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From:

Youssof Nadiri <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Sat, 27 Sep 2008 19:11:15 -0400

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text/plain (1512 lines) 

On Sat, Sep 27, 2008 at 7:00 PM, FSL automatic digest system
<[log in to unmask]> wrote:
> There is 1 message totalling 1491 lines in this issue.
>
> Topics of the day:
>
>  1. probtrackx in MNI space
>
> ----------------------------------------------------------------------
>
> Date:    Sat, 27 Sep 2008 08:20:14 -0500
> From:    Matt Glasser <[log in to unmask]>
> Subject: Re: probtrackx in MNI space
>
> This is a multi-part message in MIME format.
>
> ------=_NextPart_000_014E_01C92079.DEFB90D0
> Content-Type: text/plain;
>        charset="US-ASCII"
> Content-Transfer-Encoding: 7bit
>
> I wouldn't say that results in a given subject's DTI space are not spatially
> accurate.  If you want to compare your tractograghy results directly across
> subjects then they will need to be in a common space like MNI space.  You
> can also always transform tractography results from one space to another
> after the fact.  I personally usually track in individual subjects'
> structural spaces, as that is where I draw the ROIs, and then transform the
> results into MNI space if necessary.  I try to measure FA values in native
> DTI space, and if I look at streamlines, I use the waytotal output of
> probtrackx, rather than trying to measure anything from the path
> distribution.
>
>
>
> Peace,
>
>
> Matt.
>
>
>
>  _____
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Cherif Sahyoun
> Sent: Friday, September 26, 2008 8:36 AM
> To: [log in to unmask]
> Subject: Re: [FSL] probtrackx in MNI space
>
>
>
> Thanks Matt.
> So is it a fair rule of thumb to say that one should run probtrackx in MNI
> space for spatially accurate results, but in DTI space for quantitative
> results?
> Would you ever get #streamlines or FA in MNI space?
>
> Thanks again,
> Cherif
>
> ----------------------------------------------------------------------------
> --------------
> Cherif P. Sahyoun                                               HST-MEMP
>
> Developmental Neuroimaging of Cognitive Functions
>
> C: 617 688 8048
> H: 617 424 6956
> [log in to unmask]
>
> "Live as if this were your last day. Learn as if you'll live forever"
> Ghandi
> ----------------------------------------------------------------------------
> ---------------
>
>
>
> On Thu, Sep 25, 2008 at 1:17 PM, Matt Glasser <[log in to unmask]> wrote:
>
> If you want streamlines from DTI space you should transform your ROIs from
> MNI to each subject's DTI space before tractography.  To measure your
> subject's FA in DTI space you would do something similar.
>
>
>
> Peace,
>
>
>
> Matt.
>
>
>
>  _____
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Cherif Sahyoun
> Sent: Thursday, September 25, 2008 11:49 AM
> To: [log in to unmask]
>
>
> Subject: Re: [FSL] probtrackx in MNI space
>
>
>
> Ah! I get it! So when would you ever want to track in dti space?
>
>
> If I want to get streamline numbers/FA from a MNI space calculated tract, is
> it best to transform it down to dti space and fslstats that, or to directly
> get numbers from the MNI tracts in MNI space?
> ----------------------------------------------------------------------------
> --------------
> Cherif P. Sahyoun                                               HST-MEMP
>
> Developmental Neuroimaging of Cognitive Functions
>
> C: 617 688 8048
> H: 617 424 6956
> [log in to unmask]
>
> "Live as if this were your last day. Learn as if you'll live forever"
> Ghandi
> ----------------------------------------------------------------------------
> ---------------
>
> On Thu, Sep 25, 2008 at 11:55 AM, Saad Jbabdi <[log in to unmask]> wrote:
>
> Using a mask from a higher resolution space will not give you the same
> results because of interpolation.
>
> If you use masks in native space, the sample tracts will always start from
> the centre of the voxels. If you use a higher resolution masks, the tracts
> will start from different places within the native space voxels.
>
>
>
> Saad.
>
>
>
>
>
> On 25 Sep 2008, at 15:27, Cherif Sahyoun wrote:
>
>
>
> Thanks David and Saad!
> While we're on the subject, if I'm interested in extracting number of
> streamlines (and maybe FA) from paths, is running in MNI space buying me
> anything but a prettier picture and the ability to get a group path? I would
> think getting quantitative values is always best in native space.
> Saad and I talked briefly about it, but I'm still unsure what's best if I
> expect for ex. my groups to differ in the path probability but not in the
> location of the path.
> If I'm then looking for an average tract qualitatively, I could always just
> flirt my DTI-space tracts to MNI and save myself the many extra hours,
> right?
