> From: freesurfer-request@nmr.mgh.harvard.edu
> Subject: Freesurfer Digest, Vol 127, Issue 37
> To: freesurfer@nmr.mgh.harvard.edu
> Date: Wed, 24 Sep 2014 12:00:02 -0400
>
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>
>
> Today's Topics:
>
> 1. longitudinal analysis and linear mixed effects models
> (Emma Thompson)
> 2. Re: Pial Surface Incorrect For Native T1 (Zachary Greenberg)
> 3. Segfault Error (Nikita Zhitkevich)
> 4. how to extract the individual cortical thickness or volume
> value of significant cluster after RFT correction (wang kangcheng)
> 5. Re: how to extract the individual cortical thickness or
> volume value of significant cluster after RFT correction
> (wang kangcheng)
> 6. Re: Segfault Error (Bruce Fischl)
> 7. Re: longitudinal analysis and linear mixed effects models
> (Martin Reuter)
> 8. Re: Vertex wise analysis and area/pial area/volume
> interpretation (Las Blawimo)
> 9. Brainhack Eastern Standard Time - Boston October 18-19, 2014
> (MCLAREN, Donald)
> 10. watershed problem (Anastasia Klimovich-Smith)
> 11. Re: how to extract the individual cortical thickness or
> volume value of significant cluster after RFT correction
> (Douglas N Greve)
> 12. Re: Pial Surface Incorrect For Native T1 (Douglas N Greve)
> 13. Re: Scatter plot from mri_glmfit analyses (Douglas N Greve)
> 14. Re: possible to use freesurfer segmentations to get mean
> values for anatomic structures from other sequences (Douglas N Greve)
> 15. Re: Volume to surface coordinates (Douglas N Greve)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 23 Sep 2014 17:55:27 -0400
> From: Emma Thompson <voneconomos@gmail.com>
> Subject: [Freesurfer] longitudinal analysis and linear mixed effects
> models
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> <CA+BXJQJHWhSi2p+Yr25Cb_yUxcb-hEwPwCbdtV96Y=ub+Qh_8A@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi FS,
> I want to conduct a within-subjects longitudinal analysis, I thought I
> would be able to run a LME model in QDEC but this doesn't seem to be the
> case at all, is this correct? It seems I have to do everything using Matlab
> (big sigh).
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels
>
>
> I have already preprocessed the data: 1) cross for all time points, 2)
> base, and then 3) long according to the awesome tutorial provided by FS.
>
> I have only one group, a patient population that was scanned prior to
> (bseline) and at various time points (3 time points post) following
> treatment. Would you agree that the best analytical approach for me would
> be the LME model, especially since I have a few subjects with a couple of
> missing post-treatment time points?
>
> Is there any way you would recommend another approach using QDEC?
>
> Lastly, I have done everything in FS version 5.1, I'm considering upgrading
> to 5.3, since my freeview software seems to be out of date. It also seems
> that the Matlab tools I need to run LME are only available in FS version
> 5.2. At this point a little concerned since I'm hoping I didn't waste a
> bunch of time just realizing all this now, would upgrading to 5.3
> negatively impact all the work I've done thus far using version 5.1?
>
> Thanks for the help!!
> -------------- next part --------------
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> ------------------------------
>
> Message: 2
> Date: Tue, 23 Sep 2014 15:11:40 -0700
> From: Zachary Greenberg <zacharyigreenberg@gmail.com>
> Subject: Re: [Freesurfer] Pial Surface Incorrect For Native T1
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> <CALa=zBeoBXc3_0Fv1iaYK_dVBkv1qQk=nvMF4YfKuTqbtBBiDg@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Doug,
>
> Thanks for getting back to me and sorry for the delay. Yes I can actually.
> If I corregister the CT to orig.nii and then pick out the points in
> freeview they look pretty good. This is a pretty painful process though. Is
> there an easy way to save a set of points in a text file from freeview?
>
> Ideally, I would like to be able to do this with the native pial surface as
> well, but I still have the problem of it appearing rotated and flipped in
> freeview. Is there a way to fix this?
>
> Thanks again for your help,
>
> Best,
> -Zack
>
> On Thu, Sep 18, 2014 at 12:50 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
> > wrote:
>
> >
> > Can you get it to display correctly on the pial surface in conformed space?
> >
> > On 09/17/2014 08:04 PM, Zachary Greenberg wrote:
> > > Hello Freesurfer experts,
> > >
> > > I am having a tough time getting my pial surfaces into the correct
> > > anatomical space. I work with ECoG Patients, so we have pre-implant
> > > high resolution T1s (GE SPGR), and post-implant high resolution CTs
> > > that show the location of ECoG electrodes within the patient's skull.
> > > Our goal: display ECoG electrodes in their correct positions on the
> > > patient's native pial surface.
> > >
> > > Right now, my pipeline works like this:
> > > -ACPC align the T1, leave it in LAS orientation.
> > > -recon-all the acpc T1, using -3T -all -openmp 8 -use-gpu
> > > -corregister the CT to the acpc T1 (SPM), get electrode coords in T1
> > space
> > > -plot the electrodes on the resultant .pial surface from freesurfer
> > >
> > > The problem is, I can definitely tell that the position of the pial
> > > mesh is off (probably by 10 millimeters or so), as the electrodes
> > > (which have the correct coordinates from the T1 correg, confirmed
> > > visually by overlaying the CT on T1) are not in their correct
> > > positions on the mesh. Likewise, DTI fibers reconstructed from EPIs
> > > correctly corregistered to the T1 also appear off position within the
> > > .pial mesh.
> > >
> > > Here is what I have tried:
> > >
> > > compute the transform from .pial to .pial.native as suggested on
> > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
> > >
> > > tkregister2 --mov rawavg.mgz --targ orig.mgz --reg register.native.dat
> > --noedit --regheader
> > > mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz
> > --tval lh.pial.native --tval-xyz --hemi lh --s subjectname
> > > This results in a mesh that is flipped (left is right) and rotated
> > > such that anterior is inferior (frontal cortex is pointing downward).
> > > The mesh appears this way when plotted in any viewer besides
> > > freesurfer (MATLAB mesh, Pyqt) but appears in the correct orientation
> > > in freeview. Replacing orig.mgz with the original T1.nii in the
> > > command above produces the opposite effect, freeview plots the
> > > orientation wrong, and any other viewer plots the Mesh oriented
> > > correctly, and the mesh appears to be identical to the originally
> > > output .pial mesh (electrodes are still wrong).
> > >
> > > Any help in pin pointing what is going wrong here would be greatly
> > > appreciated. I have a feeling it has something to do with the mesh
> > > being in surface RAS and the original T1 being in LAS.
> > >
> > > Thanks a bunch,
> > > -Zack
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to whom it
> > is
> > addressed. If you believe this e-mail was sent to you in error and the
> > e-mail
> > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you in
> > error
> > but does not contain patient information, please contact the sender and
> > properly
> > dispose of the e-mail.
> >
> >
>
>
> --
> *Zachary Greenberg*
> *Assistant Imaging Specialist*
> *Department of Neurological Surgery*
> *University of California, San Francisco*
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> ------------------------------
>
> Message: 3
> Date: Tue, 23 Sep 2014 23:01:22 -0400
> From: Nikita Zhitkevich <znikitas@hotmail.com>
> Subject: [Freesurfer] Segfault Error
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <SNT147-W715A770B423545941C06D4D6B10@phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
> I am currently running Freesurfer on Linux and while trying to test it out on the bert subject I received the error message:
> ERROR: A segfault has occurred. This is not your fault, but is most likely an unrecoverable error and has made the program unstable. Please send the contents of the file .xdebug_tkmedit that should be in this directory to freesurfer@nmr.mgh.harvard.edu.
