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:
External Email - Use Caution
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
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce
<bfis...@mgh.harvard.edu>
*Sent:* Monday, April 26, 2021 5:05 PM
*To:* freesurfer@nmr.mgh.harvard.edu <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
<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
*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-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:
* External Email - Use Caution *
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
<https://secure-web.cisco.com/1UgnQVFBMbbUsDXUzai5AvAOzqeQ34tRV2D60a4CwFPoV9ELm-tRW3UuArQKODsri6BLyF4EJHmNa9nKGS6jNCozaQ7DSSoo35W2Zcq8BiNph6IZdeBEPNibwjmOvLYqUKZ0s8CGUz3jDE8YU5aGEgmDYWpSFjTol96_wyLt3oAMNC2yHszucWMRU86DbnyyzXdV62_hUR6rolZPdllR4HqwHp7lR9Fbv7Fa3VEie64eiPeN3xened9Yqs3paID3QvXxY3WNwHWdkUkXhgePXyQ/https%3A%2F%2Fonlinelibrary.wiley.com%2Fdoi%2Ffull%2F10.1002%2Fhbm.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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