Hi Doug,See attached an example of an aseg.stats file for subject e0070 (e0070_CC12_new.aseg.stats)Regards,GenevieveOn Mon, Dec 7, 2015 at 7:48 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:Can you send me one of the e0070_CC12_new.aseg.stats files?
On 12/06/2015 08:12 AM, UQAM wrote:
> Hi Bruce,
>
> We used these:
>
> mri_cc_new -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC_new.mgz -d
> 12 e0070
> ... (for all the subjects from e0042 to a0040)
>
> mri_segstats --seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC_new.mgz
> --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 --sum
> $SUBJECTS_DIR/e0070/stats/e0070_CC12_new.aseg.stats
> .... (for all the subjects from e0042 to a0040)
>
> asegstats2table --subjects e0042 e0041 e0035 e0048 e0058 e0059 e0053
> e0032 e0047 e0036 e0039 e0049 e0051 e0050 e0045 e0061 e0062 e0063
> e0064 e0065 e0066 e0067 e0068 e0070 e0071 e0072 e0073 e0074 e0075
> e0076 e0077 e0021 e0004 e0078 e0079 e0080 e0013 e0081 e0082 e0083
> a0001 a0002 a0003 a0004 a0005 a0006 a0007 a0008 a0009 a0010 a0011
> a0012 a0013 a0014 a0015 a0016 a0017 a0018 a0019 a0020 a0021 a0022
> a0023 a0024 a0025 a0026 a0027 a0028 a0029 a0030 a0031 a0032 a0033
> a0034 a0035 a0036 a0037 a0038 a0039 a0040 --meas volume --tablefile
> aseg_stats_12CC_new.txt
>
> Genevieve
>
>
> On Fri, Dec 4, 2015 at 5:56 PM, Bruce Fischl
> <fischl@nmr.mgh.harvard.edu <mailto: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
> <mailto: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 <mailto:fischl@nmr.mgh.harvard.edu>>
> wrote:
> Hi Genevieve
>
> <mailto:zkaufman@nmr.mgh.harvard.edu>> wrote:> 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
> 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>
> <mailto: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>
> <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:Freesurfer@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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Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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