Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to surface

Thu, 27 May 2021 14:48:22 -0700

No, not just volume. Example 5 has a surface example. If you want help with your mri_segstats command, send the command and the terminal output 

On 5/24/2021 2:29 PM, Jensen, Alexandria wrote:


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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


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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-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*
      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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