> I searched high and low for the .xdebug_tkmedit file but could not find it, as it seems the system is not even creating this file. Do you have any suggestions on fixing this issue?
> Sincerely,
> Nikita Zhitkevich
>
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> ------------------------------
>
> Message: 4
> Date: Wed, 24 Sep 2014 11:33:27 +0800
> From: "wang kangcheng" <kangchengwang0808@gmail.com>
> Subject: [Freesurfer] how to extract the individual cortical thickness
> or volume value of significant cluster after RFT correction
> To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <2014092411332504297610@gmail.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear experts
> I have question regarding extracting the individual cortical volume value of significant cluster after RFT correction. I have 209 subjects in an analysis and G_pariet_inf-Angular showing significant correction with score of autism after RFT correction using command of mri_surfrft_jlbr in Matlab, how
> do I export individual subjects cortical volume values for significant regions ? In addition, I did not analyze it using QDEC and just use command following reference (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis)Thank you and hope for responses.
> With best Regards,kangcheng Wang
>
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> ------------------------------
>
> Message: 5
> Date: Wed, 24 Sep 2014 11:38:49 +0800
> From: "wang kangcheng" <kangchengwang0808@gmail.com>
> Subject: Re: [Freesurfer] how to extract the individual cortical
> thickness or volume value of significant cluster after RFT correction
> To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <2014092411384754831214@gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear experts
> I am sorry. There was some wrong with previous description. The results showed that G_pariet_inf-Angular was significantly positive correlated with score of autism after RFT correction using command of mri_surfrft_jlbr.
>
> With best Regards,kangcheng Wang
>
>
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> ------------------------------
>
> Message: 6
> Date: Wed, 24 Sep 2014 08:34:14 -0400 (EDT)
> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Segfault Error
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <alpine.LRH.2.03.1409240833310.16599@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Nikita
>
> you need to give us more information if we are to help you. What was thec
> command line? What was the output of the command other than the error
> message? What version of FS and what version of Linux?
>
> cheers
> Bruce
>
>
> On Tue, 23 Sep 2014, Nikita Zhitkevich wrote:
>
> > Hi,?
> > I am currently running Freesurfer on Linux and while trying to test it out
> > on the bert subject I received the error message:?
> >
> > ERROR: A segfault has occurred. This is not your fault, but is most likely
> > an unrecoverable error and has made the program unstable.?
> > Please send the contents of the file .xdebug_tkmedit that should be in this
> > directory to?freesurfer@nmr.mgh.harvard.edu.?
> >
> > I searched high and low for the .xdebug_tkmedit file but could not find it,
> > as it seems the system is not even creating this file. Do you have any
> > suggestions on fixing this issue??
> >
> > Sincerely,?
> >
> > Nikita Zhitkevich
> >
> >
> >
>
> ------------------------------
>
> Message: 7
> Date: Wed, 24 Sep 2014 08:55:39 -0400
> From: Martin Reuter <mreuter@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] longitudinal analysis and linear mixed
> effects models
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <5422BF4B.4070307@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Emma,
>
> yes, LME is Matlab, but the wiki page describe the use step-by-step.
>
> LME makes sense in your case because some subjects have less time points
> than others.
>
> The alternative (if only a very small minority of subjects differs from
> the rest) would be the 2-stage approach, where you first reduce the
> longitudinal data to a single estimate of change (the slope of a linear
> fit within-subject) and then compare these slopes across groups. However,
> - this is not a good idea in general as it does not consider the fact
> that some subjects have less time points than others, which is
> especially problematic, if there is a bias across groups (if you did a
> group analysis)
> - also, while QDEC could be used to compare this slope/atrophy measure
> across groups, it currently does not allow 'one sample group mean' to
> check if this slope is different from zero. You'd have to use mri_glmfit
> for that.
>
> You can upgrade to 5.3 to use a more recent freeview and to run your
> post-processing (LME etc), but don't mix versions for the image
> processing part (recon-all).
>
> And finally about the design in general. Not having a control group can
> be a big problem. For example just looking at atrophy rates in your
> treatment group will not tell you anything. You'll probably find some
> atrophy here and there, but is it different from no-treatment? Is it
> different from normal ageing? You would not be able to tell. But maybe
> your design is different, e.g. you could look for a correlation with
> drug dose etc.
>
> I hope that helps.
> Best, Martin
>
> On 09/23/2014 05:55 PM, Emma Thompson wrote:
> > Hi FS,
> > I want to conduct a within-subjects longitudinal analysis, I thought I
> > would be able to run a LME model in QDEC but this doesn't seem to be
> > the case at all, is this correct? It seems I have to do everything
> > using Matlab (big sigh).
> >
> > https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels
> >
> >
> > I have already preprocessed the data: 1) cross for all time points, 2)
> > base, and then 3) long according to the awesome tutorial provided by FS.
> >
> > I have only one group, a patient population that was scanned prior to
> > (bseline) and at various time points (3 time points post) following
> > treatment. Would you agree that the best analytical approach for me
> > would be the LME model, especially since I have a few subjects with a
> > couple of missing post-treatment time points?
> >
> > Is there any way you would recommend another approach using QDEC?
> >
> > Lastly, I have done everything in FS version 5.1, I'm considering
> > upgrading to 5.3, since my freeview software seems to be out of date.
> > It also seems that the Matlab tools I need to run LME are only
> > available in FS version 5.2. At this point a little concerned since
> > I'm hoping I didn't waste a bunch of time just realizing all this
> > now, would upgrading to 5.3 negatively impact all the work I've done
> > thus far using version 5.1?
> >
> > Thanks for the help!!
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Dr. Martin Reuter
>
> Instructor in Neurology
> Harvard Medical School
> Assistant in Neuroscience
> Dept. of Radiology, Massachusetts General Hospital
> Dept. of Neurology, Massachusetts General Hospital
> Research Affiliate
> Computer Science and Artificial Intelligence Lab,
> Dept. of Electrical Engineering and Computer Science,
> Massachusetts Institute of Technology
>
> A.A.Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, MA 02129
>
> Phone: +1-617-724-5652
> Email:
> mreuter@nmr.mgh.harvard.edu
> reuter@mit.edu
> Web : http://reuter.mit.edu
>
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> ------------------------------
>
> Message: 8
> Date: Wed, 24 Sep 2014 15:30:21 +0200
> From: Las Blawimo <lasblawimo@gmail.com>
> Subject: Re: [Freesurfer] Vertex wise analysis and area/pial
> area/volume interpretation
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
> <CAKBuV=TOAK+0qJSae5uaVoUjYE8QJPKXBGKE1hE9i5d9AyuQsw@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear experts,
>
> I had a question concerning the output of the Monte Carlo Z-simulation
> (abs) in Qdec. When I run the analysis, Qdec prints out a table including
> the max vertex, p-values, and coordinates of significant clusters. However,
> when I hit the button 'Find clusters go to max', qdec provides a different
> max vertex as well as different coordinates.
>
> I was wondering what is the difference between the coordinates. Which
> output provides the coordinates of the maximum significant vertex?
>
> Thanks in advance.
>
> Kind regards,
>
> Las Blawimo
>
> # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP
> CWPLow CWPHi NVtxs Annot
> 1 3.881 94038 3103.57 * 37.7 23.7 40.4* 0.00010
> 0.00000 0.00020 5981 caudalmiddlefrontal
> 2 3.187 66622 905.91 *19.3 35.7 36.9* 0.03260
> 0.03030 0.03490 1421 superiorfrontal
> Simulation complete.
