On Fri, Dec 4, 2015 at 5:56 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

HI Genevieve

you'll need to send us all your command lines

cheers
Bruce

On Fri, 4 Dec 2015, UQAM wrote:

Hi again Bruce,
The mri_cc & mri_segstats run just fine.
- When I open the open the new segmented .mgz files (aseg.12segmentsCC_new.mgz) in tkmedit I can
clearly visualize the 12 segments.
- When I open the .stats file I get volumes for each of the 12 corpus callosum segments.

However, when I run the asegstats2table the result is a .txt file with the usual 5 segments of
the corpus callosum (anterior, ...).

Any clue why the asegstats2table doesn't take into account the new 12 segments?

See relevant files attached,

As usual thanks so much ; )
Genevieve

On Fri, Dec 4, 2015 at 3:07 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
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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