[Freesurfer] Freesurfer Template Creation

Dear experts, I'm running the Fresurfer Longitudinal Stream and I didn't realize that creating the Template file, some time points were not in the right order: recon-all -base -tp -tp -tp -tp -all instead of: recon-all -base -tp -tp -tp -tp -all Does it affect the creation

[Freesurfer] Using asegstats2table for gtm.stats.dat?

Hi Unix experts, I am trying to extract the PVC-ed values from gtm.stats.dat for every subject. Is there a fast way to do this using a similar workflow with asegstats2table? Thanks. Best Wishes, Elijah  ___ Freesurfer mailing list

Re: [Freesurfer] TRACULA: Motion measures only

Yep, you can use the dmri_motion command. Run it without any arguments to see usage info. It needs: * Your original, unprocessed DWIs * b-value table * Output from your FSL eddy correction (*.ecclog from eddy_correct or *.eddy_parameters from eddy) Hope this helps, a.y From:

[Freesurfer] TRACULA: Motion measures only

Hi All, I have already preprocessed data in FSL and only want to use TRACULA to get the motion measures to match subjects based on motion. Is there any way I can get out the motion measures without doing all of the other preprocessing steps in TRACULA? Thanks, Colleen Buckless

Re: [Freesurfer] FA ROI analysis using 6-gradient-dir DWIs

Hi Yong – Your 6 directions are on the low end for tractography. I’d recommend using TRACULA with 30 directions or more. TRACULA doesn’t use the tensor model, which you can fit with just 6 directions, but a model that can capture multiple bundles per voxel, so you need a few more directions for

[Freesurfer] web image preprocessing

Dear Freesurfer experts, Does anyone know if there is a web portal where i can upload my T1 images to preprocess them with freesurfer and download the preprocessed files? Thank you so much! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] FA ROI analysis using 6-gradient-dir DWIs

Dear Bruce, Dear Anastasia, I would like to investigate white matter changes in a group of elderly patients. The acquired DWI data are 6-gradient-direction+1-non-DWI images by a clinic routine (not by me unfortunately). The meaningful analyses may be ROI-based DTI model considering FA, MD etc.

[Freesurfer] glmfit_sim for CVS mapped data

Hi, I've been trying to run glmfit_sim on a glm analysis with data in the AVG_35_CVS space but it doesn't seem to finish (tried almost two weeks). Does anyone have an idea what might be going on here? I used mc_full for 1000 iterations for my simlation.

[Freesurfer] Design matrix for local gyrification index in QDEC

Dear all, I have a quick question regarding the appropriate design (DOSS, DODS, SOSS, SODS) to be used with QDEC when comparing LGI values for 2 groups (patients and healthy controls). I have noted that a number of publications have used DODS when comparing LGI values between 2 groups while