> ============================================================
> Generating cluster stats using min threshold of 1.3...
> Found 2 clusters
> Contrast: 'rh-Avg-thickness-SensTOTAV-Cor', 10fwhm, DOF: 185
> ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation
> --------- --- ------ --------- ---- ---- ---- ----- ----------
> 1 4.0000 49 3103.57 * 39.1 -9.6 60.8* 5981 precentral
> 2 1.4868 43 905.91 *22.0 16.7 50.8* 1421
> superiorfrontal
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> ------------------------------
>
> Message: 9
> Date: Tue, 23 Sep 2014 15:39:52 -0400
> From: "MCLAREN, Donald" <mclaren.donald@gmail.com>
> Subject: [Freesurfer] Brainhack Eastern Standard Time - Boston October
> 18-19, 2014
> To: Donald McLaren <mclaren.donald@gmail.com>
> Message-ID:
> <CAKwrF_UJigFHJqq6uYVL=VVioLA5k4SFL5R-pXLcYasgFfdcUQ@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> *Do you have a great idea for collaboration or want to collaborate on great
> ideas?*
>
> *!!!!THEN BRAINHACK IS THE PLACE FOR YOU!!!!*
>
> Brainhack is a unique conference that convenes researchers, artists, and
> members of industry from across the globe and a myriad of disciplines to
> work together on innovative projects broadly related to neuroscience. Year
> after year, global Brainhack events have brought together researchers to
> participate in open collaboration resulting in new ideas, relationships,
> and publications.
>
> Brainhack Eastern Daylight Time (EDT; http://brainhack.org/brainhack-edt/)
> will unite several regional Brainhack events during October 18 & 19, 2014.
> Having several simultaneous events will help build a critical mass for the
> regional Brainhack movement and provide opportunities for inter-Brainhack
> collaboration. The Boston Brainhack will be held at the McGovern Institute
> for Brain Research at MIT and is additionally supported by Siemens and
> Amazon.
>
> The Boston Brainhack aims to foster local collaborations across the diverse
> neuroscience interests and institutions in the Boston area.
>
> The three most common questions:
>
> *Q. What happens at a brainhack?*
>
> A. Think of it as a maker space for neuroscientists. Neuroscience is a
> complex, multidisciplinary field with many unknowns. It is often the case
> that no individual's expertise is enough to tackle research questions that
> can encompass physics, mathematics, modeling, statistics, art, etc. These
> events serve to catalyze collaboration across individuals from different
> disciplines, create local connections, and promote "thinking outside the
> box". The events also increase awareness of new and changing technologies
> around us as neuroscience move towards data and computationally intensive
> approaches. Most importantly it is the social human spirit that brings
> together people to share in efforts to solve problems together. If you have
> a scientific problem, then the Boston Brainhack can help you solve it.
> Think of it like a conference, but instead of talking about solutions,
> actually sitting down and implementing them.
>
> *Q. I am new to the field or don't know how to code, can I still come?*
>
> A. Yes! At any level or from any discipline you can make significant
> contributions. At Brainhack you will both learn and contribute. If you want
> to know how to code in a specific program, please let us know and we'll do
> our best to facilitate the learning process. If you are in a different
> field and want to hear about neuroscience problems, come on over.
>
> *Q. What do I need to do to prepare?*
>
> A. Here are a few tips
>
> 1. To help us get a rough headcount, please sign up at: http://goo.gl/tMfwa2
>
> 2. Consider questions or ideas you would like to work on at Brainhack
>
> 3. Post project ideas or become a member of a project:
>
> http://brainhack.org/brainhack-edt/
>
> 4. Bring tools, data or just enthusiasm on October 18th and 19th.
>
> 5. Start chatting at: https://gitter.im/satra/brainhackEDT/~chat#initial
> <https://gitter.im/satra/brainhackEDT/~chat%22%20%5Cl%20%22initial>
>
> or posting questions at: http://neurostars.org <%22> (tag with
> Brainhack)
>
>
> We look forward to seeing everyone at the McGovern Institute.
>
>
> Sincerely,
>
>
> The Boston Brainhack Committee
>
> Donald G McLaren, MGH/HMS
>
> Satra Ghosh, MIT
>
> Matt Hutchison, Harvard University
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> ------------------------------
>
> Message: 10
> Date: Wed, 24 Sep 2014 15:17:23 +0100
> From: Anastasia Klimovich-Smith <ak798@cam.ac.uk>
> Subject: [Freesurfer] watershed problem
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <5422D273.4040103@cam.ac.uk>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
>
> I have some unexpected results from the mne_watershed_bem script that
> uses Freesurfer mri_watershed program.
>
> For one of my subject's the inner scull surface (
> xxxx_inner_scull_surface in bem/watershed/) partially excludes
> cerebellum (the left screen shot). All my other subjects have cerebellum
> included into the inner scull (right screen shot). As a consequence
> later stage scripts (mne_setup_forward_model and
> mne_do_forward_solution) produce similarly erroneous inner scull surface
> delineation.
>
>
>
> Did anyone experience this problem before, and if so, how would you
> advise to fix it?
>
> For this subject MRI MP RAGE sequence was acquired using the 12 channel
> coil, which, compared to the 32 channel one used for other subjects,
> produced images of worse quality. However, I have other subjects with 12
> channel coil scans and their inner scull surfaces were separated
> normally (including the cerebellum).
>
> Thanks,
> Ana
>
>
>
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> ------------------------------
>
> Message: 11
> Date: Wed, 24 Sep 2014 11:33:03 -0400
> From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] how to extract the individual cortical
> thickness or volume value of significant cluster after RFT correction
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <5422E42F.2070406@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> You can run mri_glmfit-sim using the same voxel-wise threshold and
> setting the clusterwise threshold to .5. This will create several files.
> One will be called something like {csdbase}.y.ocn.annot. Load this in
> tksurfer or freeview to find which cluster corresponds to your cluster.
> Then look in {csdbase}.y.ocn.dat. This will be a matrix with number of
> rows equal to the number subjects and number of columns equal to the
> number of clusters. Take the column that corresponds to your cluster.
>
>
>
>
> On 09/23/2014 11:33 PM, wang kangcheng wrote:
> > Dear experts
> > I have question regarding extracting the individual cortical volume
> > value of significant cluster after RFT correction. I have 209 subjects
> > in an analysis and G_pariet_inf-Angularshowing significant correction
> > with score of autism after RFT correction using command of
> > mri_surfrft_jlbr in Matlab, how
> > do I export individual subjects cortical volume values for significant regions ? In addition, I did not analyze it using QDEC and just use command following reference (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis)
> > Thank you and hope for responses.
> >
> > With best Regards,
> > kangcheng Wang
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
> ------------------------------
>
> Message: 12
> Date: Wed, 24 Sep 2014 11:48:57 -0400
> From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Pial Surface Incorrect For Native T1
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <5422E7E9.8060101@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> When I run your commands, the pial is correctly oriented and placed.
> What is your freeview command? This is what I use
>
> freeview -v rawavg.mgz --surface ../surf/lh.pial.native:edgecolor=yellow
>
> On 09/23/2014 06:11 PM, Zachary Greenberg wrote:
> > Hi Doug,
> >
> > Thanks for getting back to me and sorry for the delay. Yes I can
> > actually. If I corregister the CT to orig.nii and then pick out the
> > points in freeview they look pretty good. This is a pretty painful
> > process though. Is there an easy way to save a set of points in a text
> > file from freeview?