>
> Thanks again,
> Cherif
>
> ----------------------------------------------------------------------------
> --------------
> Cherif P. Sahyoun                                               HST-MEMP
>
> Developmental Neuroimaging of Cognitive Functions
>
> C: 617 688 8048
> H: 617 424 6956
> [log in to unmask]
>
> "Live as if this were your last day. Learn as if you'll live forever"
> Ghandi
> ----------------------------------------------------------------------------
> ---------------
>
> On Thu, Sep 25, 2008 at 6:12 AM, Markus Gschwind <[log in to unmask]>
> wrote:
>
> Oh yes of course ;-)
> Thanks, Saad!
>
> 2008/9/25 Saad Jbabdi <[log in to unmask]>
>
>
>
> Hi Markus,
>
> The resolution does not matter in the process of sampling a single
> streamline (it solely depends on the step length and number of steps).
>
> However, the number of voxels of the seed mask determines the number of
> sample streamlines that probtrackx will calculate.
>
> Since changing the image resolution changes the number of voxels in the seed
> mask, resolution matters!
>
>
>
> Saad.
>
>
>
>
>
> On 25 Sep 2008, at 10:15, Markus Gschwind wrote:
>
>
>
> Hi!
>
> On the website (http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_probtrackx.html) it
> says:
>
> As explained below, results from probtrackx can be binned in any available
> space -e.g., diffusion space, structural space or standard space. Note,
> however, that tractography itself ALWAYS takes place in diffusion space - it
> is simply the results of probtrackx that are stored in the required space.
>
>
> Thus the resolution should not make a difference...?
>
> Cheers,
> Markus
>
>
>
>
> 2008/9/24 David Gutman <[log in to unmask]>
>
> time is completely based on the size of your ROI, going from a
> high-res to a DTI space (say your DTI was acquired at 2x2x2 and your
> T1 was 1mmx1mmx1mm T1) actually is an 8 fold increase in the same
> number of voxels to cover the same region-- the algorithm runs each
> voxel separately, uses the supplied transformation to map it into DTI
> space, and then back projects the data into whatever space you ran it
> in (say hi-res T1 image).
>
> So basically it should take about 8 times as long depending on the
> actual image dimensions your using.
>
> dg
>
>
>
> On Wed, Sep 24, 2008 at 10:48 AM, Cherif Sahyoun <[log in to unmask]> wrote:
>> Hi,
>>
>> I am trying to run probtrackx in MNI space, and I've noticed that for the
> same
>> tracking parameters (curvature, step length, etc.) tracking in MNI takes
> about
>> 10hrs for given single tract vs. a couple of hours when tracking in DTI
> space.
>> Does that make sense? Is it just because of the higher res?
>> Is this long a time generally normal? (note I am not using the -f option).
>>
>> Thanks for enlightening me!
>> Cherif.
>>
>
>
>
> --
> David A Gutman, M.D. Ph.D.
> Department of Psychiatry & Behavioral Sciences
> Emory University School of Medicine
>
>
>
>
> --
> Dr. med. Markus Gschwind, M.D.
> Laboratory for Neurology and Imaging of Cognition
> Dept of Neurosciences
> University Medical Center (CMU)
> 1 Michel-Servet - 1211 GENEVA - CH
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> http://labnic.unige.ch
>
> PS: Switzerland is a good place for scientists. It is the origin of special
> relativity (1905) and the World Wide Web (1990), it is associated with 105
> Nobel laureates, and boasts the world's highest number of Nobel prizes per
> capita, the highest number of publications per capita, the highest number of
> patents per capita, the highest citation impact factor, the most cited
> single-author paper, etc. Switzerland also got the highest ranking in the
> list of happiest countries :-) .
>
>
>
>
>
>
> ---------------------------------------------------------------------------
>
> Saad Jbabdi,
>
> Postdoctoral Research Assistant,
>
> Oxford University FMRIB Centre
>
>
>
> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
>
> +44 (0) 1865 222545  (fax 222717)
>
> [log in to unmask]    http://www.fmrib.ox.ac.uk/~saad
> <http://www.fmrib.ox.ac.uk/%7Esaad>
>
> ---------------------------------------------------------------------------
>
>
>
>
>
>
>
>
>
>
>
>
> --
> Dr. med. Markus Gschwind, M.D.
> Laboratory for Neurology and Imaging of Cognition
> Dept of Neurosciences
> University Medical Center (CMU)
> 1 Michel-Servet - 1211 GENEVA - CH
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> http://labnic.unige.ch
>
> PS: Switzerland is a good place for scientists. It is the origin of special
> relativity (1905) and the World Wide Web (1990), it is associated with 105
> Nobel laureates, and boasts the world's highest number of Nobel prizes per
> capita, the highest number of publications per capita, the highest number of
> patents per capita, the highest citation impact factor, the most cited
> single-author paper, etc. Switzerland also got the highest ranking in the
> list of happiest countries :-) .
