[Mristudio-users] program crashes
Anuar Imanbayev
aimanba1 at jhu.edu
Tue May 19 12:20:29 EDT 2009
Eric,
If you're still having trouble with these Siemens files and they happen to be Mosaic files,
I created a handy protocol on how to deal with these Siemens Mosaic files in DTI. There are just some adjustments to be made, that's all.
Good luck,
Anuar
----- Original Message -----
From: Hangyi Jiang <hjiang at jhmi.edu>
Date: Tuesday, May 5, 2009 11:04 am
Subject: Re: [Mristudio-users] program crashes
To: mristudio-users at mristudio.org
> mostly, this happens when the number of images doesn't match with that
> of gradients specified in the gradeint table.
> when the dataset was successfully being loaded in, the image volumes
> will be listed in the "Image List" of the "image" tab. please view
> these images, make sure the # of images are same as the # of items in
> the gradient table.
>
> another common mistake for Siemens dataset is that the images are Masaic
> format but they were loaded in as DICOM format.
>
> regards,
>
> hangyi
>
>
>
> >>> eric Q <qcdunk at hotmail.com> 05/05/09 2:05 AM >>>
>
> Hi Susumu:
>
> Thank you for answering my question regarding the gradient table.
> However the program crashes every time when I try to do a calculation
> (DTI mapping). I've tried to calculate Tensor, Color map, ADC map, Mean,
> but I always get this "The mriView3D MFC application has encountered
> a
> problem and needs to close".
>
>
> I am a new user to DTI studio, so there are probably a lot of mistakes
> I've made on my end, but could you please tell me what are the likely
> causes for the crash of my program? Your time and help is much
> appreciated.
>
> Regards
>
> Eric Q
>
> Date: Fri, 1 May 2009 09:32:56 -0400
> From: susumu at mri.jhu.edu
> To: mristudio-users at mristudio.org
> Subject: Re: [Mristudio-users] Gradient table
>
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> Hi Liang,
>
>
>
> 1) I
> am not sure which coordinates (space) the ultimate gradient table was
> relative
> to, such as frequency- and phase-encoding of image, horizontal and
> vertical
> direction of image, or magnets' x/y/z coordinates. Based on your reply,
> I think
> that it might be the last one.
>
> When you present vectors, color maps, or performing
> fiber tracking, X, Y, and Z need to be defined by the image matrix. This
> is the
> most natural way. The frequency/phase/slice and image x/y/z have
> permutation
> relationship, like frequency – image x / phase – image y / slice –
> image z or frequency – image y / phase – image x / slice – image
> z.
>
> The relationship between magnet x / y / z and image x
> / y / z could have oblique relationship if oblique scan is used, and
> therefore
> could be very complicated.
>
> The gradient table, ultimately, needs to adopt the
> image x / y / z system. Now most vendor system is adopting a way to
> deliver
> gradient application in the frequency/phase/slice system, moving away
> from
> gradient x/y/z. This means, when oblique scan is employed, the scanner
> dynamically recalculates the gradient table in the f/p/s coordinates.
> If
> the
> scanner doesn’t do this (like old Siemens system), we have to
> recalculate
> the table based on the oblique angles by ourselves. The former is more
> fool-proof.
>
>
>
> 2) In my *.PAR file, there was last 3 columns representing diffusion
> directions
> but obviously different between subjects. I don't know what diffusion
> were
> recorded in this header file.
>
> I don’t have much experience with the new PAR
> file, but if you are using oblique scans, it is not surprising the each
> patient
> have different gradient table in the “magnet” coordinate. Suppose
> we want to apply [1, 0, 0] in the first line of the gradient table,
> which is the
> “X” orientation. If we use an oblique scan, magnet X and image X
> are no longer the same. As I mentioned above, in the end, what we want
> to know
> is gradient orientation in the image coordinate. So we have two choices.
>
>
> Choice 1: deliver magnet [1, 0, 0], meaning pure X
> gradient application. This X gradient could be something like [0.9,
> 0.15, 0] in
> the image coordinate. We need to do [1, 0, 0] x ImageRotation to get
> new
> gradient table to do tensor calculation.
>
> Choice 2: deliver magnet [0.9, -0.15, 0] (I just made
> up these numbers) so that the applied gradient aligns the image X axis.
> In this
> case, we can use gradient table [1, 0, 0] for tensor calculation.
>
>
>
> I hope this makes your questions answered.
>
> Susumu
>
>
>
>
>
>
>
>
>
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>
>
>
> From:
> mristudio-users-bounces at mristudio.org
> [ On Behalf Of liang wang
>
> Sent: Saturday, AprI also have a similar question about gradient
> tables in Philips scanner.
>
>
>
>
> My data were collected using following protocols:
>
> 1) Gradient table: Medium
>
> 2) Gradient overplus: no
>
> 3) Oblique plane: yes, and different angles between subjects.
>
>
>
> Looking through your answer, I know that this set can result in the same
> gradient table input into DTIstudio for all subject. However, 1) I am
> not sure
> which coordinates (space) the ultimate gradient table was relative to,
> such as
> frequency- and phase-encoding of image, horizontal and vertical
> direction of
> image, or magnets' x/y/z coordinates. Based on your reply, I think that
> it
> might be the last one.
>
>
>
> 2) In my *.PAR file, there was last 3 columns representing diffusion
> directions
> but obviously different between subjects. I don't know what diffusion
> were
> recorded in this header file.
