What surfaces are there?
On 2/11/2021 4:35 PM, Koch, Erin M. wrote:
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Hi Douglas,
I am sorry I have to bug you once more. While the inflation step
completed with the suggested flag, as did the flattening step (for
creating a flat map), when I went to register a functional scan to the
inflated and flat map the command:
mri_vol2surf —src 'PVal_resliced' —srcreg reg.dat —projfrac 0.5
—interp nearest —hemi lh —out 'PVal_lh')
mri_vol2surf —src 'PVal_resliced' —srcreg reg.dat —projfrac 0.5
—interp nearest —hemi rh —out 'PVal_rh')
failed because the recon-all did not create a few files including:
lh.white, and rh.white
Is this due to the flags and expert options that were needed to
complete the inflation?
Can I run a separate command to create these files?
thanks,
Erin
------------------------------------------------------------------------
*From:* Koch, Erin M. <er...@caltech.edu>
*Sent:* Wednesday, January 27, 2021 10:04 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Recon-all exiting with Errors during
surface inflation
It completed! Thank you the help.
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*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Wednesday, January 27, 2021 10:00:54 AM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Recon-all exiting with Errors during
surface inflation
It should not need it for the inflation. You can try adding
-no-cortex-label and see how far you get
On 1/27/2021 12:39 PM, Koch, Erin M. wrote:
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Thanks for the info. Is it possible to put in a "fake"
aseg.presurf.mgz file? Do you think this is a possible work around,
or is the inflation for flat map generation somehow reliant on this
file now?
Erin
------------------------------------------------------------------------
*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:* Wednesday, January 27, 2021 7:40 AM
*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] Recon-all exiting with Errors during
surface inflation
It needs to be there. Sorry, I rewrote parts of the stream for v7 and
did not consider the impact on NHP streams (since they are not part
of our package). You might have to use older versions of FS to make
this work.
On 1/26/2021 11:10 PM, Koch, Erin M. wrote:
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Or, are you saying that I do not need to turn it off for NHP?
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*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 Koch,
Erin M. <er...@caltech.edu> <mailto:er...@caltech.edu>
*Sent:* Monday, January 25, 2021 10:47:34 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Recon-all exiting with Errors during
surface inflation
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Yes. I turned off aseg because this is NHP. In previous versions
of freesurfer this was fine. Do I need to add something more my
xopts file? How do I get around this problem?
Thanks,
Erin
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*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:* Monday, January 25, 2021 8:01:12 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] Recon-all exiting with Errors during
surface inflation
The problem is that it expects there to be an aseg.presurf.mgz, but
you have turned the creation of it off. Because this is NHP?
On 1/15/2021 5:40 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi
Thanks for your help. Indeed the list of commands you sent worked,
so I added the line you recommended to my xopts. This gets me
beyond my previous exit point, but now recon-all is exiting with a
new error. I will attach my recon-all log and terminal error. It
seems recon-all is trying to load an aseg file; however, I include
in my call -noaseg (and I tried adding -nosubcortseg).
Please let me know if you need anything else.
Erin
------------------------------------------------------------------------
*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 Greve,
Douglas N.,Ph.D. <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Sent:* Wednesday, December 23, 2020 9:12 AM
*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] Recon-all exiting with Errors during
surface inflation
There have been some changes that are breaking your stream. Try this
cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri
setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm
wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i
../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5
--no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze
--no-rip-lesion
If that works, then add this to your xopts file
WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa
--no-rip-freeze --no-rip-lesion
On 12/14/2020 5:35 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi all,
The lab I work in recently upgrade to
freesurfer-linux-centos7x_86_64-7.1.1
from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am
trying to use a series of shell scripts (that call freesurfer)
which we successfully used to run to create flatmaps for non-human
primate sessions. I am stuck when using recon-all to inflate the
surface. Specifically, I am running the command:
"recon-all -autorecon2-wm \
-subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\
-noaseg \
-mprage \
-xopts-use\
-debug\"
This step runs for quite some time, seemingly making progress and
then "Exits with errors" . In the terminal the error message that
I can see is: "ERROR: need seg for ripping". This is followed by:
"recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of
this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull
stripping or white matter segmentation, as the session can be
completed with the older version of freesurfer, adn I get the same
error with different sessions and subjects. Can you please shed
some light on this? The machine I am using is running Linux
3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map
creation (specifically for non-human primates) with the newer
versions of Free surfer? It is possible adapting our old pipeline
is not ideal / there are more efficient or "better" ways to do
this now.
Thank you for your help.
Best,
Erin
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