[Freesurfer] Optseq2 timing outputs

Hi all, I sent a message previously and just wanted to check in one more time about this question (apologies for the repeat message!). I’m using Optseq2 to generate stimulus / jitter schedules and, depending on the TR I use, in the output files I see onset times like 124.4001 (instead of

[Freesurfer] VBM

Hello Experts, Can we do VBM in MNI template using the outputs from recon all? Which file should I be using? And how do I smooth the volumes? Thank you for the tips! -- Shane S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] multi-frame input error with PAR/SEC origin file

Hi Idil you have to figure out what the input volume has more than 1 frame (that is, why is it 4d). It could be because you saved phase and mag, or because there are multiple echoes, but until you understand what the additional frames are we can't process it. YOu can start by bringing the

[Freesurfer] multi-frame input error with PAR/SEC origin file

Hello FreeSurfer experts, I am trying to run recon-all on a nifti file converted from PAR/SEC using dcm2niix, and this error came up pretty soon after the script started to run; >> mri_convert.bin >> /home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz >>

Re: [Freesurfer] Generating Surfaces from Labels

Hi Zach I think if you cut and flatten the cortical part of the surfaces, convert tha .annot files to separate label files, you can then use label2flat on each label to generate a flattened patch that is just taht label. I haven't used it in years (decades?), but I think it should work

[Freesurfer] Generating Surfaces from Labels

Hello All, I have been attempting to convert Label files generated using mri_annotation2label into surface files for use in external programs. In order to do this I first need to convert the label files into freesurfer binary. I have attempted to use the mri_label2vol function to generate an mgz

Re: [Freesurfer] Urgent help with stats in FreeSurfer

It sounds like you have reported everything correctly. The clusterwise p-value corresponds to a critical cluster size at the given cluster forming threshold (4), sign (neg), and fwhm (fwhm.dat in the glmdir). So the answer to the reviewer is "yes". If you want to report the critical size, then

[Freesurfer] ASL with rcbf-prep

Dear freesurfers, I have data collected here at the martinos using the Siemens ep2d_PASL sequence. I run the command "rcbf-prep —s subject —rcbf asl.nii —o tesfolder" or something like that. The resulting rcbf.nii looks good, but the values are negative? Is this just a matter of tag and ref

[Freesurfer] Urgent help with stats in FreeSurfer

Hi, One of my papers is under review showing significant differences in cortical surface area between healthy controls and patients. In this paper, regarding statistical results, for multiple comparison correction, I ran Monte Carlo simulations using following command: mri_glmfit-sim \

[Freesurfer] question about effects of changing server and freesurfer versions IF the entire study is consistent

Hello Freesurfer experts, We have processed, hand-edited, and QA'ed over 130 subjects' scans with version 5.3.0 on a linux sci6 box, and extracted the atlas-based ROI values for cortical thickness, volume, curvature, etc. The servers need upgrading but there are still whole brain analyses to

[Freesurfer] Sphere above a certain vetex

Hi everybody, I have a .annot file and I would like to display a sphere above one certain vertex. (I know the coordinates of the vertex) Someone knows a way to do that ? Thank you very much, Redwan ___ Freesurfer mailing list

Re: [Freesurfer] Cortical thickness map for a pediatric case

Thank you Bruce, sure thing :) Regards, Sneha From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Monday, August 7, 2017 6:21:57 PM To: Freesurfer support list

[Freesurfer] Matrix ill-conditioned error for dods thickness mri_glmfit analysis

Hi FreeSurfer Experts, I am trying to run a dods cortical thickness analysis examining the interaction of group on a continuous variable while controlling for other variables. Specifically, I have 6 classes (gender by three groups [zero, one, two]). I am interested in the group interaction

[Freesurfer] Linear Mixed Effects model

Dear FreeSurfer, I have a longitudinal study (patients and controls) with two time points (i.e., baseline and six-weeks follow-up). I would like to use the LME model as it can handle unequal timing and different number of time points across subjects due to missing data. I would like to test if