>
>
>
>
>
> ---------------------------------------------------------------------------
>
> Saad Jbabdi,
>
> Postdoctoral Research Assistant,
>
> Oxford University FMRIB Centre
>
>
>
> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
>
> +44 (0) 1865 222545  (fax 222717)
>
> [log in to unmask]    http://www.fmrib.ox.ac.uk/~saad
> <http://www.fmrib.ox.ac.uk/%7Esaad>
>
> ---------------------------------------------------------------------------
>
>
>
>
>
>
>
>
>
>
>
>
>
>
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>
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
> style=3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>I wouldn&#8217;t say that results =
> in a
> given subject&#8217;s DTI space are not spatially accurate.&nbsp; If you =
> want
> to compare your tractograghy results directly across subjects then they =
> will
> need to be in a common space like MNI space.&nbsp; You can also always
> transform tractography results from one space to another after the =
> fact.&nbsp;
> I personally usually track in individual subjects&#8217; structural =
> spaces, as
> that is where I draw the ROIs, and then transform the results into MNI =
> space if
> necessary.&nbsp; I try to measure FA values in native DTI space, and if =
> I look
> at streamlines, I use the waytotal output of probtrackx, rather than =
> trying to
> measure anything from the path distribution.&nbsp; =
> <o:p></o:p></span></font></p>
>
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
> style=3D'font-size:
> 10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>
>
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
> style=3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>Peace,<o:p></o:p></span></font></p>
>
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
> style=3D'font-size:
> 10.0pt;font-family:Arial;color:navy'><br>
> Matt.<o:p></o:p></span></font></p>
>
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
> style=3D'font-size:
> 10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>
>
> <div>
>
> <div class=3DMsoNormal align=3Dcenter style=3D'text-align:center'><font =
> size=3D3
> face=3D"Times New Roman"><span style=3D'font-size:12.0pt'>
>
> <hr size=3D2 width=3D"100%" align=3Dcenter tabindex=3D-1>
>
> </span></font></div>
>
> <p class=3DMsoNormal><b><font size=3D2 face=3DTahoma><span =
> style=3D'font-size:10.0pt;
> font-family:Tahoma;font-weight:bold'>From:</span></font></b><font =
> size=3D2
> face=3DTahoma><span style=3D'font-size:10.0pt;font-family:Tahoma'> =
> <st1:PersonName
> w:st=3D"on">FSL - FMRIB's Software Library</st1:PersonName>
> [mailto:[log in to unmask]] <b><span style=3D'font-weight:bold'>On =
> Behalf Of </span></b>Cherif
> Sahyoun<br>
> <b><span style=3D'font-weight:bold'>Sent:</span></b> Friday, September =
> 26, 2008
> 8:36 AM<br>
> <b><span style=3D'font-weight:bold'>To:</span></b> =
> [log in to unmask]<br>
> <b><span style=3D'font-weight:bold'>Subject:</span></b> Re: [FSL] =
> probtrackx in
> MNI space</span></font><o:p></o:p></p>
>
> </div>
>
> <p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:
> 12.0pt'><o:p>&nbsp;</o:p></span></font></p>
>
> <div>
>
> <p class=3DMsoNormal style=3D'margin-bottom:12.0pt'><font size=3D3
> face=3D"Times New Roman"><span style=3D'font-size:12.0pt'>Thanks =
> Matt.<br>
> So is it a fair rule of thumb to say that one should run probtrackx in =
> MNI
> space for spatially accurate results, but in DTI space for quantitative
> results?<br>
> Would you ever get #streamlines or FA in MNI space?<br>
> <br>
> Thanks again,<br>
> Cherif<br>
> <br clear=3Dall>
> -------------------------------------------------------------------------=
> -----------------<br>
> Cherif P. Sahyoun &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; =
> &nbsp;
> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; =
> &nbsp;
> &nbsp; &nbsp; &nbsp; &nbsp; HST-MEMP<br>
> <br>
> Developmental Neuroimaging of Cognitive Functions<br>
> <br>
> C: 617 688 8048<br>
> H: 617 424 6956<br>
> <a href=3D"mailto:[log in to unmask]">[log in to unmask]</a><br>
> <br>
> &quot;Live as if this were your last day. Learn as if you'll live =
> forever&quot;<br>
> Ghandi<br>
> -------------------------------------------------------------------------=
> ------------------<br>
> <br>
> <o:p></o:p></span></font></p>
>
> <div>
>
> <p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:
> 12.0pt'>On Thu, Sep 25, 2008 at 1:17 PM, Matt Glasser &lt;<a
> href=3D"mailto:[log in to unmask]">[log in to unmask]</a>&gt; =
> wrote:<o:p></o:p></span></font></p>
>
> <div link=3Dblue vlink=3Dblue>
>
