Freesurfer

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30070 discussions

Any large stash of labelled brain MRIs for CNN training?
by Keith E Moore 28 Apr '23

28 Apr '23

External Email - Use Caution Hi, First samseg and mri_reg are amazing tools. Thank you! I am running them on an internal dataset of images to create labelled MRIs. This is taking 45 min to an hour per grouping (T1, T1ce, T2 and FLAIR) to align and segment. It made me wonder if there is a cache of already labelled MRI images. I'm particularly looking for caudate and thalamus segmentation. Hoping I can leverage what others have done while I work on labelling my dataset. Keith

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Freesurfer mailing list submissions
by julia emily 28 Apr '23

28 Apr '23

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Automatic Calculation of White matter ADC Values using SynthSeg
by bar gen 28 Apr '23

28 Apr '23

External Email - Use Caution Dear Freesurfer experts, I hope this email finds you well. I am writing to seek your advice on a specific issue regarding a pediatric brain tumor and control group dataset that I am working with. The dataset consists of diffusion-weighted images (DWIs) with T2, b0, and b1000 trace images. My goal is to automatically calculate the Apparent Diffusion Coefficient (ADC) values in the contralateral white matter of both the childhood tumor and control groups. I have considered using b0 images segmented by SynthSeg to obtain the white matter images and then perform the measurement. However, I am not sure if this is the correct approach. When I use SynthSeg, the initial segmentation output has a resolution of 1x1x1 mm, while the ADC images have a resolution of 1.5x1.5x5 mm. I am unsure how to overcome this discrepancy in resolution. I would appreciate any guidance on whether using SynthSeg for segmenting the b0 images is the correct approach, as well as any suggestions for addressing the resolution discrepancy between the segmentation and ADC images. Additionally, if there are alternative methods or tools for automatically calculating ADC values in the contralateral white matter, I would be grateful for your recommendations. Kind regards. Barış

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Fw: repeated measures anova for 4 treatments by 2 timepoints
by Resnick, Patricia 28 Apr '23

28 Apr '23

External Email - Use Caution Tricia Stefancin Lab manager Z-lab Department of Psychology The Ohio State University ________________________________ From: Resnick, Patricia Sent: Friday, April 21, 2023 12:29 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: repeated measures anova for 4 treatments by 2 timepoints Hello, I have a total of 8 subjects with 4 treatments (A/stim, A/sham, B/stim, B/sham) each with 2 timepoints (pre, post). I subtracted the pre-post images and I am trying to compare the differences between A/stim and A/sham, B/stim and B/sham, and A/stim and B/sham. I have run the mri_glmfit command below and get the following error: matrix is ill-conditioned or badly scaled, condno = 1.33391e+07 mri_glmfit --glmdir /fs/project/PAS1305/IMPACT/glm_analysis/motor/Motor-Fix/lh/ --y /fs/project/PAS1305/IMPACT/glm_analysis/motor/Motor-Fix/lh/sigLH.nii.gz --fsgd /fs/project/PAS1305/IMPACT/glm_analysis/motor/repeated_measures.fsgd doss --C /fs/project/PAS1305/IMPACT/glm_analysis/motor/TMS_stim-sham_repeated.mtx --C /fs/project/PAS1305/IMPACT/glm_analysis/motor/PBM_stim-sham_repeated.mtx --C /fs/project/PAS1305/IMPACT/glm_analysis/motor/PBM-TMS_stim_repeated.mtx --surf fsaverage lh --fwhm 0 --sim mc-full 500 2 corrp --sim-sign abs Would someone be able to tell me why this is not going through? Best, Tricia Stefancin Lab manager Z-lab Department of Psychology The Ohio State University

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creating average labels
by Carlos Alcocer 28 Apr '23

28 Apr '23

External Email - Use Caution Good afternoon, I would like to verify that the subcallosal cingulate cortex (SCC) segmentation of my subjects are correct. I want to do this by creating an average label of the left SCC and an average label of the right SCC which I can then map onto each subject. If I save these labels from each subject as a volume (.mgz) and then run mri_concat on the left SCC labels (.mgz) and then on the right SCC labels (.mgz), would this accomplish my desired goal? Tks, Carlos

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extracting values from signifciant clusters
by Eszter Boros 28 Apr '23

28 Apr '23

External Email - Use Caution Dear FreeSurfer Team, We are doing a longitudinal analysis with Freesufer 7.1.1 (two-stage longitudinal model), and we would like to extract the Cortical thickness values from the significant clusters (before and after treatment changes) to visualize the individual values/changes. I am wondering how I can do that? Please let me know if you need any more information. Thank you for your answer in advance! All the best, Eszter Boros

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Subcortical regions of Brainnetome Atlas
by Garrett Tan 28 Apr '23

28 Apr '23

External Email - Use Caution Hi FreeSurfer Experts, I am using Brainnetome Atlas in FreeSurfer to calculate the brain volume. The cortical regions are done smoothly by using mris_ca_label->mris_anatomical_stats with materials on https://secure-web.cisco.com/1p7TY1frW67uqViolqd97Sub3WUDGgPjPK0_YAEmmtEENB… However, when I was trying to get the volume of subcortical regions (the hippocampus, amygdala, thalamus, and basal ganglia), they are excluded since the ?h.cortex.label files do not include them. My plan was to use aseg.mgz to get each subcortical regions and do the same procedure as for the cortical regions. However, mri_ca_label did not allow me to create .annot from BN_Atlas_subcortex.gca from Brainnetome website. So I continued using mris_convert to convert .gca to label.mgz, and I am stuck here. Is there any way to get the subcortical regions’ .gcs file, or even an easier way to calculate the volume of subcortical regions in brainnetome atlas from FreeSurfer? Best, Garrett

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Extracting statistical values from significant ROIs after running GLM
by Akansha Mahesh Naraindas 28 Apr '23

28 Apr '23

External Email - Use Caution Hi I have run a GLM using cortical thickness and a behavioural measure on specific ROIs, I have a query about extracting the statistical values, specifically the test statistic from the significant regions after running the GLM but prior to multiple comparison correction. Is there any way to extract the test statistic of each vertex of the significant regions? Thanks Akansha

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visualization, heatmap
by Eszter Boros 27 Apr '23

27 Apr '23

External Email - Use Caution Dear Freesurfer team, I noticed that some studies/publications add figures with heatmaps to visualize the significant cortical results (after correction), others do not. We tried to use the heat map (from yellow/red to dark blue/light blue) to visualize the group differences using Freeview but after correcting for multiple corrections (after mri_glm we used Monte Carlo simulation), we are not sure how to do that. Only the sig.mgh file can be visualized that way, right? Or that was available in tksurfer but not in Freeview? https://secure-web.cisco.com/1iHssxc0c4EPn_NgIsbQnxACsBkIj4sWVm7WSdle6CMXnC… Is tksurfer still available? We use Freesurfer 7.1.1. Thank you for your help in advance! Eszter

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FSFAST: wrong brain mask in preproc
by Elmira Hassanzadeh 27 Apr '23

27 Apr '23

External Email - Use Caution Hi everyone, We preprocessed resting-state data with preproc-sess. In the output, I noticed although *fmcpr.nii* covers the whole brain,* fmcpr.sm6.mni305.2mm.nii* is only covering brain stem+cerebellum (screenshots attached). Any clue what went wrong? This is an example of the command we ran for one of our subjects(R19): *preproc-sess -surface R19 lhrh -s R19 -fwhm 6 -fsd rest -mni305 -per-run* Thanks, Elmira

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