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-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 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-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
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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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edu mailto:BFISCHL@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto: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 mailto: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 \
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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1oAgQS75ESxIlbLn_CbYPMelz4O1gA5LetDhIiwrRSFrFR-s6afO0y1KuU7x2mDhkraWwa3fpRDUPRZd33bzp9Ojyo7XWNLrYp749S-MCcX-3HbLH4cqKQqhic0hjuZb9SLlM-fjYUJFARFoI8XgFtHMcNr77JQF0-dz4UOfqY8EVtDdw5SxsOTBf0eIZumoOsXT4WDgu3QstRu7pZTa8CFV3MMCIs2MnGBV82_nVbCy0e-xdP5wza_h5FEMuQnl54lE11uMA7hFUHKcoY7HYaA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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