Many groups simply just project to the fsaverage surface for visualization. Are you suggesting that this practice be stopped in favor of the recon-all and then mri_surf2surf process?

Are there plans to include fsFSLMNI surface and fsSPMMNI surface to aid in this shift? 

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=====================
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
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On Thu, Jun 6, 2013 at 4:39 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

The relationship of the fsaverage surface to the fsaverage volume is
complicated, to say the least. Obviously, the temptation is to think
that a volume analysis in MNI space can be mapped to the fsaverage
surface just like you would do for an individual. People do this, but we
think it is a bad idea and strongly recommend against it. The xyz
coordinates for a vertex in the fsaverage surface are the average of the
MNI coordinates for that vertex across individuals. This averaging
removes all of the small gyri and sulci making the surface have much
less area and making the surface be fairly sparse in the volume. This is
inevitable when combining subjects using a 12 DOF transform. It simply
cannot be done.

The more recent MNI template used by SPM and FSL are created with a
nonlinear transform that at least creates an identifiable cortex, but
this cortex is not matched to that in fsaverage very well. So if you
have something in SPM or FSL MNI space, then you should run the template
through recon-all to create a surface that aligns well, map your
activation to this surface, then use mri_surf2surf or mri_label2label to
map to fsaverage using the surface-based registration between the
SPM/FSL template and fsaverage. This will do a much better job than
going directly from the volume to fsaverage, but it still might not be
perfect.