> >
> > Ideally, I would like to be able to do this with the native pial
> > surface as well, but I still have the problem of it appearing rotated
> > and flipped in freeview. Is there a way to fix this?
> >
> > Thanks again for your help,
> >
> > Best,
> > -Zack
> >
> > On Thu, Sep 18, 2014 at 12:50 PM, Douglas N Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
> >
> >
> > Can you get it to display correctly on the pial surface in
> > conformed space?
> >
> > On 09/17/2014 08:04 PM, Zachary Greenberg wrote:
> > > Hello Freesurfer experts,
> > >
> > > I am having a tough time getting my pial surfaces into the correct
> > > anatomical space. I work with ECoG Patients, so we have pre-implant
> > > high resolution T1s (GE SPGR), and post-implant high resolution CTs
> > > that show the location of ECoG electrodes within the patient's
> > skull.
> > > Our goal: display ECoG electrodes in their correct positions on the
> > > patient's native pial surface.
> > >
> > > Right now, my pipeline works like this:
> > > -ACPC align the T1, leave it in LAS orientation.
> > > -recon-all the acpc T1, using -3T -all -openmp 8 -use-gpu
> > > -corregister the CT to the acpc T1 (SPM), get electrode coords
> > in T1 space
> > > -plot the electrodes on the resultant .pial surface from freesurfer
> > >
> > > The problem is, I can definitely tell that the position of the pial
> > > mesh is off (probably by 10 millimeters or so), as the electrodes
> > > (which have the correct coordinates from the T1 correg, confirmed
> > > visually by overlaying the CT on T1) are not in their correct
> > > positions on the mesh. Likewise, DTI fibers reconstructed from EPIs
> > > correctly corregistered to the T1 also appear off position
> > within the
> > > .pial mesh.
> > >
> > > Here is what I have tried:
> > >
> > > compute the transform from .pial to .pial.native as suggested on
> > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
> > >
> > > tkregister2 --mov rawavg.mgz --targ orig.mgz --reg
> > register.native.dat --noedit --regheader
> > > mri_surf2surf --sval-xyz pial --reg register.native.dat
> > rawavg.mgz --tval lh.pial.native --tval-xyz --hemi lh --s subjectname
> > > This results in a mesh that is flipped (left is right) and rotated
> > > such that anterior is inferior (frontal cortex is pointing
> > downward).
> > > The mesh appears this way when plotted in any viewer besides
> > > freesurfer (MATLAB mesh, Pyqt) but appears in the correct
> > orientation
> > > in freeview. Replacing orig.mgz with the original T1.nii in the
> > > command above produces the opposite effect, freeview plots the
> > > orientation wrong, and any other viewer plots the Mesh oriented
> > > correctly, and the mesh appears to be identical to the originally
> > > output .pial mesh (electrodes are still wrong).
> > >
> > > Any help in pin pointing what is going wrong here would be greatly
> > > appreciated. I have a feeling it has something to do with the mesh
> > > being in surface RAS and the original T1 being in LAS.
> > >
> > > Thanks a bunch,
> > > -Zack
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> > Phone Number: 617-724-2358 <tel:617-724-2358>
> > Fax: 617-726-7422 <tel:617-726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in error and
> > the e-mail
> > contains patient information, please contact the Partners
> > Compliance HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to
> > you in error
> > but does not contain patient information, please contact the
> > sender and properly
> > dispose of the e-mail.
> >
> >
> >
> >
> > --
> > *Zachary Greenberg*
> > /Assistant Imaging Specialist/
> > /Department of Neurological Surgery/
> > /University of California, San Francisco/
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
> ------------------------------
>
> Message: 13
> Date: Wed, 24 Sep 2014 11:53:46 -0400
> From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Scatter plot from mri_glmfit analyses
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <5422E90A.8060307@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> X and C have different numbers of columns. What was your mri_glmfit
> command line? If you used a --pvr, then the pcc script will not work.
> doug
>
> On 09/22/2014 01:21 PM, Celine Louapre wrote:
> > Thanks for pointing me to the file and the help. I found the info I needed
> > there fro the cache.th13.abs.y.ocn.dat file.
> >
> > For the partial correlation coefficient script fast_glm_pcc.m I could not
> > make it run however. I got this error:
> > Error using *
> > Inner matrix dimensions must agree.
> >
> > Error in fast_glm_pcc (line 28)
> > Xc = X*C';
> >
> > And also I found this info in the script WARNING: X must have a column of
> > 1s or both X and y must have been demeaned before the glm.
> > But I am not sure about what it means. Attached are Xg.dat and C.dat files.
> > Thanks again for your help
> > Celine
> >
> >>
> >> should be something like cache.th13.abs.y.ocn.dat
> >> also, you can look in mri_glmfit-sim --help to get info about each
> >> output file
> >>
> >> On 09/19/2014 04:47 PM, Celine Louapre wrote:
> >>> Indeed I ran mri_glmfit-sim. What file is the output of mri_segstat?
> >>> The cache.th13.abs.sig.ocn.annot contains the significant clusters it
> >>> that
> >>> correct? So to get individual mean values from cluster 1 for example
> >>> where
> >>> should I look?
> >>> Thanks!
> >>> Celine
> >>>
> >>>
> >>>> Have you run mri_glmfit-sim? It will create labels (ie, annotations) of
> >>>> the clusters as well as run mri_segstats to get means in each cluster
> >>>> for each subject. Try that link now
> >>>> doug
> >>>>
> >>>> On 09/18/2014 12:15 PM, Celine Louapre wrote:
> >>>>> Hi Doug and FS team
> >>>>>
> >>>>> I did glm analyses using mri_glmfit, and I was trying to plot the
> >>>>> individual values in the population for a specific significant
> >>>>> cluster.
> >>>>> However I am not sure how to extract individual values from the entire
> >>>>> cluster. (note that the concatenated surface used as input for the glm
> >>>>> contains some 0 values that I want to exclude from the mean value of
> >>>>> the
> >>>>> cluster).
> >>>>> Is there a way to build a label from a specific significant cluster?
> >>>>>
> >>>>> Then, I was thinking about using mri_segstats --avgwf on the 4D
> >>>>> concatenated file to get the average of the region but is there a way
> >>>>> to
> >>>>> not include 0 values?
> >>>>>
> >>>>> And then I was also interested in getting the correlation coefficient
> >>>>> from
> >>>>> that same cluster, so maybe the script below would be helpful for that
> >>>>> but
> >>>>> I could not open it.
> >>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_glm_pcc.m
> >>>>>
> >>>>> Thanks so much for your help
> >>>>> Best
> >>>>> Celine
> >>>>>
> >>>>> On 05/31/2012 06:09 AM, Knut J Bjuland wrote:
> >>>>>> Hi
> >>>>>>
> >>>>>> I am trying to calculate correlation coefficient using freesurfer GLM
> >>>>>> for associations between volumes and IQ. I found this ealier answar,
> >>>>>> but the matlab script but the link appear to be dead.
> >>>>>>
> >>>>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22648.html
> >>>>>>
> >>>>>> Best regards
> >>>>>>
> >>>>>> Knut J
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Freesurfer mailing list
> >>>>>> Freesurfer@nmr.mgh.harvard.edu
> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>> --
> >>>> Douglas N. Greve, Ph.D.
