[Brains-users] obtaining midline sagittal vermis measure
Cherie Marvel
cherie at psychiatry.uiowa.edu
Thu Jan 26 13:12:15 PST 2006
Ok, sounds good! Ron, Gene, thanks for the prompt response! --cherie
On Jan 26, 2006 03:00 PM, Ronald Pierson
<ronald-pierson at psychiatry.uiowa.edu> wrote:
> All that this method refers to is a trace of the three parts of the
> vermis on the single, mid-sagital slice. There is no surface
> generated,
> it is just area of that single trace. Since you are already reliable
> on
> the vermis, you can probably do these in about 2 minutes per scan.
>
> Ron
>
> On Jan 26, 2006 02:14 PM, Cherie Marvel <cherie at psychiatry.uiowa.edu>
> wrote:
>
> > Hi Folks,
> >
> > A researcher here at Hopkins is hoping to get some measures of the
> > cerebellum from his structural images of schizophrenia patients and
> > healthy controls. I've looked over his T1/T2 images, and they are OK
> > in
> > resolution. It will be too difficult to trace any structures within
> > the
> > cerebellum due to pixelation when magnified. In order to salvage any
> > kind of structural data from his scans, I was thinking that the best
> > option might be to obtain a 2D surface area measure of the midline
> > vermis. I was looking at Peg's 1999 Bio Psych paper "An MRI Study of
> > Cerbellar Vermis Morphology in Patients with Schizophrenia: Evidence
> > in
> > Support of the Cognitive Dysmetria Concept". In that paper (Table
> > 3),
> > a
> > midline sagittal surface area (in cm squared) of the vermis was
> > obtained.
> >
> > I've been playing around with lots of different features in BRAINS2,
> > including measurment of a mask, but I'm not sure that my "results"
> > are
> > valid because I can't find documentation on acquiring measurements
> > in
> > this way. Does this 2D surface area feature still exist in BRAINS2
> > (Peg
> > used BRAINS), and if so, could you direct me to the feature and/or
> > documentation that supports it?
> >
> > Thank you for your time. --cherie
> >
> > Cherie Marvel, PhD
> > Postdoctoral Fellow
> > Johns Hopkins Medical Institutions
> > Neurology, Div. of Cognitive Neuroscience
> > 1620 McElderry St., Reed Hall East-2
> > Baltimore, MD 21205
> > Phone: (410) 502-4664
> > Fax: (410) 502-2189
> > www.jhu.edu/nimlab
> >
> > On Jan 26, 2006 11:01 AM, brains-users-request at psychiatry.uiowa.edu
> > wrote:
> >
> > > Send Brains-users mailing list submissions to
> > > brains-users at www.psychiatry.uiowa.edu
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > > http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users
> > > or, via email, send a message with subject or body 'help' to
> > > brains-users-request at www.psychiatry.uiowa.edu
> > >
> > > You can reach the person managing the list at
> > > brains-users-owner at www.psychiatry.uiowa.edu
> > >
> > > When replying, please edit your Subject line so it is more
> > > specific
> > > than "Re: Contents of Brains-users digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > > 1. Re: Some questions regarding segmentation
> > > (christma at zi-mannheim.de)
> > > 2. RE: Some questions regarding segmentation (Ronald Pierson)
> > > 3. RE: Some questions regarding segmentation (Christoph
> > > Christmann)
> > > 4. RE: Some questions regarding segmentation (Ronald Pierson)
> > > 5. Re: Some questions regarding segmentation (Eugene Zeien)
> > >
> > >
> > >
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Thu, 26 Jan 2006 10:08:52 +0100
> > > From: christma at zi-mannheim.de
> > > Subject: Re: [Brains-users] Some questions regarding segmentation
> > > To: brains-users at psychiatry.uiowa.edu
> > > Message-ID: <1138266532.43d891a40cb08 at as200.zi-mannheim.de>
> > > Content-Type: text/plain; charset=iso-8859-1
> > >
> > > hi,
> > >
> > > using the workup - measure T50 volumes I get all
> > > informations about the different volumes of different parts
> > > of the brain in a window (chek T50 volumes). All volumes are
> > > in the normal range accorcing to the displayed means and
> > > standard deviations. However, while trying to UPDATE I get
> > > the following error message
> > >
> > > Failed to open global raw volume data file
> > > /raid0/data/new_data/brains2/t50/t50_volumes_raw.dat
> > >
> > > Usually I do create the missing directories manually - whta
> > > usually makes this kind of errors disappear. But I am not
> > > quite sure if I should create the directory on the root
> > > level.
