[Freesurfer] --pv flag in mri_segstats

External Email - Use Caution Hello FS team, If I want to calculate the average diffusion-weighted signal from a DWI image within WM regions using mri_segstats, would it be beneficial to use the --pv flag for "partial volume correction" , or would this only have an influence on the

[Freesurfer] Missing surface error when using tkregisterfv for checking Talairach Registration

External Email - Use Caution Hello Freesurfer, I am trying to run recon-all on a dataset, and a subset of appear to have problems with the Talairach registration. I believe that I should be able to check the Talairach registration, using this command: tkregisterfv --s $sub_id

[Freesurfer] N4BiasFieldCorrection before recon-all

External Email - Use Caution Hi there, Would it be problematic if N4BiasFieldCorrection were to be applied to the T1w before processing it in the standard recon-all pipeline? The reason is because we want and use the same T1w in other pipelines which require brain extraction an

[Freesurfer] mri_volcluster PDF multiple correction

External Email - Use Caution Dear Freesurfer support, My name is Vicente and I have a question for you regarding mri_volcluster. I am interested in using mri_volcluster to correct for multiple comparison after generating a probability distribution function (pdf) via simulation t

[Freesurfer] Longitudinal FS: does ordering of time points matter in the command

External Email - Use Caution Hi FS team, I just wanted to double check if, for the longitudinal pipeline, it matters which time point is being read first? For example, in the command below, should -tp -tp in the order of the scans being acquired? recon-all -base -tp -tp ...

[Freesurfer] Tech Support removal

External Email - Use Caution Hi, Can you please remove my email from FreeSurfer's email support. I don't want to keep receiving emails. Thank you, Sincerely, Luis Pena Marquez President of Graduate Students Association (GSA) [cid:638a6427-c72e-4c44-aebc-2e664d5d262f] ​ _

Re: [Freesurfer] Unsupported Datatype

Hi Rachel Is RGB the correct type for the file? What kind of data do you expect it to be? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Rachel Wagner Sent: Wednesday, November 16, 2022 1:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] Unsupported Datatype

Re: [Freesurfer] Unsupported Datatype

External Email - Use Caution I see, thank you! Do you know of a way I can convert it to a file type that is supported? Or what an alternative file type might be? Thank you again! Rachel From: Huang, Yujing Sent: November 16, 2022 10:29 AM To: Fr

Re: [Freesurfer] Issue with rotation during longitudinal base creation

External Email - Use Caution Hi Nathan, I am reaching out because it looks like we are coming up against a similar issue with Freesurfer's 'mri_robust_template' and I was wondering if you have been able to figure out this error for your images. I am receiving the similar erro

Re: [Freesurfer] Unsupported Datatype

Hi Rachel, It appears that your nifti has RGB datatype (128). Freesurfer doesn't support that yet. Best, Yujing From: Huang, Yujing Sent: Wednesday, November 16, 2022 7:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: RE: Unsupported Datatype Hi Rachel, Can you provide the version of Freesu

Re: [Freesurfer] Original image and the mask file dimension mismatch

Hi Padma, Freesurfer outputs volumes in conformed anatomical space (volumes in 1x1x1mm, 256x256x256). For information on how to convert volumes back to native anatomical space, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat Best, Yujing From: freesurfer-boun...@nmr.mgh.ha

Re: [Freesurfer] about using -norandomness flag with recon-all

Hi Xin, In Freesurfer 7.3, recon-all is running with ‘-norandomness’ by default unless ‘-randomness’ is specified in the command line. ‘-randomness’ uses current time and date as the seed for random number generation. This results in slightly different surfaces each run. ‘-norandomness’ ensure

Re: [Freesurfer] Unsupported Datatype

Hi Rachel, Can you provide the version of Freesurfer that you are running? Thanks. Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Rachel Wagner Sent: Tuesday, November 15, 2022 11:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Unsupported Datatype