> >>>> MGH-NMR Center
> >>>> greve@nmr.mgh.harvard.edu
> >>>> Phone Number: 617-724-2358
> >>>> Fax: 617-726-7422
> >>>>
> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> >>>> Outgoing:
> >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >>>>
> >>>> _______________________________________________
> >>>> Freesurfer mailing list
> >>>> Freesurfer@nmr.mgh.harvard.edu
> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>>
> >>>>
> >>>>
> >>> _______________________________________________
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>>
> >> --
> >> Douglas N. Greve, Ph.D.
> >> MGH-NMR Center
> >> greve@nmr.mgh.harvard.edu
> >> Phone Number: 617-724-2358
> >> Fax: 617-726-7422
> >>
> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >>
> >> _______________________________________________
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
> ------------------------------
>
> Message: 14
> Date: Wed, 24 Sep 2014 11:57:51 -0400
> From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] possible to use freesurfer segmentations to
> get mean values for anatomic structures from other sequences
> To: Salil Soman <salsoman@stanford.edu>
> Cc: free surfer <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <5422E9FF.6040009@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
> On 09/23/2014 04:05 AM, Salil Soman wrote:
> > Dear Doug,
> >
> > Thank you for your email. You were correct, there are values in the
> > output file from running mri_segstats.
> >
> > I was hoping for your advice on the following:
> >
> > 1) as I used FreeSurferColorLUT.txt and the aparc+aseg.mgz files, are
> > the values extracted from the transformed cbf images the mean value
> > per anatomic region in the same units as the original CBF image? (I am
> > under the impression yes, and so instead of interpreting the sample
> > data listed below as mm3 I would interpret the values as ml / 100 g /
> > min )
> Yes, same units as the input.
> >
> > 2) While most of the CBF to T1 registrations using the transformation
> > for the PD to the T1 image worked reasonably, there are a few where
> > the registration is a little off (almost exclusively requiring some
> > translation in the SI direction) - what is the best way to correct the
> > registration and generate a better fitting transformation matrix?
> > (either manually or using some other tool)
> What did you use to do the registration?
> >
> > 3) Do I not need to use seg-erode to minimize partial voluming?
> You may, but then you may lose an entire ROI, esp in cortex. I'll have
> some PVC software for the next release.
> >
> > 4) Is there a way I can use asegstats2table and / or aparcstats2table
> > on the output file I generate from mri_segstats to create a table with
> > values for multiple subjects? (A sample of my current output file from
> > mri_segstats is below).
> Yes, just specify --inputs /path/to/first/datfile
> /path/to/second/datfile with asegstats2table
>
>
> >
> > Thank you for all your help.
> >
> > Best wishes,
> >
> > Sal
> >
> > # Title Segmentation Statistics
> > #
> > # generating_program mri_segstats
> > # cvs_version $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve
> > Exp $
> > # cmdline mri_segstats --seg aparc+aseg.mgz --ctab
> > /farmshare/software/free/freesurfer/5.3.0/FreeSurferColorLUT.txt --i
> > JK_CBF_Reg.nii.gz --sum JK_ASL.stats --seg-erode 1
> > # sysname Linux
> > # hostname f.stanford.edu <http://f.stanford.edu>
> > # machine x86_64
> > # user soman
> > # anatomy_type volume
> > #
> > # SegVolFile aparc+aseg.mgz
> > # SegVolFileTimeStamp 2014/09/21 21:26:30
> > # ColorTable
> > /farmshare/software/free/freesurfer/5.3.0/FreeSurferColorLUT.txt
> > # ColorTableTimeStamp 2013/05/13 14:21:15
> > # InVolFile 1534_1_PRE_1200_CBF_Reg.nii.gz
> > # InVolFileTimeStamp 2014/09/21 21:26:30
> > # InVolFrame 0
> > # Only reporting non-empty segmentations
> > # VoxelVolume_mm3 1
> > # TableCol 1 ColHeader Index
> > # TableCol 1 FieldName Index
> > # TableCol 1 Units NA
> > # TableCol 2 ColHeader SegId
> > # TableCol 2 FieldName Segmentation Id
> > # TableCol 2 Units NA
> > # TableCol 3 ColHeader NVoxels
> > # TableCol 3 FieldName Number of Voxels
> > # TableCol 3 Units unitless
> > # TableCol 4 ColHeader Volume_mm3
> > # TableCol 4 FieldName Volume
> > # TableCol 4 Units mm^3
> > # TableCol 5 ColHeader StructName
> > # TableCol 5 FieldName Structure Name
> > # TableCol 5 Units NA
> > # TableCol 6 ColHeader Mean
> > # TableCol 6 FieldName Intensity Mean
> > # TableCol 6 Units unknown
> > # TableCol 7 ColHeader StdDev
> > # TableCol 7 FieldName Itensity StdDev
> > # TableCol 7 Units unknown
> > # TableCol 8 ColHeader Min
> > # TableCol 8 FieldName Intensity Min
> > # TableCol 8 Units unknown
> > # TableCol 9 ColHeader Max
> > # TableCol 9 FieldName Intensity Max
> > # TableCol 9 Units unknown
> > # TableCol 10 ColHeader Range
> > # TableCol 10 FieldName Intensity Range
> > # TableCol 10 Units unknown
> > # NRows 112
> > # NTableCols 10
> > # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev
> > Min Max Range
> > 1 0 16192691 16192691.0 Unknown 5.2913 14.7318
> > 0.0000 229.0000 229.0000
> > 2 2 139929 139929.0 Left-Cerebral-White-Matter
> > 39.5857 10.3158 0.0000 87.0000 87.0000
> > 3 4 14471 14471.0 Left-Lateral-Ventricle 27.8682
> > 9.4901 5.0000 60.0000 55.0000
> > 4 5 66 66.0 Left-Inf-Lat-Vent 31.1515
> > 6.3154 21.0000 48.0000 27.0000
> > 5 7 9041 9041.0 Left-Cerebellum-White-Matter
> > 44.4476 9.4356 17.0000 69.0000 52.0000
> > 6 8 31979 31979.0 Left-Cerebellum-Cortex 44.5335
