Oh, then you don’t need -l at all I don’t think. Have you sampled your ODI file onto the surface?

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Jensen, Alexandria
Sent: Monday, April 26, 2021 5:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to surface

External Email - Use Caution

Hi Bruce,

Thank you for the help! If the -a option is the aparc.DKTatlas.annot file and the -l option should be a label file, where does the ODI surface file come into play? My ultimate goal is to get average ODI values for each ROI in the DKT atlas.

Alexandria

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edu>
Sent: Monday, April 26, 2021 2:45 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to surface

Hi Alexandria

The file given in the -l option should be an ascii label file, not a volume.

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Jensen, Alexandria
Sent: Monday, April 26, 2021 4:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to surface

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This is the command I use for mris_anatomical_stats and the terminal output. I have taken out some of the directory information for privacy reasons.

mris_anatomical_stats \

-a /.../freesurfer/label/lh.aparc.DLTatlas.annot \

-l odi_in_cortexL.nativespace.mgh \

-b subject_xxx \

computing statistics for each annotation in /…/freesurfer/label/lh.aparc.DKTatlas.annot.

limiting computations to label ODI_in_cortexL.nativespace.mgh.

reading volume /…/freesurfer/mri/wm.mgz...

reading input surface /… /freesurfer/surf/lh.white...

Using TH3 vertex volume calc

Total face volume 227931

Total vertex volume 224122 (mask=0)

reading input pial surface /… /freesurfer/surf/lh.pial...

reading input white surface /…/freesurfer/surf/lh.white...

reading colortable from annotation file...

colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

<??q;??)?????????

error: mris_anatomical_stats: could not scan # of lines from label file

error: /…/freesurfer: could not read label ODI_in_cortexL.nativespace.mgh

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Sunday, April 25, 2021 8:35 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to surface

what is your mris_anatomical_stats command and terminal output?

On 4/22/2021 4:48 PM, Jensen, Alexandria wrote:

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Hello fellow Freesurfer users,

I am attempting to reproduce the analysis conducted by Parker et al. in their 2018 paper, “Cortical microstructure in young onset Alzheimer's disease using neurite orientation dispersion and density imaging” (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://onlinelibrary.wiley.com/doi/full/10.1002/hbm.24056). Cortical reconstruction of the T1 structural image was done in Freesurfer and NODDI processing using the NODDI toolbox in Matlab. The final steps I am attempting to complete include (1) projecting the ODI/NDI maps to an inflated surface to create surface maps (2. Materials and Methods, 2.5 Diffusion-weighted MRI processing); and (2) calculating mean ODI/NDI values across both hemispheres for a selected number of ROIs from the Desikan parcellation (2. Materials and Methods, 2.6 Cortical ROIs). The Parker et al. paper has provided the Freesurfer functions used in each of these final steps, but I am getting stuck on step (2) and am now worried that I have made an error in step (1). Below is the code I have written so far to project an ODI map onto an inflated surface:

bbregister \

--s freesurfer \

--mov odi.nii \

--init-fsl \

--reg register.dat \

--dti

tkregister2 \

--s freesurfer \

--mov odi.nii \

--reg register.dat \

--surf

mri_vol2surf \

--src odi.nii \

--out odi_in_cortex.nativespace.mgh \

--srcreg register.dat \

--hemi lh \

--projfrac 0.5

When I load lh.inflated, the lh.aparc.DKTatlas.annot annotation file, and the odi_in_cortex.nativespace.mgh overlay in Freeview, things seem to be correct. The issue I have is when I try to use mris_anatomical_stats(). I have tried different combinations of label and annotation files but am either getting errors or no errors but also no output.

Any guidance would be much appreciated! I am new to Freesurfer and have been learning it as part of my graduate research assistantship. I am using Freesurfer version 7.1.1 on a macOS Catalina, version 10.15.7 operating system for reference.

Cheers,

Alexandria Jensen
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