[Freesurfer] bbregister surfaces

Hi all, According to https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25476.html, bbregister uses the white matter surface and cortical thickness measures to perform its registrations, though there was some possibility of using the pial surface in further releases. I just want to ver

[Freesurfer] Expert file for recon-all -hires

Hi all, If I'm reading this < https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon> correctly, the current best practice for `-hires` is to include an expert file containing "mris_inflate -n 15", and that this should work for all voxel sizes (0.75mm)^3 - (1mm)^3? Or do we need to empirical

[Freesurfer] Adjust bbregister affine to target raw T1

Hi all, Suppose you have a sub-pipeline: $ recon-all -s $SUBJ -i $T1 -all $ bbregister --s $SUBJ --mov $EPI --init-fsl --t2 --reg bbreg.dat --fslmat fsl.mat Now `bbreg.dat`/`fsl.mat` is registered to `$SUBJECTS_DIR/$SUBJ/mri/T1.mgz`; what's the best way to register to $T1? I've tried: $ tkregi

Re: [Freesurfer] Adjust bbregister affine to target raw T1

t fsl did not provide a good initial registration. If > you have v6, you can leave off --init-fsl and it will use mri_coreg > (which is more robust). > > > On 03/09/2017 03:24 PM, Christopher Markiewicz wrote: > > Hi all, > > > > Suppose you have a sub-pipeline: > >

[Freesurfer] BUG: bbregister --init-best needs to unset InitCoreg

Hi all, bbregister --init-best always produces "ERROR: cannot spec an init method with --init-best", because InitCoreg is defined as 1 by default, and never set to 0 by --init-best. (Setting something else that unsets InitCoreg will trigger the same error.) Example, given SUBJ and EPI: $ bbregis

Re: [Freesurfer] Adjust bbregister affine to target raw T1

I would not worry about some > being done with coreg and some with flirt > > On 3/9/17 3:40 PM, Christopher Markiewicz wrote: > > Hi Doug, > > This is the final line with "cost" in it: > > MinCost: 0.862331 7440.183178 7411.264107 -1.819400 > >

[Freesurfer] First-level GLM on externally-preprocessed functionals

Hi list, We're working on making a preprocessing stream that will be generally accessible to different analysis streams, including FreeSurfer. One component of this is sampling functional volumes to FreeSurfer meshes, and I want to test this component by running a simple first-level GLM in FreeSur

[Freesurfer] Survey on inputs for surface-based analysis pipelines

Hi list, We're working on FMRIPREP , a pipeline aimed at performing baseline preprocessing, and producing cleaned structural and functional data which can be fed into any of a number of analysis pipelines. We've recently begun incorporating surface r

Re: [Freesurfer] negative header after preproc-sess

Hi Doug, I wonder if there's a plan to move to NIfTI-2 as the default encoding for .nii(.gz) images that would can't be encoded in a standard-conforming NIfTI-1? I believe all of the major packages support NIfTI-2 in their latest releases (with the possible exception of ANTs, which I don't beli

[Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

Hi, I've used `bbregister` to generate a transform `bold2T1.lta` from `bold.nii` to `T1.mgz` (assume we have a `T1.nii` as well for the sake of ANTs). The following produces a well-aligned output: mri_convert --apply_transform bold2T1.lta bold.nii bold_space-T1.nii As does the following:

Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

into translation, scale, and direction cosine, and then the matrix is thrown away. When a volume with the same geometry is written out, the matrix is recomputed. Some resolution is lost during the decomposition/recomposition, and we don't end up with the exact same matrix. On 10/14/17 1:30 PM, C

Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

ave a special case (e.g. maybe we never tested registration across different resolutions or whatever?). Thanks, Martin https://gate.nmr.mgh.harvard.edu/filedrop2/ On 16. Oct 2017, at 19:37, Christopher Markiewicz mailto:markiew...@stanford.edu>> wrote: Doug, Sorry if I muddied things by goi

[Freesurfer] readVolGeom corner case leads to lta_convert failures

Hi all, We've run into an issue where lta_convert is failing if the filename line in a volume geometry is of a specific length. We've identified the source of the problem, and made a pull request on GitHub that at least partially fixes the issue (https://github.com/freesurfer/freesurfer/pull/18

Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

d.edu on behalf of Christopher Markiewicz Sent: Tuesday, October 17, 2017 12:11:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms Hi Martin, I've uploaded a .tgz file with a T1w vo

[Freesurfer] RFC: Changes to nibabel API for .mgh/.mgz files

Hi all, I'd like to solicit input for the Python interface to .mgh/.mgz files in nibabel[0]. I've recently had cause to dig into this interface (MGHImage[1]), and found that the naming of header fields[2] (analogous to variable names in C structs) is inconsistent with all of my experience with

[Freesurfer] Resolution limits of FLAIR/T2w for effective pial refinement

Hi all, I wonder if people have any data (or anecdotes - I'm not picky) with regard to how high of resolution T2w or FLAIR images need to be in order to be useful for FreeSurfer's pial refinement. I've seen a couple threads suggesting the optimal is ~1mm isotropic, and that thick slice (1x1x5 m

Re: [Freesurfer] Clarification about .annot file format

External Email - Use Caution Hi all, I believe I've gotten to the bottom of this, and the problem is incorrect documentation, both in the read/write_annotation.m files and in the wiki. Taking the FreeSurfer C source as the de facto specification, we can refer to the colortab.

Re: [Freesurfer] Clarification about .annot file format

: Friday, September 28, 2018 12:47:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Clarification about .annot file format Thanks Chris, can you point us to the offending wiki page? doug On 9/28/18 12:44 PM, Christopher Markiewicz wrote: External Email - Use Caution Hi

Re: [Freesurfer] Clarification about .annot file format

bject: Re: [Freesurfer] Clarification about .annot file format Is this the offending line? or is there more? value = (A * 2563) + (B * 2562) + (G * 256) + (R) On 9/28/18 1:03 PM, Christopher Markiewicz wrote: External Email - Use Caution Hi Doug, The relevant wiki page is:

[Freesurfer] Python Surface API discussion

External Email - Use Caution Hi FreeSurfers, I wanted to reach out to this group about plans to create a new Python API for working with surface data in Nibabel. As you are all undoubtedly aware, surface meshes are too large and cumbersome to pack with data sampled on the surfac

[Freesurfer] Data formats review - Surface and surface-sampled data

External Email - Use Caution Hi all, This Friday, April 22, we at Nipy will be hosting a journal club on surface and surface-sampled data formats. We are focused on current interchange formats and possible future directions, which seems like it might be of interest to the FreeS

[Freesurfer] -gcareg dropped from -autorecon2-volonly

External Email - Use Caution Hi all, This is a duplicate of a bug report on GitHub (https://secure-web.cisco.com/1C5EnDIMtZh6wk0SJMqe8l166ycKmSdnL5atT3CIHDPAY15Ixtf93Rif0FmPFCZaftXbqlhK5AbXT22OXXCJq9JgIiSOyglr8IF1n3lOAzrtCIHcr8C2aLwqsXcMciJwp9Mz2DV4vmcWjm2v_xTUmw6hoea4u37a4hkUyIk

Re: [Freesurfer] -gcareg dropped from -autorecon2-volonly

l= 1; set DoSegStats = 0; set DoNormalization2 = 1; set DoMaskBFS= 1; set DoSegmentation = 1; set DoFill = 1; breaksw On 3/24/2023 9:57 AM, Christopher Markiewicz wrote: > External Email - Use Caution > &

Re: [Freesurfer] -gcareg dropped from -autorecon2-volonly

09:29 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -gcareg dropped from -autorecon2-volonly In my version, it appears just after DoCANormalize. Can you have grep print out one more line? On 3/28/2023 9:05 AM, Christopher Markiewicz wrote: > External Email - Use Caution

[Freesurfer] Possible bug: recon-all -i $T1 -T2 $T2 -autorecon1 attempts to run -T2pial

External Email - Use Caution Hi all, This is a reproduction of GitHub issue 1010. There is a section of recon-all (L5927-5930 in current dev) that states: # MOD: turn on T2/FLAIR pial editing when FLAIR specified # This can backfire, eg, if not all the preceeding ste