doug




On 06/06/2013 12:20 PM, McMains, Stephanie wrote:
>
> Here is the original thread (to at least most of it). Maybe I am just
> an idiot, but I cant' figure out how to easily reply from the web to
> an entire thread, and pulling it out of the digests I get is a pain!!
>
> They wanted to take an ROI from SPM and put it into free surfer to
> extract cortical thickness.  I thought going through fsaverage was a
> good way to do this.  But as I said, looking at the surface, I have
> some concerns.  I am more confused by when you tell them to run the
> MNI template through recon-all to get a surface, because I thought
> fsaverage was a kind of MNI space that has already been run through?
>
>
>
>
> Thanks,
> Stephanie
>
> what space is your VBM map in?
> doug
>
> On 06/05/2013 11:06 AM, Ozranov-Palchik, Ola wrote:
> > Hi Doug,
> >
> > Thank you for your response! I am still a bit confused about the vol2surf
> > command. I have a volumetric mask with voxels of interest based on a VBM
> > analysis  in SPM. I would like to extract the cortical thickness measurements
> > based on these voxels.  I am not clear what specifications I need to include
> > when using vol2surf. For example, what do I use as my registration matrix?
> >
> > Thank you for your help!
> > Ola
> >
> > Ola Ozranov-Palchik M.S.
> > Research Coordinator, Gaab Lab
> > Laboratories of Cognitive Neuroscience
> > Children's Hospital Boston
> > 1 Autumn Street, Mailbox # 713
> > Boston, MA 02115
> > olga.ozra...@childrens.harvard.edu  <http://childrens.harvard.edu>
> > phone: (617) 334-5046
> > main lab: (617) 355-0400
> > fax: (617) 730-0518
> >http://www.childrenshospital.org/research/gaablab
> >
> >
> > -----Original Message-----
> > From: freesurfer-boun...@nmr.mgh.harvard.edu  <http://nmr.mgh.harvard.edu>
> > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> > Sent: Tuesday, June 04, 2013 1:48 PM
> > To:freesurfer@nmr.mgh.harvard.edu  <mailto:freesurfer@nmr.mgh.harvard.edu>
> > Subject: Re: [Freesurfer] SPM ROI to Cortical Thickness
> >
> >
> > Make sure that your SPM volume is registered to the anatomical, then use
> > mri_vol2surf to map the volume to the surface, then mri_segstats to extract
> > the mean of the thickness
> >
> > doug
> >
> >
> >
> >
> > On 06/04/2013 01:45 PM, Ozranov-Palchik, Ola wrote:
> >> main lab: (617) 355-0400
> > Dear FreeSurfer Experts,
> >
> > I was wondering if anyone can advise on the best way to use an ROI mask
> > created in SPM (XjView) to extract cortical thickness values in freesurfer.
> >
> > Thank you in advance for your help!
> >
> > Ola
> >
> > Ola Ozranov-Palchik M.S.
> > Research Coordinator, Gaab Lab
> > Laboratories of Cognitive Neuroscience
> >
> > Children's Hospital Boston
> > 1 Autumn Street, Mailbox # 713
> > Boston, MA 02115
> > olga.ozra...@childrens.harvard.edu  <http://childrens.harvard.edu>
> > <mailto:olga.ozra...@childrens.harvard.edu>
> > phone: (617) 334-5046
> > main lab: (617) 355-0400
> > fax: (617) 730-0518
> >http://www.childrenshospital.org/research/gaablab
> >
>
>
>
>
> Then it goes on:
>
> Hi Ola, this probably will not work. The tal coordinate is notoriously
> inaccurate in cortex. You are verylikely to totally miss the area you
> are looking for. A better way is to run the MNI template through
> recon-all, map your VBM result to the surface of that, then use
> mri_surf2surf to map the effect to each individual.
> doug
>
>
> On 06/05/2013 02:58 PM, Ozranov-Palchik, Ola wrote:
> > Hi Doug,
> >
> > Thank you, again! I decided to try to use the Talairach coordinates from my
> > analysis for ROI extraction. I created an average  subject and preprocessed
> > the data (mris_preproc). I obtained the vertex index based on the coordinates
> > from the average subject.  Any ideas on how I can now find the corresponding
> > vertices in all my subjects?
> >
> > Thanks very much!
> > Ola
> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu  <http://nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
>>
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 6 Jun 2013 08:03:25 -0700
>> From: David Dalton <dcd4@rice.edu <mailto:dcd4@rice.edu>>
>> Subject: [Freesurfer] (no subject)
>> To: freesurfer@nmr.mgh.harvard.edu
>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>> Message-ID:
>>        <CAKg8KF6EWUxVB-ubo-5hpArsEeXnNAXQUp20j8k3VFCdQkbBjA@mail.gmail.com
>> <mailto:CAKg8KF6EWUxVB-ubo-5hpArsEeXnNAXQUp20j8k3VFCdQkbBjA@mail.gmail.com>>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hello,
>>
>> I am currently attempting to download the freesurfer software onto my mac
>> device from the website, but I am having trouble.  None of the links will
>> open, and when I tried typing the wget (curl-O for me) command into my
>> command line, nothing happened.  Any suggestions?
>>
>> Thanks,
>> David
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
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>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130606/1b440137/attachment-0001.html
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Thu, 06 Jun 2013 11:04:30 -0400
>> From: Douglas N Greve <greve@nmr.mgh.harvard.edu
>> <mailto:greve@nmr.mgh.harvard.edu>>
>> Subject: Re: [Freesurfer] SPM ROI to Cortical Thickness
>> To: freesurfer@nmr.mgh.harvard.edu
>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <51B0A4FE.6020909@nmr.mgh.harvard.edu