>
>
>
> Many thanks
>
>
>
> Liang
>
>
>
> 2009/4/16 susumu <susumu at mri.jhu.edu>
>
>
>
>
>
> Hi Eric,
>
>
>
>
>
> For Philips scanner there are several types of gradient
> tables you can specify in the scanner. Please check your protocol for
> the
> following points;
>
>
>
>
>
> 1) Gradient table: High (32-orientation)/ Medium (15-orientation)
> /
> Low (6-orientation)
>
> 2) Overplus (ON / OFF)
>
> 3) Oblique plane (X/Y/Z angles)
>
>
>
>
> The first option has 3 choices and the second option has 2
> choices. Therefore, there are 3 x 2 = 6 gradient tables.
>
>
> If the second option (Overplus) is NO, the third option has
> no effect. If the second option is YES, the gradient table has to be
> rotated
> based on the oblique angles.
>
>
>
>
>
> To simplify the DTI processing, we recommend Overplus = NO.
>
>
>
>
>
> We have the basic 6 tables, which can be used as is if you
> use Overplus = OFF or Oblique angles = 0/0/0 degree.
>
>
> Please let us know which options you are using.
>
>
>
>
>
> Susumu
>
>
>
>
>
>
>
>
>
>
>
>
>
> From: mristudio-users-bounces at mristudio.org
> [
> On Behalf Of eric Q
>
> Sent: Thursday, April 16, 2009
> 9:44 PM
>
>
>
>
>
>
> To: mristudio-users at mristudio.org
>
>
>
> Subject: Re:
> [Mristudio-users] Gradient table
>
>
>
>
>
>
>
>
>
>
> Hello Dear DTIstudio users:
>
>
>
> I am new to DTIstudio, I was hoping someone could give me some much
> needed
> advises for beginners.
>
>
>
>
>
> I was trying to obtain the FA values for my brain phantom (PHILIP 3T
> scanner).
> When I clicked on "DTI mapping", it prompted me to enter the
> "gradient table", how do I calculate the "gradient table"?
>
>
>
> Thanks in advanced
>
>
>
> Best regards
>
>
>
> Eric
>
>
>
>
>
>
>
>
>
>
>
> Date: Thu, 9 Apr 2009 11:04:09
> -0400
>
> From: susumu at mri.jhu.edu
>
> To: mristudio-users at mristudio.org
>
> Subject: Re: [Mristudio-users] MriView3D application close
>
> Hi Hugh,
>
>
>
>
>
> When you got this error, please suspect one of the following
> two reasons;
>
>
>
>
>
> 1) Memory shortage:
>
>
>
>
>
> Even if you have many GB of memories, 32-bit Windows system
> can allocate only 1 - 1.5 GB to each program. To check if you have the
> memory
> problem, please restrict the slices to be calculated. In the
> initial data parameter window, there is a section called "Slices to
> be processed". Here you can specify only a portion of slices to be
> processed. Please limit the slices to, for example, 0-9 and see how it
> goes. If
> you can calculate tensors without errors, then you have the memory
> problem. The
> solution is; a) upgrade to the 64-bit system or b) devide the
> calculation to 2
> batches (e.g. slice 0-29 for the first batch and 30-59 for the second
> batch),
> calculate all maps (e.g. FA), and later combine them.
>
>
>
>
>
> 2) Mismatch between the gradient table and the number of
> images:
>
>
>
>
>
> For example, if you specify 12-orientation table and 30
> volume images, then you get the error. After loading the data and before
> you go
> to the Dti Map tab, make sure that you have 1 b0 + 64 DWIs in the
> pull-down
> menu in the right column of the Image tab. If you have the correct
> number of
> the images, then you might have an error in your gradient
> tab"DtiMapping" in the "File" button again, d) the window still
> remembers the gradient table you entered last time. This remembered
> window
> tells how DtiStudio interpreted your gradient table. If there is any
> syntax
> errors, you may find them much easier. For example, if you enter, "4:
> 1
> 0.5 0", instead of "4: 1, 0.5, 0", then you would find, "4:
> 1, 0, 0".
>
>
>
>
>
> If any of these do not solve the issue, please let us know.
>
>
>
>
>
> Susumu
>
>
>
>
>
>
>
>
>
>
>
> From: mristudio-users-bounces at mristudio.org
> [
> On Behalf Of Hugh Wang
>
> Sent: Wednesday, April 08, 2009
> 6:30 PM
>
> To: mristudio-users at mristudio.org
>
> Subject: [Mristudio-users]
> MriView3D application close
>
> Hi,
>
>
>
> I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM
> diffusion images (1baseline,64 gradients). After successfully loading
> the
> images, I click the "dti map" option at lower right corner. Whatever
> calculation I choose, it always gives me an error:
>
>
>
> "MriView3D MFC Application has encountered a problem and needs to
> close. We are sorry for the inconvenience."
>
>
>
> I tried several PCs, and the problem keeped the same. I would appreciate
> that
> if there's anyone having any idea on how to solve it. Thanks.
>
>
> Best,
>
> Hugh
>
>
>
>
>
>
>
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>
> --
>
> Liang Wang, PhD
>
> Postdoctoral Fellow
>
> Woodward Lab
>
> Department of Psychiatry
>
> University of British Columbia
>
> BC Mental Health & Addiction Services
>
> 938 West 28th Avenue
>
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>
> Telephone: 1-604-875-2000 (ext. 4735)
>
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> Email: wanglbit at gmail.com
>
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