Freesurfer June 2024

freesurfer@nmr.mgh.harvard.edu

47 participants
51 discussions

TRACULA multiple sessions output question
by Fotiadis, Panagiotis 18 Jun '24

18 Jun '24

External Email - Use Caution Hello, First of all, thank you for the fantastic software! I have a cohort of individuals with multiple DWI sessions each, and I have been using TRACULA with a configuration file similar to that of Example 3 (“Cross-sectional study, multiple diffusion scans per session”) shown in https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc to analyze them. I have ran all three steps of the analysis (preproc, bedp, and path) successfully for all subjects, but I was a little confused as to whether TRACULA can save the individual statistics for each DWI session of each subject. So far, when I’m looking under each subject’s …/dpath/$white_matter_tract/ directory I can see only one pathstats.byvoxel.txt (and one pathstats.overall.txt) file. 1. Does that correspond to only one (perhaps the least noisy) or the average stats file across all DWI sessions for that subject? 2. I can see that some files (such as the control point niftis) are saved for all DWI sessions, but is there a way to get the aforementioned stats files (and corresponding diffusion measure and white matter tract maps) for each DWI session per subject? Thank you in advance! Best, Panos ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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Brain in a Box
by Hebah Tanveer 18 Jun '24

18 Jun '24

External Email - Use Caution I'm trying to determine the smallest rectangular prism that a brain will fit in based on its MRI scan. My strategy is as follows: I am moving through the brain axially, sagittally, and coronally to see where the brain "starts" appearing and "stops" appearing. Then, I'm subtracting the amount of no-brain slices from the total number of slices and multiplying the result by the slice thickness. This should get me the length (sagittal plane), width (coronal plane), and height (axial plane) of a box that contains the brain. Is there a function within FreeSurfer that can automate this process of determining "first and last sight of brain" ? It is quite time consuming to manually check hundreds of patients! Best, Hebah

3 2

freesurfer launching error
by yunus soleymani 18 Jun '24

18 Jun '24

External Email - Use Caution hi everyone, recently after a major Windows 11 update, I can not launch Freeview in my WSL Ubuntu machine despite having VcXsrv working in the background, and encountered the following error: QXcbConnection: Could not connect to display 10.255.255.254:0Could not connect to any X display. do you have any idea to troubleshoot this error? I appreciate any help you can provideBest,Yunus

1 0

Cannot find mri/transforms/talairach.m3z file
by Dan Levitas 17 Jun '24

17 Jun '24

External Email - Use Caution Hello, I am following the longitudinal freesurfer pipeline ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) and getting this error on the final (LONG) portion: *ERROR: cannot find or read transforms/talairach.m3z* I can confirm that recon-all ran successfully during the CROSS and BASE portions; it is only when I attempt to perform recon-all -long that things fail. My suspicion is that CA registration was not performed during CROSS, as I used -synthseg (and -synthstrip) in that recon-all command. I'm unsure if I need to go back and specify -careg in the CROSS recon-all command (e.g. *recon-all -autorecon2 -careg*), or if there is some way to bypass this error. I tried appending -nocareg to the end of my LONG recon-all command, but this errored out with the following output: *mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/transforms/cc_up.lta sub-1000_ses-2pre.long.sub-1000 will read input aseg from aseg.auto_noCCseg.mgzwriting aseg with cc labels to aseg.auto.mgzwill write lta as /N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/transforms/cc_up.ltareading aseg from /N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/aseg.auto_noCCseg.mgzerror: mghRead(/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/aseg.auto_noCCseg.mgz, -1): could not open file* Thanks for the assistance. Dan

2 4

How to get the parcellations to the initial space as before running recon all
by Reji, A. (Amal, Student M-EE) 17 Jun '24

17 Jun '24

External Email - Use Caution Hi, I was trying to get the mesh files for cortical parcellations after running recon all. I used the Ernie data set which is the example dataset given by SimNIBS.<https://simnibs.github.io/simnibs/build/html/dataset.html> I did recon all to the Ernie dataset and I got the parcellations. Now I want to get these parcellations to the same space as the space of Ernie. How can I convert the parcellations in the initial space? Looing forward to hearing from you Regards Amal Reji

2 3

recon-all clinical : usage with contrast-enhanced T1-weighted images?
by Barbara Bellenberg 14 Jun '24

14 Jun '24

External Email - Use Caution Dear all, I would like to use the recon-all-clinical pipeline with Gadolinium contrast-enhanced 3D-T1 weighted images. Can you tell me if recon-all-clinical is suitable for this purpose? Thanks in adcance for your support! Barbara

3 2

Probability density function
by Jingjing Liu 13 Jun '24

13 Jun '24

External Email - Use Caution Dear Freesurfer team, I am looking for the answer that where I can find the document of Probability density function in voxels of each brain volume after preprocessing. Because I need these indicators. Thank you so much in advance for your reply! Sincerely, Jingjing Liu

2 1

BIANCA Sensitivity/Robustness to non-brain material in skull-strip
by CRISTIAN MOJICA 13 Jun '24

13 Jun '24

External Email - Use Caution Hello, I will be running BIANCA in FSL after some quality control with the requisite files to be listed in the Masterfile. I am examining my skull-strip files (in FLAIR space), and most skull strips still have some dura or black space occupied by CSF leftover. How sensitive is BIANCA to some leftover non-cortical material, or is anyone aware of an analysis that examines BIANCA's output as a function of thoroughness of skull strip, or (on the Freesurfer side) have suggestions for gcut or wsthresh parameters that are good for BIANCA? The skull strip was done in Freesurfer's recon-all process, then the resulting brainmask was registered into FLAIR space with FSL. Thanks in advance!

2 1

PETSurfer: pvc'ed and scaled output nifti image
by Sneha Pandya 12 Jun '24

12 Jun '24

External Email - Use Caution Dear team, I am using mri_gtmpvc to obtain PVC'ed regional data which we will use as an input TAC to perform kinetic analysis. In addition, we are also doing static SUVR analysis (sum of frames from 60-90 mins) in which I am scaling input PET data with gray matter cerebellum. In the output folder I see that upon scaling (when using --save-input flag) we get a scaled input image which can be used as SUVR. However, is this scaled image also PVC corrected or just scaled? If not, then is it possible to get PVC'ed and scaled nifti image? Thank you, Sneha

2 2

Does motion correction command mc-sess do censoring of high motion timepoints?
by Possidente, Thomas 12 Jun '24

12 Jun '24

External Email - Use Caution Hi there, I'm using this version of Freesurfer: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 I'm using mc-sess to run motion correction on some functional task and resting state data. I would like to perform censoring on high motion timepoints in order to reduce spurious correlations due to movement during connectivity analysis. My main question is: does mc-sess include censoring? If so, what are the threshold parameters? If not, are there any optional arguments to turn censoring on? If not, how do you recommend doing motion correction with censoring using Freesurfer? I know mc-sess uses AFNI's motion correction, just not sure if it utilizes censoring. Thank you, Tom

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Freesurfer June 2024