[Freesurfer] Thalamic nuclei segmentation
External Email - Use Caution Hi! Few weeks ago I found the thalamic nuclei segmentation tool in Freesurfer development version and I had it working fine. However, I can’t find the web page anymore with the instructions how to use the tool. Is the tool still in use and if so, where can I find the instructions? Also, does free surfer have a similar segmentation tool for cerebellar subsegments? Thank you in advance! -Antti ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Thalamic nuclei longitudinal analysis
External Email - Use Caution Dear FS experts, I'm using the thalamic nuclei segmentation on T1-images. Is it possible to perform longitudinal analysis with this data, or could I just segment the different time points separately to see volume reduction of specific nuclei? Best, Antti Cajanus PhD student ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] dt_recon error: dimension mismatch between y and X
External Email - Use CautionDear FS experts,I’m attempting to run dt_recon on my own DWI DICOM file with registration to corresponding structural data, as described in FS diffusion tutorial (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0) I’m using FS version freesurfer-darwin-macOS-7.1.1-20200811-8b40551 on Mac (MacOS Big Sur v. 11.1). I’ve already succesfully run recon-all on the T1 scan. However, when I’m running the dt_recon, I’m getting the following error:Command I’m using: dt_recon --i $TUTORIAL_DIR/$subj/orig/DTI/S142783/NIFD_1_S_0001_MR_dti_WIP_b2000_64dir__br_raw_20120306104435815_50_S142783_I288323.dcm --s $subj --o $TUTORIAL_DIR/$subj/dtreconERROR: dimension mismatch between y and X. y has 65 inputs, X has 66 rows.I’ve searched the archive, however not finding any similar issues. Does anyone have an idea how to solve this error? Attached is the dt_recon.log.Best,Antti Cajanus dt_recon.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Group comparison with MD
External Email - Use Caution Dear Freesurfer experts, I’m trying to do a group comparison of cortical mean diffusivity. The study subjects form 2 groups (demented vs. non-demented). I’ve run recon-all and dt_recon on all of my study subjects. My goal is to create a surface, that has the mean diffusivity values sampled from the midpoint of the cortical thickness (50% the distance between WM and pia). I’m puzzled about three things; 1) Can I use the adc.nii created by dt_recon to represent the mean diffusivity or should I use something else? 2) Can I obtain the MD values from the midpoint of cortical thickness using mri_vol2surf command, using the optional ”–projfrac 0.5” flag? i.e. mri_vol2surf –src adc.nii.gz --out adc-to-midthick.mgz --hemi lh --projfrac 0.5 --srcreg register.dat 3) I want to smooth the the data with FWHM 15mm. Should I apply the smoothing in the mri_vol2surf (as registering the adc.nii to cortical ribbon) or in the mri_surf2surf phase (as registering the adc-to-midthick.mgz to fsaverage)? Thank you already in advance! Best, Antti Cajanus___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