> <div>
>
> <p><font size=3D2 color=3Dnavy face=3DArial><span =
> style=3D'font-size:10.0pt;font-family:
> Arial;color:navy'>If you want streamlines from DTI space you should =
> transform
> your ROIs from MNI to each subject's DTI space before =
> tractography.&nbsp; To
> measure your subject's FA in DTI space you would do something =
> similar.</span></font><o:p></o:p></p>
>
> <p><font size=3D2 color=3Dnavy face=3DArial><span =
> style=3D'font-size:10.0pt;font-family:
> Arial;color:navy'>&nbsp;</span></font><o:p></o:p></p>
>
> <p><font size=3D2 color=3Dnavy face=3DArial><span =
> style=3D'font-size:10.0pt;font-family:
> Arial;color:navy'>Peace,</span></font><o:p></o:p></p>
>
> <p><font size=3D2 color=3Dnavy face=3DArial><span =
> style=3D'font-size:10.0pt;font-family:
> Arial;color:navy'>&nbsp;</span></font><o:p></o:p></p>
>
> <p><font size=3D2 color=3Dnavy face=3DArial><span =
> style=3D'font-size:10.0pt;font-family:
> Arial;color:navy'>Matt.</span></font><o:p></o:p></p>
>
> <p><font size=3D2 color=3Dnavy face=3DArial><span =
> style=3D'font-size:10.0pt;font-family:
> Arial;color:navy'>&nbsp;</span></font><o:p></o:p></p>
>
> <div>
>
> <div class=3DMsoNormal align=3Dcenter style=3D'text-align:center'><font =
> size=3D3
> face=3D"Times New Roman"><span style=3D'font-size:12.0pt'>
>
> <hr size=3D2 width=3D"100%" align=3Dcenter>
>
> </span></font></div>
>
> <p><b><font size=3D2 face=3DTahoma><span =
> style=3D'font-size:10.0pt;font-family:Tahoma;
> font-weight:bold'>From:</span></font></b><font size=3D2 =
> face=3DTahoma><span
> style=3D'font-size:10.0pt;font-family:Tahoma'> <st1:PersonName =
> w:st=3D"on">FSL -
>  FMRIB's Software Library</st1:PersonName> [mailto:<a
> href=3D"mailto:[log in to unmask]" =
> target=3D"_blank">[log in to unmask]</a>] <b><span
> style=3D'font-weight:bold'>On Behalf Of </span></b>Cherif Sahyoun<br>
> <b><span style=3D'font-weight:bold'>Sent:</span></b> Thursday, September =
> 25, 2008
> 11:49 AM<br>
> <b><span style=3D'font-weight:bold'>To:</span></b> <a
> href=3D"mailto:[log in to unmask]" =
> target=3D"_blank">[log in to unmask]</a><o:p></o:p></span></font></p>
>
> <div>
>
> <p class=3DMsoNormal><font size=3D2 face=3DTahoma><span =
> style=3D'font-size:10.0pt;
> font-family:Tahoma'><br>
> <b><span style=3D'font-weight:bold'>Subject:</span></b> Re: [FSL] =
> probtrackx in
> MNI space<o:p></o:p></span></font></p>
>
> </div>
>
> </div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>&nbsp;<o:p></o:p></span></font></p>
>
> <div>
>
> <p style=3D'margin-bottom:12.0pt'><font size=3D3 face=3D"Times New =
> Roman"><span
> style=3D'font-size:12.0pt'>Ah! I get it! So when would you ever want to =
> track in
> dti space?<o:p></o:p></span></font></p>
>
> <div>
>
> <div>
>
> <p class=3DMsoNormal style=3D'margin-bottom:12.0pt'><font size=3D3
> face=3D"Times New Roman"><span style=3D'font-size:12.0pt'><br>
> If I want to get streamline numbers/FA from a MNI space calculated =
> tract, is it
> best to transform it down to dti space and fslstats that, or to directly =
> get
> numbers from the MNI tracts in MNI space?<br clear=3Dall>
> -------------------------------------------------------------------------=
> -----------------<br>
> Cherif P. Sahyoun &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; =
> &nbsp;
> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; =
> &nbsp;
> &nbsp; &nbsp; &nbsp; &nbsp; HST-MEMP<br>
> <br>
> Developmental Neuroimaging of Cognitive Functions<br>
> <br>
> C: 617 688 8048<br>
> H: 617 424 6956<br>
> <a href=3D"mailto:[log in to unmask]" =
> target=3D"_blank">[log in to unmask]</a><br>
> <br>
> &quot;Live as if this were your last day. Learn as if you'll live =
> forever&quot;<br>
> Ghandi<br>
> -------------------------------------------------------------------------=
> ------------------<o:p></o:p></span></font></p>
>
> </div>
>
> </div>
>
> <div>
>
> <div>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>On Thu,
> Sep 25, 2008 at 11:55 AM, Saad Jbabdi &lt;<a =
> href=3D"mailto:[log in to unmask]"
> target=3D"_blank">[log in to unmask]</a>&gt; =
> wrote:<o:p></o:p></span></font></p>
>
> <div>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>Using a
> mask from a higher resolution space will not give you the same results =
> because
> of interpolation.&nbsp;<o:p></o:p></span></font></p>
>
> </div>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>If you
> use masks in native space, the sample tracts will always start from the =
> centre
> of the voxels. If you use a higher resolution masks, the tracts will =
> start from
> different places within the native space =
