[Freesurfer] using different versions of Freesurfer?

Hi Freesurfer team, I have currently used version 5.3. for all my cortical parcellations of MRI data, but for PET images of those same subjects I used the gtmseg, mri_coregister, gtmpvc of the 6.0 beta version to get partial volume effect-corrected SUVR(standard uptake value ratios). I am awa

[Freesurfer] TRACULA Error in virtualbox

I am trying to run TRACULA and keep getting the error FSLDIR: Undefined Variable. I have looked at the answers to this question that have been previously posted but cannot seem to remedy this problem. I'm running freesurfer 5.3 via virtualbox on windows. I have applied for a license and added that

[Freesurfer] Reconstructing cerebellum in FreeSurfer 5.3

Hi, I have been trying to figure out how to extract and reconstruct the cerebellum and possible the pons and brain stem. I have already ran recon-all and extracted the hemispheres but cannot seem to find any documentation on how to extract the other structures. I am running version 5.3 on Windows v

[Freesurfer] Trouble with Two Stage Longitudinal Analysis

FreeSurfer experts, I am attempting to use the two stage model for longitudinal analysis, however I keep receiving an error message that my design matrix is poorly scaled. I belive I have cross-checked my qdec, fsgd, design matrix, and contrast files and they all match so I do not think the probl

[Freesurfer] Request for patch for mri_convert, nifti1Read(): unsupported slice timing pattern 5 error

Hello Freesurfer experts, I'm trying to run the TRACULA preprocessing pipeline using data in NIFTI-1 format, but am receiving the following error: "nifti1Read(): unsupported slice timing pattern 5" Several other users have run into this problem. In the archives, there are a few links to dead fil

Re: [Freesurfer] Freeview -dti Display as Vectors Discrepancy

Hi Doug - Yes, there used to be a bug in how freeview used to interpret orientation info from the header of volumes loaded with the -dti option. Hopefully it's fixed now! a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]

[Freesurfer] Freeview -dti Display as Vectors Discrepancy

Hello experts, I have come across what I think could be an inconsistency with how freeview interprets and/or displays dti data as vectors. Specifically, the x component seems to be inverted in freeview from freesurfer-Darwin-lion-stable-pub-v5.3.0 as compared to fslview (version 509) AND freevi

[Freesurfer] Multiple Frames Error

Hello, I’ve been having a problem with recon-all lately. I’m relatively new to FreeSurfer and the processes that I have done in the past have been done on sample individualized scans in my lab and I ran into an issue once I started trying to run FreeSurfer on fMRI data provided by our lab. Whene

Re: [Freesurfer] mris_make_surfaces in longitudinal stream - explanation of parameters

Hi Antonin, we start slightly inside as surfaces expand more easily than shrink. This way even for the further atrophied time points there is a higher chance that it will be slightly inside it’s final position. The mris_longitudinal_surfaces is over 11 years old and was used for testing other

[Freesurfer] Overlap parcellation

Hello, I’d like to ask couple of questions regarding parcellation: First, we used aparc.DKTatalas40.annot implemented in Freesurfer; 1) we used the command mris_make_face_parcellation to have a first parcellation: mri_annotation2label --subject ${subjid1} --hemi lh --annotation ${S

[Freesurfer] QDEC versus R

Hello, As a PhD student, I send you this mail because i am meeting a misunderstanding with QDEC. In a few words : I made an analysis thanks to the QDEC tool : * I tested a correlation between an inhibition score and cortical thickness, corrected for age (continuous = inhibition score ; n