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My apologies if I am missing something obvious, but isn't mri_segstats used to
compute statistics on segmented volumes? I have moved my ODI map onto an
inflated surface using the mri_vol2surf command, which is why I was attempting
to use mris_anatomical_stats.
My attempts at using mri_segstats for this purpose have been resulting in
errors, which is why I am asking.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: Monday, May 10, 2021 9:23 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to
surface
You can use mri_segstats on the output to get your table of values for each
ROI. Run it with --help and see example 5
On 4/27/2021 1:50 PM, Jensen, Alexandria wrote:
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I believe I have using the code below, though I am not fully certain of it:
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_cortexL.nativespace.mgh \
--srcreg register.dat \
--hemi lh \
--projfrac 0.5
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Fischl, Bruce
<bfis...@mgh.harvard.edu><mailto:bfis...@mgh.harvard.edu>
Sent: Monday, April 26, 2021 5:05 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to
surface
Oh, then you don’t need -l at all I don’t think. Have you sampled your ODI file
onto the surface?
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
On Behalf Of Jensen, Alexandria
Sent: Monday, April 26, 2021 5:01 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to
surface
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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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>>
Sent: Monday, April 26, 2021 2:45 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Jensen, Alexandria
Sent: Monday, April 26, 2021 4:26 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to
surface
External Email - Use Caution
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 \
lh
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>
Sent: Sunday, April 25, 2021 8:35 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto: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
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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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