

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mri_glmfit-sim - Clusterwise correction for multiple comparisons.
by Guthrie, Andrew J. 15 Oct '23

15 Oct '23

External Email - Use Caution Hi all, I took the freesurfer course in the recent past, and I am now beginning to run some glm thickness analyses! Currently I am doing a thickness analysis looking at the difference between two groups while controlling for age, and two continuous measures of depression and anxiety. The general commands I run are as follows: mris_preproc --fsgd [fsgd filename] --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --o lh.[filename].thickness.10.mgh mris_preproc --fsgd [fsgd filename] --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi rh --o rh.[filename].thickness.10.mgh mri_glmfit --y lh.[filename].thickness.10.mgh --fsgd [fsgd filename] doss --C contrast.mtx --surf fsaverage lh --glmdir lh_[filename]_fwhm10.glmdir mri_glmfit --y rh.[filename].thickness.10.mgh --fsgd [fsgd filename] doss --C contrast.mtx --surf fsaverage rh --glmdir rh_[filename]_fwhm10.glmdir mri_glmfit-sim --glmdir lh_[filename]_fwhm10.glmdir --cwpvalthresh .05 --cache 2.0 abs --2spaces mri_glmfit-sim --glmdir rh_[filename]_fwhm10.glmdir --cwpvalthresh .05 --cache 2.0 abs --2spaces I noticed that in some analyses there would be no significant clusters when the threshold is set at 2.0 (p<0.01) but if you were to run the same analyses with a threshold at 2.3 (p<0.005) there would be a significant cluster, in the lingual for example. If I go one step further and set the threshold to 3.0 there is also a significant cluster - however the cluster is now in the isthmuscingulate. Am I doing something incorrectly or is this possible? And if so, could you help me understand what is going on here. Best, Andrew

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Use of *inflated resulst from recon-all
by Lesage, Anne-Cecile 15 Oct '23

15 Oct '23

External Email - Use Caution Dear Freesurfer teams I am working on sEEG data to help localize the epileptogenic zone at UTMB. We were wondering with Dr Karas if we could use the *.inflated surface to view better the electrodes in contact with the cortex. Do the *inflated surfaces have the same number of vertices and faces than the *pial ones? Does the *inflated surface respect the same geodesic distance between vertices than the *pial ones? Thank you Best Regards Anne-Cecile Lesage, PhD Research Scientist Department of neurosurgery University of Texas Medical Branch anlesage(a)utmb.edu

2 1

convert to fsaverage
by Sam W 15 Oct '23

15 Oct '23

External Email - Use Caution Hello! I have a volumetric mask of the cuneus and I would like to convert it to a label and then convert that label to fsaverage space. So far I did mri_vol2label --i cuneus.nii.gz --l cuneus.label But how can I now convert cuneus.label to fsaverage? Thanks! Best regards, Sam

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Freesurfer September 2023