> voxels.<o:p></o:p></span></font></p>
>
> </div>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>&nbsp;<o:p></o:p></span></font></p>
>
> </div>
>
> <div>
>
> <p><font size=3D3 color=3D"#888888" face=3D"Times New Roman"><span =
> style=3D'font-size:
> 12.0pt;color:#888888'>Saad.</span></font><o:p></o:p></p>
>
> </div>
>
> <div>
>
> <div>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>&nbsp;<o:p></o:p></span></font></p>
>
> </div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>&nbsp;<o:p></o:p></span></font></p>
>
> <div>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>On 25 Sep
> 2008, at 15:27, Cherif Sahyoun wrote:<o:p></o:p></span></font></p>
>
> </div>
>
> <p style=3D'margin-bottom:12.0pt'><font size=3D3 face=3D"Times New =
> Roman"><span
> style=3D'font-size:12.0pt'><o:p>&nbsp;</o:p></span></font></p>
>
> <div>
>
> <p style=3D'margin-bottom:12.0pt'><font size=3D3 face=3D"Times New =
> Roman"><span
> style=3D'font-size:12.0pt'>Thanks David and Saad!<br>
> While we're on the subject, if I'm interested in extracting number of
> streamlines (and maybe FA) from paths, is running in MNI space buying me
> anything but a prettier picture and the ability to get a group path? I =
> would
> think getting quantitative values is always best in native space.<br>
> Saad and I talked briefly about it, but I'm still unsure what's best if =
> I
> expect for ex. my groups to differ in the path probability but not in =
> the
> location of the path.<br>
> If I'm then looking for an average tract qualitatively, I could always =
> just
> flirt my DTI-space tracts to MNI and save myself the many extra hours, =
> right?<br>
> <br>
> Thanks again,<br>
> Cherif<br>
> <br clear=3Dall>
> -------------------------------------------------------------------------=
> -----------------<br>
> Cherif P. Sahyoun &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; =
> &nbsp;
> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; =
> &nbsp;
> &nbsp; &nbsp; &nbsp; &nbsp; HST-MEMP<br>
> <br>
> Developmental Neuroimaging of Cognitive Functions<br>
> <br>
> C: 617 688 8048<br>
> H: 617 424 6956<br>
> <a href=3D"mailto:[log in to unmask]" =
> target=3D"_blank">[log in to unmask]</a><br>
> <br>
> &quot;Live as if this were your last day. Learn as if you'll live =
> forever&quot;<br>
> Ghandi<br>
> -------------------------------------------------------------------------=
> ------------------<o:p></o:p></span></font></p>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>On Thu,
> Sep 25, 2008 at 6:12 AM, Markus Gschwind &lt;<a
> href=3D"mailto:[log in to unmask]" =
> target=3D"_blank">[log in to unmask]</a>&gt;
> wrote:<o:p></o:p></span></font></p>
>
> <div>
>
> <p style=3D'margin-bottom:12.0pt'><font size=3D3 face=3D"Times New =
> Roman"><span
> style=3D'font-size:12.0pt'>Oh yes of course ;-)<br>
> Thanks, Saad!<o:p></o:p></span></font></p>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>2008/9/25
> Saad Jbabdi &lt;<a href=3D"mailto:[log in to unmask]" =
> target=3D"_blank">[log in to unmask]</a>&gt;<o:p></o:p></span></font></p=
>>
>
> <div>
>
> <div>
>
> <blockquote style=3D'border:none;border-left:solid windowtext =
> 1.0pt;padding:0in 0in 0in 6.0pt;
> margin-left:4.8pt;margin-top:5.0pt;margin-right:0in;margin-bottom:5.0pt;
> border-color:-moz-use-text-color -moz-use-text-color -moz-use-text-color =
> rgb(204, 204, 204)'>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>&nbsp;<o:p></o:p></span></font></p>
>
> <div>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>Hi
> Markus,<o:p></o:p></span></font></p>
>
> </div>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>The
> resolution does not matter in the process of sampling a single =
> streamline (it
> solely depends on the step length and number of =
> steps).<o:p></o:p></span></font></p>
>
> </div>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>However,
> the <i><span style=3D'font-style:italic'>number of =
> voxels</span></i>&nbsp;of the
> seed mask determines the number of sample streamlines that probtrackx =
> will
> calculate.<o:p></o:p></span></font></p>
>
> </div>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>Since
> changing the image resolution changes the number of voxels in the seed =
> mask,
> resolution matters!<o:p></o:p></span></font></p>
>
> </div>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>&nbsp;<o:p></o:p></span></font></p>
>
> </div>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>Saad.<o:p></o:p></span></font></p>
>
> </div>
>
> <div>
>
> <div>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>&nbsp;<o:p></o:p></span></font></p>