> > >
> > > Thanks for any hints in advance
> > >
> > > Christoph
> > >
> > >
> > >
> > >
> > > **********************************************************************************************
> > > IMPORTANT: The contents of this email and any attachments are
> > > confidential. They are intended for the
> > > named recipient(s) only.
> > > If you have received this email in error, please notify the system
> > > manager or the sender immediately and do
> > > not disclose the contents to anyone or make copies thereof.
> > > *** eSafe scanned this email for viruses, vandals, and malicious
> > > content. ***
> > >
> > >
> > >
> > > **********************************************************************************************
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 2
> > > Date: Thu, 26 Jan 2006 06:36:43 -0600
> > > From: "Ronald Pierson" <ronald-pierson at uiowa.edu>
> > > Subject: RE: [Brains-users] Some questions regarding segmentation
> > > To: <christma at zi-mannheim.de>, <brains-users at psychiatry.uiowa.edu>
> > > Message-ID: <000501c62275$2a3dd090$6501a8c0 at basement>
> > > Content-Type: text/plain; charset="us-ascii"
> > >
> > > Hi - sounds like you are making good progress!
> > >
> > > This is a single file where the data from all of the scans that
> > > you
> > > process will end up. It is not necessary to update the global data
> > > file, as the data for each scan is there in the 10_ACPC/standard
> > > directory. However, for us this makes it easy to put all the data
> > > in
> > > one spot. At Iowa we have about 10 different people doing standard
> > > workup for the various researchers, and there are several thousand
> > > scans. For the data manager, this makes it simple because nobody
> > > has
> > > to
> > > let him know when a scan is done, the data just ends up in the
> > > global
> > > data file. In one file he can see the new data from all of the
> > > scans
> > > that have been completed.
> > >
> > > This file name and path for this global data file can be changed
> > > when
> > > you measure the volumes, or it can be changed permanently in a
> > > file
> > > called brains2rc. There is one of these files located somewhere in
> > > the
> > > brains2 program folders, I don't recall where at the moment and
> > > I'll
> > > email that later today when I am in the office. You should copy
> > > that
> > > file over to your linux home directory and modify it for your own
> > > preferences. Save it as .brains2rc (that makes it a hidden file).
> > > The
> > > settings you make in the brains2rc file in your home directory
> > > will
> > > override those of the global one, so you can have your own
> > > personal
> > > settings. Somewhere near the bottom the brains2rc file the global
> > > data
> > > file is set, just change it to whatever you want for your system.
> > >
> > > FYI - the T50 volumes will probably not be useful to you, as they
> > > are
> > > simply CSF vs. Tissue on the T1 image. Segmentation volumes use
> > > the
> > > tissue classified image, and divide the measures into gray, white,
> > > csf,
> > > blood, and unclassified.
> > >
> > > Ronald
> > >
> > >
> > > -----Original Message-----
> > > From: brains-users-bounces at psychiatry.uiowa.edu
> > > [mailto:brains-users-bounces at psychiatry.uiowa.edu] On Behalf Of
> > > christma at zi-mannheim.de
> > > Sent: Thursday, January 26, 2006 3:09 AM
> > > To: brains-users at psychiatry.uiowa.edu
> > > Subject: Re: [Brains-users] Some questions regarding segmentation
> > >
> > > hi,
> > >
> > > using the workup - measure T50 volumes I get all
> > > informations about the different volumes of different parts
> > > of the brain in a window (chek T50 volumes). All volumes are
> > > in the normal range accorcing to the displayed means and
> > > standard deviations. However, while trying to UPDATE I get
> > > the following error message
> > >
> > > Failed to open global raw volume data file
> > > /raid0/data/new_data/brains2/t50/t50_volumes_raw.dat
> > >
> > > Usually I do create the missing directories manually - whta
> > > usually makes this kind of errors disappear. But I am not
> > > quite sure if I should create the directory on the root
> > > level.
> > >
> > > Thanks for any hints in advance
> > >
> > > Christoph
> > >
> > >
> > >
> > >
> > > ************************************************************************
> > > **********************
> > > IMPORTANT: The contents of this email and any attachments are
> > > confidential. They are intended for the
> > > named recipient(s) only.
