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Can you try using lh.thickness.mgz instead of just lh.thickness?
On 5/23/2023 1:12 PM, Malav Shah wrote:
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Hi there,
I believe the problem occured, because I generated pial surface by
segmenting, and then tessellating that label volume, instead the way I
see in log file of the subject 'bert' where standard autorecon
achieves it using the 'mris_place_surface' command
(mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg
aseg.presurf.mgz --threads 8 --wm wm.mgz --invol brain.finalsurfs.mgz
--rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0
--rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall
../label/rh.cortex.label --aparc ../label/rh.aparc.annot
--repulse-surf ../surf/rh.white --white-surf ../surf/rh.white)
Therefore, to go that way, I tried to "cheat" freesurfer with
"mris_place_surface --adgws-in autodet.gw.stats.lh.dat --invol
vol_seg.nii.gz --lh --i lh.wm.5smth --o lh.pial.nofix --pial
--repulse-surf lh.wm.5smth"
command using (following) made-up files....
- vol_seg.nii.gz- segmentation volume with voxel-intensities 1
(pial-matter), 2 (gray matter) and 3 (white matter)
- lh.wm.smth- white matter surface generated using white matter
segmentation's tessellation, and then smootheed with n_smooth = 5
- autodet.gw.stats.lh.pial is duplicated from the subject "bert" file
with following values
hemicode 1
white_border_hi 3
white_border_low 3
white_outside_low 3
white_inside_hi 3
white_outside_hi 3
pial_border_hi 1
pial_border_low 1
pial_outside_low 1
pial_inside_hi 1
pial_outside_hi 1
use_mode 1
variablesigma 1.000000
std_scale 1.000000
adWHITE_MATTER_MEAN 3
MAX_WHITE 3.00000
MIN_BORDER_WHITE 2.500000
MAX_BORDER_WHITE 2.5000000
MAX_GRAY 2.000000
MID_GRAY 2.000000
MIN_GRAY_AT_CSF_BORDER 1.5000000
MAX_GRAY_AT_CSF_BORDER 1.5000000
MIN_CSF 0.000000
adMAX_CSF 1.0000000
white_mean 3.000000
white_mode 3.000000
white_std 0
gray_mean 2.000000
gray_mode 2.000000
gray_std 0
min_border_white 2.000000
max_border_white 3.0
min_gray_at_white_border 1.5
max_gray 2.00
min_gray_at_csf_border 1.500
max_gray_at_csf_border 2.44
min_csf 1.000000
max_csf 1.000000
max_gray_scale 0.000000
max_scale_down 0.200000
However...I am getting the segmenetation fault error when it reads the
surface
cd
/Volumes/experiment/share/Malav/Ele_ana_cortexMRI/pipelines/dumba_piece/fs_trl2
setenv SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects/
mris_place_surface --adgws-in autodet.gw.stats.lh.dat --invol
vol_seg.nii.gz --lh --i lh.wm.5smth --o lh.pial.nofix --pial
--repulse-surf lh.wm.5smth
Reading in input surface lh.wm.5smth
ERROR: MRISedges(): too many faces: 181 938 n=7, m=3, k=2
Segmentation fault: 11
Any suggestions?
Thanks in advance,
malav
------------------------------------------------------------------------
*From: *"Malav Shah" <malav.s...@bccn-berlin.de>
*To: *"Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
*Sent: *Monday, May 22, 2023 5:35:56 PM
*Subject: *Re: [Freesurfer] Cortical thickness of elephant brain
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Thank you for a swift reply, Doug.
Upon running the command "mris_diff --debug --min-dist lh.pial.5smth
lh.wm.5smth 1 lh.thickness", the command line throws error that it
can't find file.
outcome:
5 --min-dist
Use Exact = 1
Writing mindist to lh.thickness
error: unknown file type for file (lh.thickness)
mris_diff done
I tried with an absolute file path which also didn't work.
Strangely, when mentioned no file location, but giving in a directory
"mris_diff --debug --min-dist lh.pial.5smth lh.wm.5smth 1
/Users/user-name/Desktop/",
2 files namely COR-info and COR-001 are created on Desktop, and
COR-info can be loaded as 'overlay' for a surface. Unfortunately,
these curvature values are not within range at all.
For further details, using the command with --debug flag gives the
following outcome (on command line)
Use Exact = 0
Writing mindist to /Users/monster/Desktop/
non-standard value for imnr1 (1, usually 256) in volume structure
non-standard value for type (3, usually 0) in volume structure
non-standard value for width (177753, usually 256) in volume structure
non-standard value for height (1, usually 256) in volume structure
mris_diff done
Here I attach a couple of screenshots to elaborate the outcome.
Kindly let me know how I can rectify the issue.
Thanks and regards,
malav
------------------------------------------------------------------------
*From: *"Douglas N. Greve" <dgr...@mgh.harvard.edu>
*To: *"freesurfer" <freesurfer@nmr.mgh.harvard.edu>
*Sent: *Monday, May 22, 2023 3:32:28 PM
*Subject: *Re: [Freesurfer] Cortical thickness of elephant brain
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Hi Malav, try
mris_diff --min-dist lh.wm.smth5 lh.pial.smth5 1 lh.thickness
The output will be on the pial surface. Reverse the surface order to
get it on the white surface
doug
On 5/22/2023 5:48 AM, Malav Shah wrote:
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Dear freeSurfer team,
I am trying to extract cortical thickness in a postmortem elephant
(structural) MRI scan.
I initiated the process with the segmentation of white (wm) and
pial matter, using MATLAB image processing tools.
Having satisfied white and pial matter labels, I "tesselated"
these volumes to generate pial and wm surfaces.
Then, with 'mris_smooth' command, I smoothed these surfaces.
When attempted to estimate cortical thickness between these
surfaces (lh.pial.smth5 and lh.wm.smth5), I get the following error.
command: mris_place_surface --thickness lh.pial.smth5 lh.wm.smth5
20 5 lh.thickness
error: No such file or directory
error:
ERROR:
MRISreadVertexPositions(/Volumes/experiment/share/Malav/Ele_ana_cortexMRI/pipelines/dumba_piece/lh.wm.smth5):
surfaces differ. Main: 177753 verts 365096 faces, lh.wm.smth5:
145095 verts 298436 faces
Surfaces may be out-of-date
I understand there is a mismatch in the number of nodes of these
surfaces. How can I rectify this issue to get to the thickness?
Thanks and regards,
malav
Malav Shah
PhD candidate, Michael Brecht Lab,
Humboldt University zu Berlin.
(+49) 163-216-9391
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