>
> </div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>&nbsp;<o:p></o:p></span></font></p>
>
> <div>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>On 25 Sep
> 2008, at 10:15, Markus Gschwind wrote:<o:p></o:p></span></font></p>
>
> </div>
>
> <p style=3D'margin-bottom:12.0pt'><font size=3D3 face=3D"Times New =
> Roman"><span
> style=3D'font-size:12.0pt'><o:p>&nbsp;</o:p></span></font></p>
>
> <div>
>
> <p style=3D'margin-bottom:12.0pt'><font size=3D3 face=3D"Times New =
> Roman"><span
> style=3D'font-size:12.0pt'>Hi!<br>
> <br>
> On the website (<a =
> href=3D"http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_probtrackx.html"
> target=3D"_blank">http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_probtrackx.html</=
> a>) it
> says:<o:p></o:p></span></font></p>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>As
> explained below, results from <b><span =
> style=3D'font-weight:bold'>probtrackx</span></b>
> can be binned in any available space -e.g., diffusion space, structural =
> space
> or standard space. Note, however, that tractography itself ALWAYS takes =
> place
> in diffusion space - it is simply the <i><span =
> style=3D'font-style:italic'>results</span></i>
> of <b><span style=3D'font-weight:bold'>probtrackx</span></b> that are =
> stored in
> the required space.<o:p></o:p></span></font></p>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'><br>
> Thus the resolution should not make a difference...?<br>
> <br>
> Cheers,<br>
> Markus <br>
> &nbsp;<o:p></o:p></span></font></p>
>
> </div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>&nbsp;<o:p></o:p></span></font></p>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>2008/9/24
> David Gutman &lt;<a href=3D"mailto:[log in to unmask]" =
> target=3D"_blank">[log in to unmask]</a>&gt;<o:p></o:p></span></font></p>=
>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>time is
> completely based on the size of your ROI, going from a<br>
> high-res to a DTI space (say your DTI was acquired at 2x2x2 and your<br>
> T1 was 1mmx1mmx1mm T1) actually is an 8 fold increase in the same<br>
> number of voxels to cover the same region-- the algorithm runs each<br>
> voxel separately, uses the supplied transformation to map it into =
> DTI<br>
> space, and then back projects the data into whatever space you ran =
> it<br>
> in (say hi-res T1 image).<br>
> <br>
> So basically it should take about 8 times as long depending on the<br>
> actual image dimensions your using.<br>
> <br>
> dg<o:p></o:p></span></font></p>
>
> <div>
>
> <div>
>
> <p style=3D'margin-bottom:12.0pt'><font size=3D3 face=3D"Times New =
> Roman"><span
> style=3D'font-size:12.0pt'><br>
> <br>
> On Wed, Sep 24, 2008 at 10:48 AM, Cherif Sahyoun &lt;<a
> href=3D"mailto:[log in to unmask]" target=3D"_blank">[log in to unmask]</a>&gt; =
> wrote:<br>
> &gt; Hi,<br>
> &gt;<br>
> &gt; I am trying to run probtrackx in MNI space, and I've noticed that =
> for the
> same<br>
> &gt; tracking parameters (curvature, step length, etc.) tracking in MNI =
> takes
> about<br>
> &gt; 10hrs for given single tract vs. a couple of hours when tracking in =
> DTI
> space.<br>
> &gt; Does that make sense? Is it just because of the higher res?<br>
> &gt; Is this long a time generally normal? (note I am not using the -f =
> option).<br>
> &gt;<br>
> &gt; Thanks for enlightening me!<br>
> &gt; Cherif.<br>
> &gt;<br>
> <br>
> <o:p></o:p></span></font></p>
>
> </div>
>
> </div>
>
> <p><font size=3D3 color=3D"#888888" face=3D"Times New Roman"><span =
> style=3D'font-size:
> 12.0pt;color:#888888'>--<br>
> David A Gutman, M.D. Ph.D.<br>
> Department of Psychiatry &amp; Behavioral Sciences<br>
> <st1:place w:st=3D"on"><st1:PlaceName w:st=3D"on">Emory</st1:PlaceName> =
> <st1:PlaceType
>  w:st=3D"on">University</st1:PlaceType> <st1:PlaceType =
> w:st=3D"on">School</st1:PlaceType></st1:place>
> of Medicine</span></font><o:p></o:p></p>
>
> </div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'><br>
> <br clear=3Dall>
> <br>
> -- <br>
> Dr. med. Markus Gschwind, M.D.<br>
> Laboratory for Neurology and Imaging of Cognition<br>
> Dept of Neurosciences<br>
> <st1:place w:st=3D"on"><st1:PlaceType =
> w:st=3D"on">University</st1:PlaceType> <st1:PlaceName
>  w:st=3D"on">Medical</st1:PlaceName> <st1:PlaceType =
> w:st=3D"on">Center</st1:PlaceType></st1:place>
> (CMU)<br>
> 1 Michel-Servet - 1211 <st1:City w:st=3D"on"><st1:place =
> w:st=3D"on">GENEVA</st1:place></st1:City>
> - CH<br>
> <br>
> Tel 0041 (0) 22 379 5324<br>
> Fax 0041 (0) 22 379 5402<br>