> > > If you have received this email in error, please notify the system
> > > manager or the sender immediately and do
> > > not disclose the contents to anyone or make copies thereof.
> > > *** eSafe scanned this email for viruses, vandals, and malicious
> > > content. ***
> > >
> > >
> > >
> > > ************************************************************************
> > > **********************
> > >
> > > _______________________________________________
> > > Brains-users mailing list
> > > Brains-users at www.psychiatry.uiowa.edu
> > > http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users
> > >
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 3
> > > Date: Thu, 26 Jan 2006 16:50:03 +0100
> > > From: Christoph Christmann <christma at zi-mannheim.de>
> > > Subject: RE: [Brains-users] Some questions regarding segmentation
> > > To: <brains-users at psychiatry.uiowa.edu>
> > > Message-ID: <6.2.5.6.2.20060126164937.02e93318 at zi-mannheim.de>
> > > Content-Type: text/plain; charset="us-ascii"; format=flowed
> > >
> > > 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
> > >
> > >
> > >
> > > --
> > > Christoph Christmann christma at as200.zi-mannheim.de
> > > Psychologist, MEE Fon/Fax +49 621 1703 63 18/05
> > > Central Institute of Mental Health http://www.zi-mannheim.de
> > > Department of Neuropsychology D-68159 Mannheim J5
> > > and Clinical Psychology
> > >
> > >
> > >
> > >
> > > **********************************************************************************************
> > > IMPORTANT: The contents of this email and any attachments are
> > > confidential. They are intended for the
> > > named recipient(s) only.
> > > If you have received this email in error, please notify the system
> > > manager or the sender immediately and do
> > > not disclose the contents to anyone or make copies thereof.
> > > *** eSafe scanned this email for viruses, vandals, and malicious
> > > content. ***
> > >
> > >
> > >
> > > **********************************************************************************************
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 4
> > > Date: Thu, 26 Jan 2006 09:58:36 -0600
> > > From: "Ronald Pierson" <ronald-pierson at uiowa.edu>
> > > Subject: RE: [Brains-users] Some questions regarding segmentation
> > > To: "'Christoph Christmann'" <christma at zi-mannheim.de>,
> > > <brains-users at psychiatry.uiowa.edu>
> > > Message-ID: <001201c62291$5e4c5160$6d01a8c0 at pierson>
> > > Content-Type: text/plain; charset="us-ascii"
> > >
> > > 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
> > >
> > >
> > >
> > > --
> > > Christoph Christmann christma at as200.zi-mannheim.de
> > > Psychologist, MEE Fon/Fax +49 621 1703 63 18/05
> > > Central Institute of Mental Health http://www.zi-mannheim.de
> > > Department of Neuropsychology D-68159 Mannheim J5
> > > and Clinical Psychology
> > >
> > >
> > >
> > >
> > > ****************************************************************************
> > > ******************
> > > IMPORTANT: The contents of this email and any attachments are
> > > confidential.
> > > They are intended for the
> > > named recipient(s) only.
> > > If you have received this email in error, please notify the system
> > > manager
> > > or the sender immediately and do
> > > not disclose the contents to anyone or make copies thereof.
> > > *** eSafe scanned this email for viruses, vandals, and malicious
> > > content.
> > > ***
> > >
> > >
> > >
> > > ****************************************************************************
> > > ******************
> > >
> > > _______________________________________________
> > > Brains-users mailing list
> > > Brains-users at www.psychiatry.uiowa.edu
> > > http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users
> > >
> > >
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 5
> > > Date: Thu, 26 Jan 2006 11:01:05 -0600
> > > From: Eugene Zeien <eugene-zeien at uiowa.edu>
> > > Subject: Re: [Brains-users] Some questions regarding segmentation
> > > To: "brains-users at psychiatry.uiowa.edu"
> > > <brains-users at psychiatry.uiowa.edu>
> > > Message-ID: <43D90051.8020801 at uiowa.edu>
> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> > >
> > > 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
> > > >
> > > >
> > > >
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > _______________________________________________
> > > Brains-users mailing list
> > > Brains-users at www.psychiatry.uiowa.edu
> > > http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users
> > >
> > >
> > > End of Brains-users Digest, Vol 7, Issue 10
> > > *******************************************
> > >
> >
> > _______________________________________________
> > Brains-users mailing list
> > Brains-users at www.psychiatry.uiowa.edu
> > http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users
> >
>
More information about the Brains-users
mailing list