> > 8.8930 14.0000 88.0000 74.0000
> > 7 10 5372 5372.0 Left-Thalamus-Proper 35.8096
> > 17.4881 11.0000 95.0000 84.0000
> > 8 11 1889 1889.0 Left-Caudate 22.4314 7.9514
> > 8.0000 58.0000 50.0000
> > 9 12 3145 3145.0 Left-Putamen 27.5463 6.7851
> > 10.0000 57.0000 47.0000
> > 10 13 954 954.0 Left-Pallidum 25.0922 5.8356
> > 14.0000 50.0000 36.0000
> > 11 14 1102 1102.0 3rd-Ventricle 35.0554 12.4595
> > 8.0000 60.0000 52.0000
> > 12 15 1698 1698.0 4th-Ventricle 38.9694 8.9711
> > 18.0000 59.0000 41.0000
> > 13 16 17721 17721.0 Brain-Stem 37.2733 8.1110
> > 12.0000 62.0000 50.0000
> > 14 17 2187 2187.0 Left-Hippocampus 36.8834
> > 10.7569 13.0000 86.0000 73.0000
> > 15 18 636 636.0 Left-Amygdala 29.3239 5.4794
> > 17.0000 42.0000 25.0000
> > 16 24 387 387.0 CSF 24.8398 9.1261 7.0000
> > 49.0000 42.0000
> > 17 26 202 202.0 Left-Accumbens-area 44.8267
> > 11.7573 15.0000 67.0000 52.0000
> > 18 28 2301 2301.0 Left-VentralDC 33.1521 8.6387
> > 8.0000 57.0000 49.0000
> > 19 30 3 3.0 Left-vessel 27.6667 4.0415
> > 24.0000 32.0000 8.0000
> > 20 31 408 408.0 Left-choroid-plexus 26.4951
> > 6.9254 14.0000 45.0000 31.0000
> > 21 41 144265 144265.0 Right-Cerebral-White-Matter
> > 38.9664 10.8617 0.0000 87.0000 87.0000
> > 22 43 14126 14126.0 Right-Lateral-Ventricle 29.9931
> > 9.8450 9.0000 60.0000 51.0000
> > 23 44 128 128.0 Right-Inf-Lat-Vent 28.5391
> > 5.1770 18.0000 41.0000 23.0000
> > 24 46 9402 9402.0 Right-Cerebellum-White-Matter
> > 40.2174 7.6558 19.0000 63.0000 44.0000
> > 25 47 31954 31954.0 Right-Cerebellum-Cortex 44.5438
> > 9.7131 17.0000 78.0000 61.0000
> > 26 49 4703 4703.0 Right-Thalamus-Proper 36.6517
> > 15.8310 11.0000 86.0000 75.0000
> > 27 50 1621 1621.0 Right-Caudate 21.8803 6.6455
> > 10.0000 58.0000 48.0000
> > 28 51 2955 2955.0 Right-Putamen 30.2964 7.2943
> > 12.0000 60.0000 48.0000
> > 29 52 793 793.0 Right-Pallidum 28.2472 6.3972
> > 12.0000 45.0000 33.0000
> > 30 53 2466 2466.0 Right-Hippocampus 37.5037
> > 11.7375 13.0000 87.0000 74.0000
> > 31 54 719 719.0 Right-Amygdala 33.6120 6.4086
> > 17.0000 53.0000 36.0000
> > 32 58 246 246.0 Right-Accumbens-area 36.3293
> > 12.9949 9.0000 61.0000 52.0000
> > 33 60 2141 2141.0 Right-VentralDC 35.2429 8.7845
> > 11.0000 58.0000 47.0000
> > 34 62 7 7.0 Right-vessel 30.1429 2.7343
> > 27.0000 34.0000 7.0000
> > 35 63 689 689.0 Right-choroid-plexus 25.5268
> > 5.6117 12.0000 46.0000 34.0000
> > 36 77 168 168.0 WM-hypointensities 31.5714
> > 5.8141 16.0000 43.0000 27.0000
> > 37 85 12 12.0 Optic-Chiasm 48.7500 8.2476
> > 42.0000 65.0000 23.0000
> > 38 251 402 402.0 CC_Posterior 43.4677 8.6258
> > 29.0000 65.0000 36.0000
> > 39 252 93 93.0 CC_Mid_Posterior 45.2903
> > 6.5816 31.0000 57.0000 26.0000
> > 40 253 125 125.0 CC_Central 45.2080 8.9093
> > 31.0000 57.0000 26.0000
> > 41 254 162 162.0 CC_Mid_Anterior 43.3519 6.0232
> > 27.0000 49.0000 22.0000
> > 42 255 339 339.0 CC_Anterior 42.9734 10.9373
> > 21.0000 61.0000 40.0000
> > 43 1000 41 41.0 ctx-lh-unknown 37.9268
> > 6.1983 23.0000 49.0000 26.0000
> > 44 1001 524 524.0 ctx-lh-bankssts 43.5973
> > 7.2795 26.0000 72.0000 46.0000
> > 45 1002 468 468.0 ctx-lh-caudalanteriorcingulate
> > 46.5150 9.3055 29.0000 75.0000 46.0000
> > 46 1003 1455 1455.0 ctx-lh-caudalmiddlefrontal
> > 43.3966 10.4078 9.0000 71.0000 62.0000
> > 47 1005 535 535.0 ctx-lh-cuneus 42.1850
> > 11.6290 15.0000 73.0000 58.0000
> > 48 1006 773 773.0 ctx-lh-entorhinal 35.2574
> > 5.9514 18.0000 48.0000 30.0000
> > 49 1007 3584 3584.0 ctx-lh-fusiform 39.9163
> > 9.9257 7.0000 95.0000 88.0000
> > 50 1008 3063 3063.0 ctx-lh-inferiorparietal 42.1329
> > 10.4487 19.0000 79.0000 60.0000
> > 51 1009 3197 3197.0 ctx-lh-inferiortemporal 46.8877
> > 8.9039 25.0000 74.0000 49.0000
> > 52 1010 710 710.0 ctx-lh-isthmuscingulate 50.0577
> > 12.7209 16.0000 78.0000 62.0000
> > 53 1011 2680 2680.0 ctx-lh-lateraloccipital 46.9022
> > 10.6538 13.0000 84.0000 71.0000
> > 54 1012 2014 2014.0 ctx-lh-lateralorbitofrontal
> > 38.0447 10.3773 13.0000 76.0000 63.0000
> > 55 1013 1915 1915.0 ctx-lh-lingual 44.2522
> > 8.7790 20.0000 73.0000 53.0000
> > 56 1014 1136 1136.0 ctx-lh-medialorbitofrontal
> > 42.8310 8.3573 11.0000 69.0000 58.0000
> > 57 1015 4187 4187.0 ctx-lh-middletemporal 40.0339
> > 9.4288 0.0000 86.0000 86.0000
> > 58 1016 782 782.0 ctx-lh-parahippocampal 40.9923
> > 7.7781 24.0000 73.0000 49.0000
> > 59 1017 816 816.0 ctx-lh-paracentral 44.5846
> > 10.0558 24.0000 69.0000 45.0000
> > 60 1018 1178 1178.0 ctx-lh-parsopercularis 44.0688
> > 9.2176 19.0000 70.0000 51.0000
> > 61 1019 469 469.0 ctx-lh-parsorbitalis 48.9296
> > 10.4027 11.0000 75.0000 64.0000
> > 62 1020 983 983.0 ctx-lh-parstriangularis 41.9664
> > 9.7837 0.0000 74.0000 74.0000
> > 63 1021 250 250.0 ctx-lh-pericalcarine 42.3400
> > 8.8072 20.0000 69.0000 49.0000
> > 64 1022 2438 2438.0 ctx-lh-postcentral 45.2994
> > 12.9843 0.0000 78.0000 78.0000
> > 65 1023 595 595.0 ctx-lh-posteriorcingulate
> > 46.9244 5.9274 25.0000 61.0000 36.0000
> > 66 1024 4243 4243.0 ctx-lh-precentral 44.1237
> > 13.6463 0.0000 104.0000 104.0000
> > 67 1025 1831 1831.0 ctx-lh-precuneus 46.9700
> > 10.3497 21.0000 75.0000 54.0000
> > 68 1026 603 603.0 ctx-lh-rostralanteriorcingulate
> > 48.3333 8.1835 14.0000 61.0000 47.0000
> > 69 1027 3801 3801.0 ctx-lh-rostralmiddlefrontal
> > 37.6959 12.5454 0.0000 81.0000 81.0000
> > 70 1028 7274 7274.0 ctx-lh-superiorfrontal 35.8754
> > 20.2344 0.0000 99.0000 99.0000
> > 71 1029 2502 2502.0 ctx-lh-superiorparietal 38.4592
> > 11.2217 13.0000 71.0000 58.0000
> > 72 1030 4193 4193.0 ctx-lh-superiortemporal 37.8710