>> <http://nmr.mgh.harvard.edu>>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Hi Stephanie, I don't know which recommendation you are referring to. We
>> get a lot of emails, and I can't remember each one. Can you repost with
>> the full thread?
>> doug
>>
>>
>> On 06/06/2013 10:40 AM, McMains, Stephanie wrote:
>>> I am wondering why you didn't tell them to go through fsvarege space?
>>> I thought that was an easy way to go from SPM MNI to freesurfer land.
>>>
>>>> /tksurfer fsaverage lh inflated -aparc -mni152reg -overlay
>>>> /pathname/to/spm/roi/yourfile.img/
>>>
>>>
>>> I am wondering because when I look at the segmentation for fsaverage,
>>> it seems like it is missing a lot of the gray matter, particularly in
>>> the big sulci, most likely from the 'smoothing' that comes with
>>> averaging subjects together.  And therefore I wonder if this is the
>>> best thing to use as an intermediate step.  Are you instead suggesting
>>> (as it seemed like in this thread), to put the SPM roi into individual
>>> subject space and then somehow project it to the surface in free surfer?
>>>
>>> Thanks,
>>> Stephanie
>>>
>>>
>>> +++++++++++++++++++++++++
>>>
>>> Stephanie McMains
>>> Neuroimaging Staff Scientist
>>> Center for Brain Science
>>> Harvard University
>>> 52 Oxford Street
>>> Cambridge, MA 02138
>>>
>>> +++++++++++++++++++++++++
>>> For answers to frequently asked questions:
>>> http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/information-investigators/faq
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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 <mailto: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: 4
>> Date: Thu, 06 Jun 2013 11:06:38 -0400
>> From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] problem about file format
>> To: freesurfer@nmr.mgh.harvard.edu
>> Message-ID: <51B0A57E.8000605@nmr.mgh.harvard.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>
>> There is still something wrong with these files. Probably a problem with
>> copying it back and forth.
>> doug
>>
>> On 06/05/2013 08:19 PM, huang bs wrote:
>>> Let me send you again the files because in the previous reply the
>>> attachments were more than 500k.
>>>
>>>
>>> On 05/06/2013, huang bs <huangbs@gmail.com> wrote:
>>>> Dear Bruce,
>>>>
>>>> Yes, sure. I printed the screens and showed you two cases. One can be
>>>> recognized, the other one can not. Please find attached for the six
>>>> figures. I also attached the files talairach.xfm and
>>>> talairach.auto.xfm for the subject linziyi.
>>>>
>>>> One more question: how to extend the hard disk space in Xubuntu,
>>>> especially in the folder /home/virtualuser/freesurfer/subjects ? If
>>>> possible, I don't want to move the data to the shared folder and then
>>>> face such problem.
>>>>
>>>> Sorry I am quite new to Linux so some questions may be quite stupid.
>>>>
>>>> Thank you very much!
>>>>
>>>> On 05/06/2013, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
>>>>> no, I haven't seen that before. Can you cat
>>>>> /home/virtualuser/freesurfer/subjects/linziyi/mri/transforms/talairach.xfm
>>>>>
>>>>> and send us the contents?
>>>>>
>>>>> Bruce
>>>>> On
>>>>> Wed, 5 Jun 2013, huang bs wrote:
>>>>>
>>>>>> Hi All,
>>>>>>
>>>>>> Sorry to take up your time.
>>>>>>
>>>>>> My freesurfer now can not recognize the re-con files (such as the
>>>>>> .mgz
>>>>>> files, or .xfm files, etc).
>>>>>> For example, I run this command to check the talairach transform:
>>>>>> tkregister2 --mgz --s linziyi --fstal --surf orig
>>>>>> The terminal then reports:
>>>>>> ERROR:
>>>>>> /home/virtualuser/freesurfer/subjects/linziyi/mri/transforms/talairach.xfm
>>>>>> does not start as 'MNI Transform File
>>>>>> This file talairach.xfm does exist. But under Xubuntu, this
>>>>>> talairach.auto.xfm file has a different icon and appears as
>>>>>> "executable
>>>>>> file". That's quite strange because I did not make such change to it.
>>>>>>
>>>>>> These files did work when I just finished the re-con. But afer the
>>>>>> re-con,
>>>>>> I
>>>>>> moved them from the freesurfer subjects folder to the shared folder
>>>>>> (shard
>>>>>> with XP), because the freesurfer subjects folder has a limited space.
>>>>>> After
>>>>>> a few days, I moved them back to the subjects folder for doing the
>>>>>> statistical analysis, and then I have such problem. Even under the
>>>>>> shared
>>>>>> folder, the files can not be read either.
>>>>>>
>>>>>> For the cases I just re-con, since they are not moved to elsewhere,
>>>>>> everything seems OK.
>>>>>>
>>>>>> Have you guys had such problem before and how to fix it? Thanks!
>>>>>>
>>>>>> --
>>>>>> Best Regards,
>>>>>>
>>>>>> B Huang
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> 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.
>>>>>
>>>>
>>>> --
>>>> Best Regards,
>>>>
>>>> Bingsheng Huang
>>>> Postdoctoral Research Fellow
>>>> Diagnostic Radiology, The University of Hong Kong
>>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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: 5
>> Date: Thu, 06 Jun 2013 11:27:31 -0400
>> From: Z K <zkaufman@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] (no subject)
>> To: David Dalton <dcd4@rice.edu>
