[Freesurfer] ROIs defined in MNI space and vol2surf

All, I have a question regarding the required registration file in mri_vol2surf. I have some spherical ROI's in MNI space produced via 3dUndump--they're volume files that show up in the correct places when loaded in with an MNI standard subject such as fsaverage. I also have some patients scan

[Freesurfer] Question about Cortical Thickness

I have a few questions regarding the instructions at: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness The instructions assume that there is an ROI in the same space as the T1.mgz map. Then they do the following: 1) Register the T1 to fsaverage 2) resample the ROI to the co

[Freesurfer] mri_convert scaling

All, I have some DICOM files from a pet scan and an MRI. I viewed the files in three different ways: 1. Opened the DICOM's directly in a viewer (Pmod) 2. Used mri_convert to change the DICOMs to a .nii, and opened them. 3. Used dcm2nii to change the DICOMS to a .nii and opened them.

[Freesurfer] FNIRT all NaN's

Freesurfer experts, I have a few fractional anisotropy images linearly registered to an FA atlas. I'd like to run FNIRT on them with reference the FA Atlas, but when I do, the output is entirely NaNs. I ran the program in verbose mode--and everything is NaN's. e.g.: SSD = -nann = 0

Re: [Freesurfer] FNIRT all NaN's

Sent this to the wrong list. Apologies. Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003 From: Funk, Quentin Sent: Wednesday, February 8, 2017 11:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: FNIRT all NaN's Freesurfer experts, I

[Freesurfer] TRACULA anterior/posterior

Freesurfer experts: I'm interested in comparing anterior and posterior pieces of a tract generated by TRACULA. Ideally, I'd like to take the probabilistic map (i.e. the path.pd.nii.gz from one of the folders in SUBJECT/dpath) and obtain a "posterior part" and an "anterior part" by masking. The

Re: [Freesurfer] TRACULA anterior/posterior

hing like that, to get the two endings of the tract that you care about. Hope this helps, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Funk, Quentin [qf...@houstonmethodist.org] Sent: Thursday, April 27, 201

[Freesurfer] QDec not allowing keyboard input on Display or Subjects Page

Freesurfer experts, QDEC won't allow me to type any information in on the subjects of Display page--i.e. in the FDR rate box, or in either threshold box. I found some emails regarding this from 2013, but no information that helps vis a vis the newest version. Is there a reason this is happen

[Freesurfer] Lookup table to surface overlay

External Email - Use Caution Freesurfer experts, I have some lookup table volume files in MNI space that I'd like to overlay on a surface (say, fsaverage's lh.pial). Currently I'm using this command: mri_vol2surf --mov look_up_table.nii --regheader fsaverage --interp nearest

Re: [Freesurfer] Lookup table to surface overlay

t/plain; charset="windows-1252" You might be sampling outside of the brain. Try adding --projabs -2 To sample 2mm below the pial surface On 5/25/18 10:32 AM, Funk, Quentin wrote: > > > Freesurfer experts, > > > I have some lookup table volume files in MNI space

[Freesurfer] Confusion about MRI_GLMFIT

External Email - Use Caution Freesurfer experts, I'm trying to figure out what values I get from mri_glmfit as in the tutorial. In particular, I'm interested in how I can compare these values to what I get fro

[Freesurfer] Strange annotations in Freeview?

External Email - Use Caution See the link here: https://imgur.com/a/ACsG73A [https://i.imgur.com/1zEaYUT.jpg?fb] Annotations? imgur.com Post with 0 views. Annotations? There's not actually any voxel values in those r

[Freesurfer] Siemens Enhanced DICOM

External Email - Use Caution Hey all- Freesurfer's recon-all fails if I try to give it a dicom from the new Siemens Enhanced format. Are there any workarounds that don't involve converting to nifti with a different software first? Thanks! Quentin Funk, PhD Houston Methodist Re

[Freesurfer] Reconstruction on BLADE sequences

External Email - Use Caution Freesurfer experts, We're attempting to get some reconstructions on MRI's for very advanced alzheimer's subjects. Many of these subjects have pretty extensive motion artifacts in their acquisitions. There has been some work with the so-called BLADE

[Freesurfer] ROIs to surface overlays / Arithmetic on surface overlays

External Email - Use Caution Freesurfer experts, I have a volumetric ROI (integer valued) in MNI space. I'd really like to display them on the fsaverage brain as a surface overlay so that it's clear what regions I'm looking at. Using something like this, I get pretty good resul

[Freesurfer] Different results on same MRI in different space ?

External Email - Use Caution Freesurfer experts, I have two MRIs for a patient separated by 5 years. I would like to look at progression of atrophy. These MRIs are different, however, firstly in terms of resolution (new one is 1x1x1, old one is 1.05x1.05x1.2), and secondly just

Re: [Freesurfer] Different results on same MRI in different space ?

External Email - Use Caution I used the SPM default coregistration settings -- which it calls "4th degree B-spline". From: "Douglas N. Greve" Subject: Re: [Freesurfer] Different results on same MRI in different space ? To: Message-ID: Content-Type: text/plain; char

[Freesurfer] Two questions about FDR correction

External Email - Use Caution Freesurfer experts, I have two questions that probably show my lack of understanding of many things related to thickness comparisons. I have a group of controls and a single subject with pathology. I'd like to run a thickness analysis comparing them

[Freesurfer] Update FS version and manually edited controls

External Email - Use Caution Freesurfer experts, I have a collection of older controls that I have reconstructed with FS 5.3. Due to age, many of these controls have hypointensities in the white matter that led to some errors in reconstruction that needed to be manually fixed.