> > 9.7801 12.0000 70.0000 58.0000
> > 73 1031 2981 2981.0 ctx-lh-supramarginal 41.4270
> > 9.2431 12.0000 68.0000 56.0000
> > 74 1032 184 184.0 ctx-lh-frontalpole 28.1087
> > 8.1776 15.0000 49.0000 34.0000
> > 75 1033 806 806.0 ctx-lh-temporalpole 37.2395
> > 8.7618 21.0000 70.0000 49.0000
> > 76 1034 200 200.0 ctx-lh-transversetemporal
> > 46.8550 6.7893 32.0000 64.0000 32.0000
> > 77 1035 2509 2509.0 ctx-lh-insula 40.5050
> > 8.8055 20.0000 60.0000 40.0000
> > 78 2000 27 27.0 ctx-rh-unknown 37.8148
> > 6.6912 24.0000 45.0000 21.0000
> > 79 2001 808 808.0 ctx-rh-bankssts 44.1015
> > 7.3096 15.0000 63.0000 48.0000
> > 80 2002 676 676.0 ctx-rh-caudalanteriorcingulate
> > 42.1213 8.2041 18.0000 61.0000 43.0000
> > 81 2003 1477 1477.0 ctx-rh-caudalmiddlefrontal
> > 40.6391 22.0031 0.0000 87.0000 87.0000
> > 82 2005 608 608.0 ctx-rh-cuneus 42.1447
> > 11.9201 16.0000 65.0000 49.0000
> > 83 2006 548 548.0 ctx-rh-entorhinal 40.8303
> > 6.2827 26.0000 56.0000 30.0000
> > 84 2007 4445 4445.0 ctx-rh-fusiform 41.6220
> > 11.9162 9.0000 75.0000 66.0000
> > 85 2008 3984 3984.0 ctx-rh-inferiorparietal 41.0595
> > 12.4253 10.0000 85.0000 75.0000
> > 86 2009 2909 2909.0 ctx-rh-inferiortemporal 45.6710
> > 9.9779 18.0000 77.0000 59.0000
> > 87 2010 568 568.0 ctx-rh-isthmuscingulate 47.7500
> > 12.4814 10.0000 67.0000 57.0000
> > 88 2011 3119 3119.0 ctx-rh-lateraloccipital 51.3071
> > 9.7769 21.0000 80.0000 59.0000
> > 89 2012 1865 1865.0 ctx-rh-lateralorbitofrontal
> > 32.3861 8.7282 11.0000 60.0000 49.0000
> > 90 2013 2193 2193.0 ctx-rh-lingual 43.8171
> > 8.2956 22.0000 73.0000 51.0000
> > 91 2014 1536 1536.0 ctx-rh-medialorbitofrontal
> > 45.0983 10.2363 13.0000 82.0000 69.0000
> > 92 2015 4616 4616.0 ctx-rh-middletemporal 43.2000
> > 11.1110 17.0000 75.0000 58.0000
> > 93 2016 989 989.0 ctx-rh-parahippocampal 39.0172
> > 7.3277 16.0000 63.0000 47.0000
> > 94 2017 834 834.0 ctx-rh-paracentral 44.9532
> > 15.9802 0.0000 86.0000 86.0000
> > 95 2018 1059 1059.0 ctx-rh-parsopercularis 41.9122
> > 10.1778 16.0000 74.0000 58.0000
> > 96 2019 761 761.0 ctx-rh-parsorbitalis 44.6636
> > 11.4619 13.0000 71.0000 58.0000
> > 97 2020 770 770.0 ctx-rh-parstriangularis 35.3675
> > 9.9894 14.0000 63.0000 49.0000
> > 98 2021 311 311.0 ctx-rh-pericalcarine 50.3055
> > 6.9137 30.0000 70.0000 40.0000
> > 99 2022 2362 2362.0 ctx-rh-postcentral 39.3971
> > 15.8836 0.0000 76.0000 76.0000
> > 100 2023 800 800.0 ctx-rh-posteriorcingulate
> > 42.1250 8.6638 23.0000 70.0000 47.0000
> > 101 2024 4120 4120.0 ctx-rh-precentral 38.4903
> > 19.2733 0.0000 89.0000 89.0000
> > 102 2025 2278 2278.0 ctx-rh-precuneus 51.4719
> > 10.8414 0.0000 74.0000 74.0000
> > 103 2026 847 847.0 ctx-rh-rostralanteriorcingulate
> > 44.3093 8.4714 17.0000 67.0000 50.0000
> > 104 2027 3884 3884.0 ctx-rh-rostralmiddlefrontal
> > 37.5881 14.9279 0.0000 77.0000 77.0000
> > 105 2028 6878 6878.0 ctx-rh-superiorfrontal 32.7812
> > 20.7192 0.0000 92.0000 92.0000
> > 106 2029 2313 2313.0 ctx-rh-superiorparietal 38.3312
> > 13.7339 0.0000 76.0000 76.0000
> > 107 2030 4177 4177.0 ctx-rh-superiortemporal 39.0893
> > 10.6739 9.0000 72.0000 63.0000
> > 108 2031 2662 2662.0 ctx-rh-supramarginal 39.5586
> > 9.4404 16.0000 70.0000 54.0000
> > 109 2032 300 300.0 ctx-rh-frontalpole 43.1600
> > 12.4866 8.0000 71.0000 63.0000
> > 110 2033 1068 1068.0 ctx-rh-temporalpole 32.2996
> > 8.3381 14.0000 56.0000 42.0000
> > 111 2034 295 295.0 ctx-rh-transversetemporal
> > 48.2644 8.0202 33.0000 64.0000 31.0000
> > 112 2035 2511 2511.0 ctx-rh-insula 38.9263
> > 6.8398 18.0000 55.0000 37.0000
> >
> >
> >
> >
> > On Thu, Sep 18, 2014 at 2:05 PM, Douglas N Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
> >
> >
> > Are you sure that *all* are 0? By passing it
> > FreeSurferColorLUT.txt, you force it to report hundreds (or
> > thousands) of ROIs which are not represented in the
> > aparc+aseg.mgz. Also, try removing --seg-erode.
> >
> > On 09/18/2014 04:43 PM, Salil Soman wrote:
> >
> > Dear Doug,
> >
> > Thank you for your email.
> >
> > The registration overlap looks reasonable. Thank you for
> > considering this question.
> >
> > Best wishes,
> >
> > Sal
> >
> > On Thu, Sep 18, 2014 at 12:14 PM, Douglas N Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> >
> > When you look at SUBJECT_ID_CBF_reg.nii.gz, does it look
> > reasonable? Does it overlay correctly on the T1.mgz?
> > doug
> >
> > On 09/14/2014 11:40 PM, Salil Soman wrote:
> >
> > Thank you Doug. I am having trouble with extracting
> > statistics using this method.
> >
> > I am able to use bbregister to get a transformation that
> > registers the PD image of the ASL to the T1. I then
> > used this
> > transformation matrix to register the CBF map for the ASL
> > study into the T1.mgz space. Checking the images, the
> > registration looked reasonable. However, when I try to
> > extract
> > the values from the registered image using the vois from
> > aparc+aseg.mgz, and the FreeSurferColorLUT I get all 0
> > values.
> >
> > *The command I ran is:*
> >
> > mri_segstats --seg
> > $SUBJECTS_DIR/SUBJECT_ID/mri/aparc+aseg.mgz
> > --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i
> > SUBJECT_ID_CBF_reg.nii.gz --sum SUBJECT_ID_ASL.stats
> > --seg-erode 1
> >
> > *where SUBJECT_ID_CBF_reg.nii.gz was generated by
> > running:*
> >
> > mri_vol2vol --mov SUBJECT_ID_CBF.nii.gz --targ T1.mgz
> > --interp
> > nearest --o SUBJECT_ID_CBF_reg.nii.gz --reg SUBJECT_ID.dat
> > --no-save-reg
> >
> > (and this was run with T1.mgz and
> > SUBJECT_ID_CBF.nii.gz in the
> > same folder).
