Re: [Freesurfer] -hippo-subfields

[Eugenio Iglesias]

Hi Greg,
I would suggest that you only do it with either autorecon2 or  autorecon3. With 
autorecon1, it will fail because it won't find aseg.mgz. You should still be 
able to run autorecon2 after this mistake, but I wouldn't do it (why let the 
software exit with an error without need?). If you do it both with both 
autorecon2 and autorecon3, I believe that the code will be run twice.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: "Gregory Kirk" 
To: "free" 
Sent: Thursday, August 7, 2014 5:05:27 PM
Subject: [Freesurfer] -hippo-subfields



we have freesurfer set up on our big condor cluster, i asked that the

-hippo-subfields be added. they have it set up to run in 3 stages
autorecon1 autorecon2 autorecon3 
they added the flag to all 3, i think it would only be needed on autorecon3, 
but don't think it would
cause harm, just be ignored in the first 2 ?

thanks

greg
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Re: [Freesurfer] Interpreting clusters 'holistically' vs in terms of max coordinates

[Francesco Puccettone]

Hello Doug,
thank you very much for your answer. But how I can find which other areas
the cluster  overlaps, since QDEC only gives the name of the parcel that
contains the max point?
Is there any other (semi)automated way of obtaining the names of the other
structures that the cluster contains (either in whole or parts of)?
Or is it just down to one's own knowledge of brain anatomy?
--Francesco


On 6 August 2014 23:12, Douglas N Greve  wrote:

>
> I would definitely show a picture of it, say which areas it overlaps,
> and spec the coordinates for the max (which is what QDEC reports).
> doug
>
> On 08/05/2014 06:39 PM, Francesco Puccettone wrote:
> > Hello,
> >
> > If a QDEC analysis returns a certain cluster as being significantly
> > different between the groups (after MC correction) in terms of some
> > measure, which part of this cluster's description should my
> > interpretation of this result be based on: its spatial extent (how it
> > looks when projected onto the template brain, and what your knowledge
> > of brain anatomy makes of that) or the coordinates of its maxima (as
> > reported in the terminal window)?
> >
> > For instance, my result cluster is labeled as the postcentral gyrus, I
> > guess because that is the parcel that overlaps most with the cluster
> > (or perhaps because that is where the maximum point of the cluster
> > falls?!), but looking at the cluster, it clearly extends into the
> > parietal lobe:
> >
> >
> > So how does one go about describing this cluster and interpreting the
> > meaning of the effect in a Discussion section? Should I focus on the
> > postcentral gyrus label and link it to other PCG effects in the
> > literature? Or should I instead try to find in the literature maxima
> > coordinates that are similar to what I get here?
> >
> > Any help much appreciated!
> > --Francesco
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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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[Freesurfer] New longitudinal Tracula version?

[Chung, Yoonho]

Dear Freesurfer Experts
We decided to reprocess our T1 and DTI data with the latest stream v.5.3 – we 
would like to give TRACULA longitudinal stream a try. Before we go ahead and 
reprocess our recons and DTI data with FS v 5.3 we were wondering if you plan 
to release a new version of the TRACULA DTI longitudinal stream anytime soon.
I think I saw somewhere in the email chain that this is likely to happen soon 
with additional features and bug fixes. If so, I think it would be worth a wait.

Thank you!

Yoon


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Re: [Freesurfer] proportion of surface area of significant region

[Lars M. Rimol]

Thanks, Doug!

So I tried this method using fsaverage/surf/lh.white.avg.area.mgh. The
results seem to be reasonably consistent with the ones I get when
eyeballing the p-maps overlayed on fsaverage in tksurfer. Would you agree
that's a reasonable "sanity check"?

When I compare the results to just counting vertices, there doesn't seem to
be a huge difference between proportion of #vertices and proportion of
surface area. So either there isn't a lot of variance in the sizes of the
faces, or the variance is evenly distributed.

Finally, if I want to convert from an individual map or the cohort mean map
to mm² units, can I do it by scaling the ico area vertex values by the
ratio between native and ico total area?  So:  (vertex value from mean
cohort map * total area for cohort mean map) / total area for
fsaverage/surf/lh.white.avg.area.mgh, where total area would be the sum of
all vertex values?



Thank you!