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Message-ID: <51B0AA63.6070603@nmr.mgh.harvard.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> David,
>>
>> Are you using the links from this page?
>>
>> http://surfer.nmr.mgh.harvard.edu/fswiki/Download
>>
>> I just tested the download from two different computers on two different
>> networks and both were successful. There was another post to the
>> freesurfer list a couple weeks ago claiming to have the same problem so
>> Im open to attempting to diagnose the issue, but all tests on my end
>> fail to replicate it. I have a couple questions:
>>
>> 1) Is it only the Mac downloads that dont work? What happens when you
>> click the linux distibutions?
>>
>> 2) Can you provide a snapshot of the terminal after you type the "curl"
>> command?
>>
>> -Zeke
>>
>>
>> On 06/06/2013 11:03 AM, David Dalton wrote:
>>> Hello,
>>>
>>> I am currently attempting to download the freesurfer software onto my
>>> mac device from the website, but I am having trouble.  None of the links
>>> will open, and when I tried typing the wget (curl-O for me) command into
>>> my command line, nothing happened.  Any suggestions?
>>>
>>> Thanks,
>>> David
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Thu, 6 Jun 2013 11:48:10 -0400 (EDT)
>> From: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] averaging tracts?
>> To: "Hoptman, Matthew" <Hoptman@nki.rfmh.org>
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Message-ID: <alpine.LRH.2.03.1306061140300.18006@nmr.mgh.harvard.edu>
>> Content-Type: text/plain; charset="iso-8859-15"
>>
>>
>> Hi Matt - Thanks for your kind words!
>>
>> The merged_*.mgz file is just a 4D mgz file where each frame corresponds
>> to one of the 18 tracts. The only special thing about this mgz file is
>> that it has some special fields in its header that tell freeview how to
>> display each tract (color, name, and threshold). I haven't tried
>> this, but
>> I would guess that if you performed any operation on that mgz file, those
>> header fields would be preserved. And if they're not they should be,
>> so we
>> should know about it.
>>
>> You can try to map each mgz file from individual DWI space to a common
>> space with mri_vol2vol and then average them with mri_concat. Let us know
>> if this ends up working or if you have any questions about these steps.
>>
>> Thanks!
>> a.y
>>
>> On Thu, 6 Jun 2013, Hoptman, Matthew wrote:
>>
>>>
>>> Hi all,
>>>
>>> Thanks for tracula , which I think is a terrific tool.? Is there any
>>> way to
>>> average tracts across subjects for viewing purposes?? I have in mind
>>> somehting along the line of a group average merged_avg33_mni_bbi.mgz.
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>> ?
>>>
>>> Matthew J. Hoptman, PhD
>>> Research Scientist V
>>> Nathan S. Kline Institute for Psychiatric Research
>>>
>>> Research Associate Professor in Psychiatry
>>> NYU School of Medicine
>>>
>>> ?
>>>
>>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
>>> recipient. It may contain confidential information which is legally
>>> privileged or otherwise protected by law. If you received this
>>> e-mail in error or from someone who was not authorized to send it to
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>>> you are strictly prohibited from reviewing, using, disseminating,
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>>> PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND
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>>> MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
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>>>
>>> ____________________________________________________________________________
>>> Conserve Resources. Print only when necessary.
>>>
>>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
>>> recipient. It may contain confidential information which is legally
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>>> E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your
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>>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
>>> recipient. It may contain confidential information which is legally
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>>
>> ------------------------------
>>
>> Message: 7
>> Date: Thu, 6 Jun 2013 15:58:07 +0000
>> From: pablo najt <pablonajt@hotmail.com>
>> Subject: [Freesurfer] Enquire about running FreeSurfer {Disarmed}
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <BLU176-W40FB3B3E607B0A8BAA0697AE980@phx.gbl>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hello I have a question regarding the installation/running
>> FreeSurfer.I have just completed the installation and got the
>> confirmation that Free surfer was installed. Please see
>> snapshot.However when I follow the steps for testing
>> (https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer), I
>> always get "command not found". I was wondering if you would be able
>> to help me.Thanks,Pablo
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>> ------------------------------
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> End of Freesurfer Digest, Vol 112, Issue 17
>> *******************************************
>
>
>
> _______________________________________________
> 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/

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