> >
> > *for which SUBJECT_ID.dat was generated by running the
> > code:*
> >
> > bbregister --s SUBJECT_ID --mov
> > SUBJECT_ID_ASL_PD.nii.gz --reg
> > SUBJECT_ID.dat --t1 --init-fsl
> >
> > Thank you for your consideration of this question.
> >
> > Best wishes,
> >
> > Salil Soman, MD, MS
> >
> >
> >
> >
> > On Sun, Sep 14, 2014 at 3:32 PM, Douglas Greve
> > <greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote:
> >
> > yep, you can use it for anything.
> > doug
> >
> >
> > On 9/14/14 12:52 PM, Salil Soman wrote:
> >
> > Dear Doug,
> >
> > Thank you again for this email. Do you think it is
> > possible to
> > use this method for ASL images as well? If so, how
> > would you
> > change the options?
> >
> > Best wishes,
> >
> > Salil Soman, MD, MS
> >
> > On Sat, May 25, 2013 at 11:51 AM, Douglas Greve
> > <greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu>
> >
> > <mailto:greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote:
> >
> >
> > On 5/25/13 1:39 PM, Salil Soman wrote:
> >
> > Thank you Doug.
> >
> > Just so I am clear - is the
> > anatomical the
> > nifti T1.mgz or
> > is it a different file. From your email I
> > gather should do
> > the following:
> >
> > *1) Use bbregister to register the
> > lowb image
> > to the
> > anatomical. This creates a
> > registration matrix.*
> >
> > bbregister -s SUBJECTNAME --mov lowb.nii
> > --initfsl --reg
> > register.dat
> >
> > That is right, but add --t2 (since it is
> > t2 weighted).
> >
> >
> > *2) Use mri_vol2vol and the
> > registration to
> > map the ADC map
> > to the anatomical*
> > mri_vol2vol --mov lowb.nii --targ $vol
> > --inv
> > --interp nearest --o $vol2diff --reg
> > $outdir/register.dat --no-save-reg
> >
> > Use the ADC as the moveable (not lowb, but
> > use the
> > lowb for
> > bbregister). The target volume should be the
> > T1.mgz (or any
> > conformed volume). The output will be the
> > adc in the
> > anatomical space (not sure why you call it
> > vol2diff).
> >
> > *3) use mri_segstats to extract the
> > values*
> > *mri_segstats* --seg
> > $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab
> > $FREESURFER_HOME/FreeSurferColorLUT.txt --i
> > lowb.nii
> > --sum fa.stats
> >
> > The input would be the adc volume mapped the
> > anatomical
> > space. I would use WMParcStatsLUT.txt or else
> > you'll get a
> > billion different areas not represented in
> > wmparc.
> > You may
> > also want to add "--seg-erode 1" to erode the
> > segmentations
> > by a voxel. This helps to prevent partial
> > voluming.
> >
> > doug
> >
> >
> > Where lowb.nii is the other MRI tissue
> > sequence I am
> > analyzing (e.g. ADC), $vol2diff is the
> > output
> > image of the
> > registration, and fa.stats will be my
> > output
> > stats table?
> >
> > I suspect there is part of the syntax for
> > these tools I do
> > not understand. Also, what input would
> > $vol be?
> >
> > Best wishes,
> >
> > Sal
> >
> >
> > On Sat, May 25, 2013 at 10:06 AM,
> > Douglas Greve
> > <greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu>
> >
> > <mailto:greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote:
> >
> >
> > Hi Sal, yes you can. Use bbregister to
> > register the lowb
> > image to the anatomical. This
> > creates a
> > registration
> > matrix. Use mri_vol2vol and the
> > registration to map the
> > ADC map to the anatomical, then use
> > mri_segstats to
> > extract the values
> > doug
> >
> > ps. Please post questions to the
> > FS list
> > instead of us
> > directly so that others can
> > benefit and it
> > gets
> > archived. thanks!
> >
> >
> >
> > On 5/25/13 1:03 PM, Salil Soman wrote:
> >
> > Dear Dr. Greve,
> >
> > Is it possible to register a
> > nonstructural MR
> > sequences (e.g. an ADC map)
> > with the
> > aseg.mgz file
> > (or aparc+aseg.mgz file, etc) and
> > then, using the
> > segmentation from the aseg (or
> > aparc+aseg) file to
> > output a mean ADC value for each
> > anatomic area
> > segmented?
> >
> > Thank you for your time and
> > consideration.
> >
> > Best wishes,
> >
> > Sal
> >
> > Salil Soman, MD, MS
> >
> >
> >
> >
> > The information in this e-mail is
> > intended
> > only for the
> > person to whom it is
> > addressed. If you believe this
> > e-mail was
> > sent to you in
> > error and the e-mail
> > contains patient information, please
> > contact the
> > Partners Compliance HelpLine at
> > http://www.partners.org/complianceline . If the e-mail
> > was sent to you in error
> > but does not contain patient
> > information,
> > please contact
> > the sender and properly
> > dispose of the e-mail.
> >
> >
> >
> >
> >
> >
> > -- Salil Soman, MD, MS
> > Postdoctoral Research Fellow - Stanford
> > Radiological
> > Sciences
> > Laboratory
> > Fellow - Palo Alto War Related Illness and Injury
> > Study Center
> > WOC Neuroradiology Attending - Veterans
> > Affairs Palo
> > Alto Health
> > Care System
> >
> >
> >
> >
> >
> > -- Salil Soman, MD, MS
> > Postdoctoral Research Fellow - Stanford Radiological
> > Sciences
> > Laboratory
> > Fellow - Palo Alto War Related Illness and Injury
> > Study Center
> > WOC Neuroradiology Attending - Veterans Affairs Palo Alto
> > Health Care System
> >
> >
> > -- Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:617-724-2358>
> > <tel:617-724-2358 <tel:617-724-2358>>
> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
> > <tel:617-726-7422>>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> >
> >
> >
> >
> > --
> > Salil Soman, MD, MS
> > Postdoctoral Research Fellow - Stanford Radiological Sciences
> > Laboratory
> > Fellow - Palo Alto War Related Illness and Injury Study Center
> > WOC Neuroradiology Attending - Veterans Affairs Palo Alto
> > Health Care System
> >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> > Phone Number: 617-724-2358 <tel:617-724-2358>
> > Fax: 617-726-7422 <tel:617-726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> >
> >
> >
> >
> > --
> > Salil Soman, MD, MS
> > Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
> > Fellow - Palo Alto War Related Illness and Injury Study Center
> > WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care
> > System
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
> ------------------------------
>
> Message: 15
> Date: Wed, 24 Sep 2014 11:58:51 -0400
> From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Volume to surface coordinates
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <5422EA3B.8000505@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> See if this page gives you the answer you need
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
>
>
> On 09/23/2014 10:39 AM, Michael WOODMAN wrote:
> > Hello freesurfers,
> >
> > I would like to identify, in surface/vertex coordinates, certain points
> > in a volume. Is there a straightforward way to obtain relevant transform?
> >
> > Thank you,
> > Marmaduke Woodman
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
> ------------------------------
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> End of Freesurfer Digest, Vol 127, Issue 37
> *******************************************