[Freesurfer] Longitudinal pipeline in pediatric sample with TIV difference

External Email - Use Caution Hello Freesurfers experts, I have a pediatric sample and I wanted to use the longitudinal pipeline (the time acquisitions are 8 years apart and age range is from 6 years to 17). I saw that longitudinal pipeline assumes that TIV doesn't change, which in

[Freesurfer] Label on fsaverage failure

External Email - Use Caution Dear Freesurfer developers, We have a series of MRI scans and we are trying to extract cortical thickness in certain regions of interest. The ROIs already exist - some are in .img and some in NIFTI format - and we want to tranform them into labels and

[Freesurfer] POSTDOC POSITION - modeling the functional and structural architecture of the visual system

External Email - Use Caution POSTDOCTORAL SCHOLAR We are recruiting a Post Doctoral Scholar in the Cognition and Brain Circuitry Laboratory of Dr. David Osher at the Ohio State University. The Post Doctoral Scholar will plan, design, and conduct research using computational mode

[Freesurfer] Two research assistant positions

External Email - Use Caution RESEARCH ASSISTANT We are recruiting 2 technical research assistants in the Cognition and Brain Circuitry Laboratory of Dr. David Osher at the Ohio State University. Primary duties for both positions include: conducting neuroscience research on the f

[Freesurfer] Postdoctoral position: Neuroimaging, PCAN lab, University of Calgary, Canada, 2 years

External Email - Use Caution Dear All, The PCAN lab: http://pcanlab.ca has a two-year funded postdoctoral research fellow position under the supervision of Dr. Oury Monchi starting immediately to work on the following project: *Neuroimaging and other predictors of cognitive and

Re: [Freesurfer] Bounding box dimensions for mri_cvs_register (MNI space)

Hi Liz, (1) Given that the included MNI template lives in the 1mm isotropic space, the output will also live there. Your two commands seem to be the right for to achieve what you intend to do. (2) I suspect there was a dimensionality difference between your fMRI and sMRI images even before the

Re: [Freesurfer] Longitudinal Stream Problem

Hi Laura, it looks like there is a bug in v6 that does not transfer the edits correctly. This is fixed in v7, but I'm looking into getting you a version of mri_mask that will work in v6. doug On 6/23/2020 1:49 PM, Danielian, Laura (NIH/NINDS) [E] wrote: External Email - Use Caution

Re: [Freesurfer] How much recon editing is appropriate?

No, not needed, if you are only working with subcortical volumes. On 6/30/2020 8:55 PM, Wakim, Kathryn-Mary wrote: > External Email - Use Caution > > Hi everyone! > > Quick question. For my specific analysis, I’m most interested in the values > given in the aseg.stats file. I’m comparing

Re: [Freesurfer] Sub-cortical areas and other atlases

You can't run mri_glmfit-sim on ROI output. mri_glmfit-sim is for correcting multiple comparisons on maps. For ROIs, you'll have to leave them uncorrecrted or correct with Bonferonni or FDR. In theory, you could use permutation. On 6/30/2020 9:54 PM, Martin Juneja wrote: External Ema

Re: [Freesurfer] error for input volume

External Email - Use Caution The error is 'no space left on device'. Please check your hard disk space, the drive may be full (or your quota reached on multi-user storage). Best, Tim > On July 1, 2020 at 11:41 AM N Saf wrote: > > > External Email - Use Caution

[Freesurfer] error for input volume

External Email - Use Caution Dear Freesurfer experts, I've tried to perform an autorecon1 for a patient's brain MRI(T1). There are some dark regions in white matter areas. an error has occurred which I've attached the corresponding log file here as well as the raw nii data. I wond

[Freesurfer] Bounding box dimensions for mri_cvs_register (MNI space)

External Email - Use Caution Hi guys, I have a couple of queries regarding the output dimensions for mri_cvs_register. 1. If I am registering my images to MNI space, can the command give me a 2mm image, or will I only get a 1mm image which I then need to convert into a 2mm?