> email: <a href=3D"mailto:[log in to unmask]" =
> target=3D"_blank">[log in to unmask]</a><br>
> <a href=3D"http://labnic.unige.ch" =
> target=3D"_blank">http://labnic.unige.ch</a><br>
> <br>
> PS: <st1:country-region w:st=3D"on"><st1:place =
> w:st=3D"on">Switzerland</st1:place></st1:country-region>
> is a good place for scientists. It is the origin of special relativity =
> (1905)
> and the World Wide Web (1990), it is associated with 105 Nobel =
> laureates, and
> boasts the world's highest number of Nobel prizes per capita, the =
> highest
> number of publications per capita, the highest number of patents per =
> capita,
> the highest citation impact factor, the most cited single-author paper, =
> etc. <st1:country-region
> w:st=3D"on"><st1:place =
> w:st=3D"on">Switzerland</st1:place></st1:country-region>
> also got the highest ranking in the list of happiest countries :-) =
> .<o:p></o:p></span></font></p>
>
> </div>
>
> </div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>&nbsp;<o:p></o:p></span></font></p>
>
> </div>
>
> </div>
>
> <div><span style=3D'border-spacing: 0px;word-spacing:0px'>
>
> <div><span style=3D'border-spacing: 0px;word-spacing:0px'>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>--------------------------------------=
> -------------------------------------</span></font><o:p></o:p></p>
>
> </div>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>Saad =
> Jbabdi,&nbsp;</span></font><o:p></o:p></p>
>
> </div>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>Postdoctoral Research =
> Assistant,&nbsp;&nbsp;</span></font><o:p></o:p></p>
>
> </div>
>
> <div>
>
> <p><st1:place w:st=3D"on"><st1:PlaceName w:st=3D"on"><font size=3D1 =
> color=3Dblack
>  face=3DHelvetica><span =
> style=3D'font-size:9.0pt;font-family:Helvetica;color:black'>Oxford</span>=
> </font></st1:PlaceName><font
>  size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;font-family:
>  Helvetica;color:black'> <st1:PlaceType =
> w:st=3D"on">University</st1:PlaceType></span></font></st1:place><font
> size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;font-family:
> Helvetica;color:black'> FMRIB Centre</span></font><o:p></o:p></p>
>
> </div>
>
> <div style=3D'min-height: 14px'>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>&nbsp;</span></font><o:p></o:p></p>
>
> </div>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>FMRIB, JR Hospital, Headington, =
> <st1:place
> w:st=3D"on"><st1:City =
> w:st=3D"on">Oxford</st1:City>&nbsp;&nbsp;<st1:PostalCode
>  w:st=3D"on">OX3 9DU</st1:PostalCode>, <st1:country-region =
> w:st=3D"on">UK</st1:country-region></st1:place></span></font><o:p></o:p><=
> /p>
>
> </div>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>+44 (0) 1865 222545&nbsp;&nbsp;(fax =
> 222717)</span></font><o:p></o:p></p>
>
> </div>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'><a =
> href=3D"mailto:[log in to unmask]"
> target=3D"_blank">[log in to unmask]</a>&nbsp; &nbsp;&nbsp;<a
> href=3D"http://www.fmrib.ox.ac.uk/%7Esaad" =
> target=3D"_blank">http://www.fmrib.ox.ac.uk/~saad</a></span></font><o:p><=
> /o:p></p>
>
> </div>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>--------------------------------------=
> -------------------------------------</span></font><o:p></o:p></p>
>
> </div>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>&nbsp;</span></font><o:p></o:p></p>
>
> </div>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>&nbsp;</span></font><o:p></o:p></p>
>
> </div>
>
> <p style=3D'margin-bottom:12.0pt'><font size=3D3 face=3D"Times New =
> Roman"><span
> style=3D'font-size:12.0pt'><o:p>&nbsp;</o:p></span></font></p>
>
> </div>
>
> </div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'></span></span>&nbsp;<o:p></o:p></span></font><=
> /p>
>
> </div>
>
> </blockquote>
>
> </div>
>
> </div>
>
> </div>
>
> <div>
>
> <div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'><br>
> <br clear=3Dall>
> <br>
> -- <br>
> Dr. med. Markus Gschwind, M.D.<br>
> Laboratory for Neurology and Imaging of Cognition<br>
> Dept of Neurosciences<br>
> <st1:place w:st=3D"on"><st1:PlaceType =
> w:st=3D"on">University</st1:PlaceType> <st1:PlaceName
>  w:st=3D"on">Medical</st1:PlaceName> <st1:PlaceType =
> w:st=3D"on">Center</st1:PlaceType></st1:place>
> (CMU)<br>
> 1 Michel-Servet - 1211 <st1:City w:st=3D"on"><st1:place =
> w:st=3D"on">GENEVA</st1:place></st1:City>
> - CH<br>
> <br>
> Tel 0041 (0) 22 379 5324<br>
> Fax 0041 (0) 22 379 5402<br>
> email: <a href=3D"mailto:[log in to unmask]" =
> target=3D"_blank">[log in to unmask]</a><br>
> <a href=3D"http://labnic.unige.ch" =
