[Brains-users] obtaining midline sagittal vermis measure
Cherie Marvel
cherie at psychiatry.uiowa.edu
Thu Jan 26 12:14:30 PST 2006
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:
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> 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
>
>
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> ------------------------------
>
> 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
>
>
> ************************************************************************
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> 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.
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> _______________________________________________
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>
>
> ------------------------------
>
> 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. ***
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> **********************************************************************************************
>
>
>
> ------------------------------
>
> 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.
> ***
>
> ****************************************************************************
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>
> _______________________________________________
> 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
> >
> >
> >
>
>
>
> ------------------------------
>
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>
> End of Brains-users Digest, Vol 7, Issue 10
> *******************************************
>
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