Hi Genevieve
I just reran it locally and confirmed that the segments start at 230 for me, so I'm not sure what's going on. Still, maybe it meets your needs for now (but be aware that when we release V6 the segment numbering is likely to start at 230)
cheers
Bruce
On Fri, 4 Dec 2015, UQAM wrote:
Hi Bruce,
We were using the correct mri_cc, but our segments were numbered 251 to 262 instead of 230 to 241
in the CColorLUT.txt. With this adjustment, the mri_cc now runs perfectly and segments in 12.
Many thanks for your support!
Best,
Genevieve
On Fri, Nov 27, 2015 at 3:58 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Genevieve
are you sure you are using the correct mri_cc? I used your command line and got 12
segments. How many segents do you get? It should generate segments numbered 230-241 I
think. You'll need to make your own entries in the ColorLUT.txt file if you want to see
them in prespecified colors and names and such
cheers
Bruce
On Fri, 27 Nov 2015, UQAM wrote:
Hi Zeke,
We tried the new version of mri_cc and we still do not get 12 segments of
the corpus callosum when we open
the aseg.12segmentsCC.mgz in a viewer.
Could you send us the script you launch after the recon_all to get aseg.mgz
files with 12 segments?
basically the mri_cc
Could you also please explain how to edit the ColorLut.txt file
Finally, what is the precise script of the mri_segstats to generate stats
tables.
Thanks again,
Cheers,
Genevieve
On Tue, Nov 24, 2015 at 11:20 PM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote:
Hello Genevieve,
Below is a link to the newest version of mri_cc. Please copy it to
your FREESURFER_HOME
directory and backup the original.
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_cc
Hope this help.
-Zeke
On 11/24/2015 05:56 AM, UQAM wrote:
Hi Bruce,
DELL R910
Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores)
32 Go RAM
CentOS release 5.10 (Final)
kernel 2.6.18-371.3.1.el5
On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>> wrote:
Hi Genevieve
I just tracked this down and it is a bug in mri_cc. If you
tell Zeke
your hardware/software environment he can get you a new
version that
should work
cheers
Bruce
On Mon, 23 Nov 2015, UQAM wrote:
Hi Bruce,
Please find the two files attached.
Genevieve
On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>>
wrote:
Hi Geneviève
if you send us the $SUBJECTS_DIR/CColorLUT.txt
and
$SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we
will take a
look
cheers
Bruce
On Mon, 23 Nov 2015, UQAM wrote:
Hi,
This a a "re-posting" of a question I've
raised
last week ; )
I would like to segment the corpus
callosum
into twelve even lenght segments
instead of the five segments that
freesurfer
includes by default.
- First I ran a mri_cc on subject e0070:
mri_cc -aseg aseg.auto_noCCseg.mgz -o
aseg.12segmentsCC.mgz -d 12 e0070
- Then I edited the ColorLUT.txt file and
renamed
it CColorLUT.txt (see
attachment, segments 251 to 262).
- Finally I ran a mri_segstats to compute
the
statistics on segmented
volumes.
mri_segstats seg
$SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab
$SUBJECTS_DIR/CColorLUT.txt --nonempty
--excludeid
0 sum
--e0070_CC12.aseg.stats
The e0070_CC12.aseg.stats file still
displays only
five segments of the
corpus callosum.
Any tips or clues on how I could do things
differently to get 12 segments?
Thanks in advance,
Geneviève
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