Re: [Freesurfer] Calculating local gyrification using CIVET's surface file ('.obj')
Hi Kie Woo, The other thing that you might want to check is that the pial-outer-smoothed surface and the pial surface match, in case the transformation from the CIVET format induced any strange translation in space and they don't line up. Just open them both on a volume using tkmedit or freeview. Best, Marie On Oct 1, 2015, at 8:54 AM, Bruce Fischl wrote: > Hi Kie Woo > > can you run mris_euler_number on those surfaces to see if they are > topologically correct? > > cheers > Bruce > > > On Thu, 1 Oct 2015, Nam, Kie Woo wrote: > >> Dear experts, >> >> I’m trying to calculate local gyrifcation index using CIVET’s surface file >> (‘.obj’). >> >> >> >> >> First, I’ve successfully done ‘CIVET --> FreeSurfer’ conversion and created >> a ‘.pial’ file - below are the commands that worked for ‘CIVET --> >> FreeSurfer’ and ‘FreeSurfer --> CIVET’ conversions. >> CIVET (MNI obj) --> FreeSurfer (ASCII) --> FreeSurfer (BINARY_BE (Big >> Endian)): “ConvertSurface -i_mni CIVET_2.0_icbm_avg_mid_sym_mc_left.obj >> -o_fs lh.pial; mris_convert lh.pial.asc lh.pial” >> FreeSurfer (BINARY_BE (Big Endian)) --> CIVET (MNI obj): “ConvertSurface >> -i_fs lh.pial -o_mni lh.pial” >> >> >> >> >> Then, I ran “recon-all -s Subject -localGI”, but it keeps crashing with the >> following message. >> >> lGI for vertex number 5501 of the outer mesh is 4.1122 >> lGI for vertex number 5601 of the outer mesh is 0.86156 >> lGI for vertex number 5701 of the outer mesh is 3.8343 >> ... remeasuring lGI value for vertex iV = 5801. It may take a few minutes. >> WARNING -- Problem for vertex iV = 5801, lGI value is aberrantly high >> (lGI=62.3205)... >> ...lGI computation will be stopped. This may be caused by topological >> defects, check mris_euler_number on the pial surface. >> >> >> The link below suggests rerunning “recon-all -autorecon2-wm -randomness”, >> but it’s not an option for me because I have no other FreeSurfer compatible >> files except “.pial”. >> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg18228.html >> >> >> >> So, could there be any solution for this? >> >> >> >> Best wishes, >> >> Kie Woo > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Calculating local gyrification using CIVET's surface file ('.obj')
Hi Kie Woo can you run mris_euler_number on those surfaces to see if they are topologically correct? cheers Bruce On Thu, 1 Oct 2015, Nam, Kie Woo wrote: Dear experts, I’m trying to calculate local gyrifcation index using CIVET’s surface file (‘.obj’). First, I’ve successfully done ‘CIVET --> FreeSurfer’ conversion and created a ‘.pial’ file - below are the commands that worked for ‘CIVET --> FreeSurfer’ and ‘FreeSurfer --> CIVET’ conversions. CIVET (MNI obj) --> FreeSurfer (ASCII) --> FreeSurfer (BINARY_BE (Big Endian)): “ConvertSurface -i_mni CIVET_2.0_icbm_avg_mid_sym_mc_left.obj -o_fs lh.pial; mris_convert lh.pial.asc lh.pial” FreeSurfer (BINARY_BE (Big Endian)) --> CIVET (MNI obj): “ConvertSurface -i_fs lh.pial -o_mni lh.pial” Then, I ran “recon-all -s Subject -localGI”, but it keeps crashing with the following message. lGI for vertex number 5501 of the outer mesh is 4.1122 lGI for vertex number 5601 of the outer mesh is 0.86156 lGI for vertex number 5701 of the outer mesh is 3.8343 ... remeasuring lGI value for vertex iV = 5801. It may take a few minutes. WARNING -- Problem for vertex iV = 5801, lGI value is aberrantly high (lGI=62.3205)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. The link below suggests rerunning “recon-all -autorecon2-wm -randomness”, but it’s not an option for me because I have no other FreeSurfer compatible files except “.pial”. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg18228.html So, could there be any solution for this? Best wishes, Kie Woo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Calculating local gyrification using CIVET's surface file ('.obj')
Dear experts,
I'm trying to calculate local gyrifcation index using CIVET's surface file
('.obj').
First, I've successfully done 'CIVET --> FreeSurfer' conversion and created a
'.pial' file - below are the commands that worked for 'CIVET --> FreeSurfer'
and 'FreeSurfer --> CIVET' conversions.
CIVET (MNI obj) --> FreeSurfer (ASCII) --> FreeSurfer (BINARY_BE (Big Endian)):
"ConvertSurface -i_mni CIVET_2.0_icbm_avg_mid_sym_mc_left.obj -o_fs lh.pial;
mris_convert lh.pial.asc lh.pial"
FreeSurfer (BINARY_BE (Big Endian)) --> CIVET (MNI obj): "ConvertSurface -i_fs
lh.pial -o_mni lh.pial"
Then, I ran "recon-all -s Subject -localGI", but it keeps crashing with the
following message.
lGI for vertex number 5501 of the outer mesh is 4.1122
lGI for vertex number 5601 of the outer mesh is 0.86156
lGI for vertex number 5701 of the outer mesh is 3.8343
... remeasuring lGI value for vertex iV = 5801. It may take a few minutes.
WARNING -- Problem for vertex iV = 5801, lGI value is aberrantly high
(lGI=62.3205)...
...lGI computation will be stopped. This may be caused by topological defects,
check mris_euler_number on the pial surface.
The link below suggests rerunning "recon-all -autorecon2-wm -randomness", but
it's not an option for me because I have no other FreeSurfer compatible files
except ".pial".
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg18228.html
So, could there be any solution for this?
Best wishes,
Kie Woo
___
Freesurfer mailing list
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
