[Freesurfer] Annualised percentage change within linear mixed models
Hi FreeSurfer team, I was wondering if it is possible to use a measure of annualised percentage change instead of raw thickness within the FreeSurfer toolbox for Matlab (i.e. when running linear mixed models)? Thanks for your help, Nandi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Downsampling data and writing mgh file
Dear FreeSurfer Experts, I'm trying to downsample the thickness info of subjects (with longitudinal data) to the same number of vertices as fsaverage6, and would like to save this output as an mgh file for use in Matlab. I was able to downsample a single subject using the following command: mri_surf2surf --hemi lh --srcsubject 'subjID' --srcsurfval thickness --src_type curv --trgsubject fsaverage6 --trgsurfval 'output name' --trg_type mgh However, it won't allow me to enter multiple subject IDs into the same command. I'm wondering what's the best way to do this, with the aim of getting a single mgh file that has the thickness data for all subjects. Do I have to create a separate downsampled mgh file for each subject and then merge them? Thanks, Nandi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FDR correction in Matlab
Hi FS team, I was wondering if you could help me with FDR correction for linear mixed models within Matlab. I have run FDR2 correction using the following command: *dvtx = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0); *However, dvtx was empty, so I would like to try lme_mass_FDR instead. Could you please help me with the command for FDR correction, as well as how to visualise the corrected significance map in FreeSurfer? Thank you, Nandi Vijayakumar MPsych (Clinical Neuropsychology) / PhD Candidate ADAPT | Adolescent Development and Psychopathology Team Melbourne School of Psychological Sciences University of Melbourne Email: *n.vijayaku...@student.unimelb.edu.au * ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FreeSurfer6 hires patch for longitudinal output
External Email - Use Caution Dear FreeSurfer team, I have processed my data through the longitudinal stream of FreeSurfer6 using the -hires flag. I would like to apply the patch to fix the global metrics, but seem to run into an error when supplying the longitudinal subject directory. I've tried running the following command: recon-all -long sub-001_wave1.long.sub-001 sub-001 -segstats -parcstats -parcstats2 -parcstats3 -wmparc -balabels But get the following error: Unmatched ". The command seems to work fine on the cross-sectional directories. So I'm wondering if the patch can be applied to longitudinal directories? Thanks, Nandi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] N3 correction issues
Hi all, We are processing longitudinal structural MRI data on Freesurfer 5. 0. As our images have some intensity problems, we were running an N3 correction outside of FreeSurfer using a mask in order to maximize this step (as per recommended by Boyes et al., 2008). We first ran autorecon1 and then used the brainsmask.mgz as a mask for the N3 correction, using the following steps. mri_convert orig.mgz orig.mnc mri_binarize --i brainmask.mgz --min 1 --o binmask.mgz* mri_convert binmask.mgz binmask.mnc* mincnorm orig.mnc orig_norm.mnc nu_correct -mask binmask.mnc -distance 50 -iterations 1000 -stop 0.0001 -shrink 2 -fwhm .05 orig_norm.mnc nu.mnc mri_convert nu.mnc nu.mgz* This nu.mgz was then fed into freesurfer and autorecon1 was run over again without nuintensity correction. However, during this step, many of our scans are crashing, with the T1.mgz being very dark. When the same scans were run through Freesurfer with the nuintensitycor-3T flag (without using a mask), there were no crashes. Do you have any advice on why the N3 correction using the mask is crashing when re-running autorecon 1? Should we be using different nu_correct parameters to help the process? Thanks for your help! Nandi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