> target=3D"_blank">http://labnic.unige.ch</a><br>
> <br>
> PS: <st1:country-region w:st=3D"on"><st1:place =
> w:st=3D"on">Switzerland</st1:place></st1:country-region>
> is a good place for scientists. It is the origin of special relativity =
> (1905)
> and the World Wide Web (1990), it is associated with 105 Nobel =
> laureates, and
> boasts the world's highest number of Nobel prizes per capita, the =
> highest
> number of publications per capita, the highest number of patents per =
> capita,
> the highest citation impact factor, the most cited single-author paper, =
> etc. <st1:country-region
> w:st=3D"on"><st1:place =
> w:st=3D"on">Switzerland</st1:place></st1:country-region>
> also got the highest ranking in the list of happiest countries :-) =
> .<o:p></o:p></span></font></p>
>
> </div>
>
> </div>
>
> </div>
>
> </div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>&nbsp;<o:p></o:p></span></font></p>
>
> </div>
>
> </div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>&nbsp;<o:p></o:p></span></font></p>
>
> <div><span style=3D'border-spacing: 0px;word-spacing:0px'>
>
> <div><span style=3D'border-spacing: 0px;word-spacing:0px'>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>--------------------------------------=
> -------------------------------------</span></font><o:p></o:p></p>
>
> </div>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>Saad =
> Jbabdi,&nbsp;</span></font><o:p></o:p></p>
>
> </div>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>Postdoctoral Research =
> Assistant,&nbsp;&nbsp;</span></font><o:p></o:p></p>
>
> </div>
>
> <div>
>
> <p><st1:place w:st=3D"on"><st1:PlaceName w:st=3D"on"><font size=3D1 =
> color=3Dblack
>  face=3DHelvetica><span =
> style=3D'font-size:9.0pt;font-family:Helvetica;color:black'>Oxford</span>=
> </font></st1:PlaceName><font
>  size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;font-family:
>  Helvetica;color:black'> <st1:PlaceType =
> w:st=3D"on">University</st1:PlaceType></span></font></st1:place><font
> size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;font-family:
> Helvetica;color:black'> FMRIB Centre</span></font><o:p></o:p></p>
>
> </div>
>
> <div style=3D'min-height: 14px'>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>&nbsp;</span></font><o:p></o:p></p>
>
> </div>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>FMRIB, JR Hospital, Headington, =
> <st1:place
> w:st=3D"on"><st1:City =
> w:st=3D"on">Oxford</st1:City>&nbsp;&nbsp;<st1:PostalCode
>  w:st=3D"on">OX3 9DU</st1:PostalCode>, <st1:country-region =
> w:st=3D"on">UK</st1:country-region></st1:place></span></font><o:p></o:p><=
> /p>
>
> </div>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>+44 (0) 1865 222545&nbsp;&nbsp;(fax =
> 222717)</span></font><o:p></o:p></p>
>
> </div>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'><a =
> href=3D"mailto:[log in to unmask]"
> target=3D"_blank">[log in to unmask]</a>&nbsp; &nbsp;&nbsp;<a
> href=3D"http://www.fmrib.ox.ac.uk/%7Esaad" =
> target=3D"_blank">http://www.fmrib.ox.ac.uk/~saad</a></span></font><o:p><=
> /o:p></p>
>
> </div>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>--------------------------------------=
> -------------------------------------</span></font><o:p></o:p></p>
>
> </div>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>&nbsp;</span></font><o:p></o:p></p>
>
> </div>
>
> <div>
>
> <p><font size=3D1 color=3Dblack face=3DHelvetica><span =
> style=3D'font-size:9.0pt;
> font-family:Helvetica;color:black'>&nbsp;</span></font><o:p></o:p></p>
>
> </div>
>
> <p style=3D'margin-bottom:12.0pt'><font size=3D3 face=3D"Times New =
> Roman"><span
> style=3D'font-size:12.0pt'><o:p>&nbsp;</o:p></span></font></p>
>
> </div>
>
> </div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'></span></span>&nbsp;<o:p></o:p></span></font><=
> /p>
>
> </div>
>
> </div>
>
> </div>
>
> </div>
>
> <p><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:12.0pt'>&nbsp;<o:p></o:p></span></font></p>
>
> </div>
>
> </div>
>
> </div>
>
> </div>
>
> </div>
>
> </div>
>
> <p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
> style=3D'font-size:
> 12.0pt'><o:p>&nbsp;</o:p></span></font></p>
>
> </div>
>
> </div>
>
> </body>
>
> </html>
>
> ------=_NextPart_000_014E_01C92079.DEFB90D0--
>
> ------------------------------
>
> End of FSL Digest - 26 Sep 2008 to 27 Sep 2008 (#2008-266)
> **********************************************************
>



-- 
City Council member Alan J. Gerson
49-51 Chambers St., Suite 429
New York, NY  10007
Tel: (212) 788-7722
Fax: (212)788-7727

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