[Brains-users] Some questions regarding segmentation
Eugene Zeien
eugene-zeien at uiowa.edu
Thu Jan 26 09:01:05 PST 2006
brains2rc file options:
# To set the directory where scripts are saved,
# to "your home directory"/scripts
B2_EVAL_TCL "B2_WORK_DIR" "set B2_WORK_DIR ${HOME}/scripts ; "
# To redirect brains2 measures
B2_EVAL_TCL "B2_SCV_FILE" "b2 file saved-class-volume filename= ${HOME}/data/Class_Volumes"
B2_EVAL_TCL "B2_SSM_FILE" "b2 file saved-surface-measures filename= ${HOME}/data/Surface_Measures"
brains2 help on "b2 file":
Usage b2 file <file-type> <filename= filename>
Description Specifies an alternate file to which to write the
measurement data, as well as the standard data file.
If no filename is given, then the filename specified
is cleared and only the default file will be used.
<file-type> Must be one of: saved-volume | saved-class-volume |
saved-surface-measures | saved-distance |
saved-image-stats
<filename= filename> The name of the alternate file to which to write the
measurement data.
Return Upon successful completion, 0 is returned,
I have not found an option for changing the default group from "stdwkup" to something else.
Ronald Pierson wrote:
> The permissions/group errors are due to the way we use groups locally, and I
> think that it is documented somewhere on the WIKI page. We use a stdwrkup
> group to make sure only those who are supposed to do standard workup have
> the ability to modify key files. You may either need to add that group, or
> possibly modify the brains2 configuration so that this group isn't needed by
> brains2. Anyone have a better answer for that?
>
> The problem of no csf is one I just noticed yesterday on a scan I was
> running, and I hadn't submitted a bug report yet because I needed to verify
> I hadn't introduced a problem in the workup myself. Since you get the same
> problem as I got, I am beginning to think it probably is a bug, and will
> need to submit it. I think everyone should check into how to report bugs
> and also to see what bugs are reported. This is on the web site.
>
> I'll keep you posted on the histogram/T50 CSF bug or problem, as I don't
> know what the problem is quite yet.
>
> Ron
>
>
>
> -----Original Message-----
> From: brains-users-bounces at psychiatry.uiowa.edu
> [mailto:brains-users-bounces at psychiatry.uiowa.edu] On Behalf Of Christoph
> Christmann
> Sent: Thursday, January 26, 2006 9:50 AM
> To: brains-users at psychiatry.uiowa.edu
> Subject: RE: [Brains-users] Some questions regarding segmentation
>
> Dear Eugene, dear Ronald,
>
> I am did good progress in correcting the brain mask.
> However, using the T50 algorithm I ended up with two error
> messages
>
> Error: Failed to change group and permission on old
> measurement file /home/.../Pat6_10_ACPC/standard/
> Standard_Volumes.old
>
> and
>
> Error: Failed to change group and permission on standard
> measurement file /home/.../Pat6_10_ACPC/standard/
> Standard_Volumes
>
> Between both messages I get the message
>
> "failed to generate histogram threshold module" in the
> terminal window. I end up with the following data - there is
> obviously no CSF measured.
>
>
> Thanks again for any hint!
>
> Christoph
>
>
> Left Brain Tissue 568.790 621.980 67.980
> Left Brain CSF 0.000 82.140 27.
> 600
> Right Brain Tissue 569.151 634.270 70.
> 720
> Right Brain CSF 0.000 78.290 26.
> 800
> Left Cranial Box Tissue 568.705 621.820 68.
> 000
> Left Cranial Box CSF 0.000 81.970 27.
> 550
> Right Cranial Box Tissue 569.112 634.100 70.
> 750
> Right Cranial Box CSF 0.000 78.100 26.
> 740
> Left nFrontal Box Tissue 187.224 198.020 26.
> 370
> Left nFrontal Box CSF 0.000 30.970 12.
> 530
> Right nFrontal Box Tissue 181.408 210.220 28.
> 870
> Right nFrontal Box CSF 0.000 29.580 12.
> 590
> Left Temporal Box Tissue 99.858 112.370 12.
> 750
> Left Temporal Box CSF 0.000 14.970 5.
> 430
> Right Temporal Box Tissue 100.437 113.750 13.
> 140
> Right Temporal Box CSF 0.000 12.070 4.
> 710
> Left Parietal Box Tissue 106.293 119.200 14.
> 680
> Left Parietal Box CSF 0.000 14.650 6.
> 320
> Right Parietal Box Tissue 109.642 121.620 15.
> 300
> Right Parietal Box CSF 0.000 14.210 6.
> 170
> Left Occipital Box Tissue 49.095 62.580 10.
> 420
> Left Occipital Box CSF 0.000 5.190 3.
> 020
> Right Occipital Box Tissue 53.678 58.210 9.
> 910
> Right Occipital Box CSF 0.000 5.340 3.
> 000
> Left Cerebellum Box Tissue 61.491 67.440 9.
> 420
> Left Cerebellum Box CSF 0.000 7.620 2.
> 990
> Right Cerebellum Box Tissue 62.638 66.040 9.
> 170
> Right Cerebellum Box CSF 0.000 7.640 2.
> 960
> Left Subcortical Box Tissue 44.809 47.190 5.
> 390
> Left Subcortical Box CSF 0.000 4.750 1.
> 950
> Right Subcortical Box Tissue 43.473 48.170 5.
> 480
> Right Subcortical Box CSF 0.000 5.190 2.
> 010
> Left Brainstem Box Tissue 18.380 16.210 2.
> 520
> Left Brainstem Box CSF 0.000 3.930 1.
> 860
> Right Brainstem Box Tissue 16.531 17.020 2.
> 650
> Right Brainstem Box CSF 0.000 4.190 1.
> 990
> Left Ventricle-2 Box Tissue 59.649 60.690 7.
> 740
> Left Ventricle-2 Box CSF 0.000 7.850 4.
> 550
> Right Ventricle-2 Box Tissue 58.947 62.880 7.
> 800
> Right Ventricle-2 Box CSF 0.000 7.700 4.
> 380
> Left Ventricle Box Tissue 110.283 119.590 13.
> 390
> Left Ventricle Box CSF 0.000 9.430 5.
> 280
> Right Ventricle Box Tissue 107.108 122.980 13.
> 710
> Right Ventricle Box CSF 0.000 9.510 5.
> 180
>
>
>
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