Hi Doug,

 I am sorry that I am slow to understand. This is all new to me!

To clarify:

1) I will run my SPM mask (with significant clusters) through the recon-all pipeline. Are there any specific flags that I need to include?  

2) How do I map the anatomical clusters to the surface?

 Thanks again for your help!

Ola

On Jun 6, 2013, at 12:39 PM, Douglas N Greve 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


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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
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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
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addressed. If you believe this e-mail was sent to you in error and the
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HelpLine at
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--
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

?

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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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------------------------------

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End of Freesurfer Digest, Vol 112, Issue 17
*******************************************



_______________________________________________
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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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