LMR


---

You don't want to get the surface area from the faces of fsaverage.
Instead use the values in fsaverage/surf/lh.white.avg.area.mgh (this is
the average of the group used to create fsaverage), or, probably better,
get an average area map for your cohort
doug

On 07/30/2014 08:38 AM, Lars M. Rimol wrote:
> Hi Bruce,
>
> I would like to be able to tell what proportion of a region of
> interest (ROI), as defined in atlas space by e.g. Desikan-Killiany,
> that shows a significant effect (based on a p-map). For now I overlay
> the p-map on the inflated surface of fsaverage in tksurfer and eyeball
> the proportion.
>
> Given a p-map, if I find the FDR threshold and identify the vertices
> within a given ROI that have a p-value greater than the threshold,
> then I can find the proportion of the ROI that is suprathreshold.
> E.g., I find 1986 suprathreshold vertices in "bankssts" out of 2137,
> so 93% of vertices in bankssts show a significant effect.
>
> My question is: Does that tell me anything about what proportion of
> the ROI's surface area is affected in atlas space? Obviously, if the
> faces were uniform, there would be a 1 to 1 relationship between
> #vertices and area. In the original tesselation of any dataset the
> size of the faces is uniform, but that changes with topology fix and
> deformation. I assume that is true also for fsaverage? (so I can't
> assume [#sig vertices] / [# tot vertices] == the proportion of the
> ROI's area that is significant in atlas space)
>
> I can find the surface area of the suprathreshold region for my sample
> (or any subset thereof) by looking at a mean area map. But I'm unsure
> how to do that for fsaverage itself? Is there information on regional
> surface area directly available? Or would using  getFaceArea.m or
> getFacesArea.m or similar functions be a solution?
>
>
> Thank you!








-- 
yours,

Lars M. Rimol, PhD
St. Olavs Hospital
Trondheim,
Norway
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[Freesurfer] Tool which will return the labels associated with a RAS vector ?

[Krieger, Donald N.]

Hi,

I am almost there and now need to produce what you might call an atlas for an 
individual.
I have a large set of current source locations extracted from MEG recordings 
for each volunteer.
They are in the individual's RAS MRI coordinates so I can easily convert them 
to tkr or another of the coordinate systems used by freesurfer.
I then need to find or create a tool to which I can hand that vector and get 
back the labels which have been assigned to it.
Can you see a way to do it  with existing freesurfer tools, even if it's 
awkward?

Thanks,
 
Don


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Re: [Freesurfer] Tool which will return the labels associated with a RAS vector ?

[Bruce Fischl]

Hi Don

what kind of label do you mean? Volume (aseg) or surface (annot). I guess 
you could just pick out the aparc+aseg.mgz label and get both.

cheers
Bruce

On Fri, 8 Aug 2014, Krieger, 
Donald N. wrote:

> Hi,
>
> I am almost there and now need to produce what you might call an atlas for an 
> individual.
> I have a large set of current source locations extracted from MEG recordings 
> for each volunteer.
> They are in the individual's RAS MRI coordinates so I can easily convert them 
> to tkr or another of the coordinate systems used by freesurfer.
> I then need to find or create a tool to which I can hand that vector and get 
> back the labels which have been assigned to it.
> Can you see a way to do it  with existing freesurfer tools, even if it's 
> awkward?
>
> Thanks,
>
> Don
>
>
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Re: [Freesurfer] Tool which will return the labels associated with a RAS vector ?

[Krieger, Donald N.]

Hi Bruce,

Thanks for responding so quickly.  I think it's the volume label I want 
although honestly, I'm still not confident that I understand the language.
The vectors for which I need the associated label(s) can be almost anywhere in 
the volume of the head.
And for each one, I need to get the label(s) for the nearest vector that 
freesurfer has identified.
It would work for my purpose if that label was for the nearest vector on a 
surface, particularly orig, white, or pial.

Don

Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, August 08, 2014 11:15 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tool which will return the labels associated with a   
RAS vector ?

Hi Don

what kind of label do you mean? Volume (aseg) or surface (annot). I guess
you could just pick out the aparc+aseg.mgz label and get both.

cheers
Bruce

On Fri, 8 Aug 2014, Krieger,
Donald N. wrote:

> Hi,
>
> I am almost there and now need to produce what you might call an atlas for an 
> individual.
> I have a large set of current source locations extracted from MEG recordings 
> for each volunteer.
> They are in the individual's RAS MRI coordinates so I can easily convert them 
> to tkr or another of the coordinate systems used by freesurfer.
> I then need to find or create a tool to which I can hand that vector and get 
> back the labels which have been assigned to it.
> Can you see a way to do it  with existing freesurfer tools, even if it's 
> awkward?
>
> Thanks,
>
> Don
>
>
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Re: [Freesurfer] insula on medial surface

[Harms, Michael]

Hi Christophe,
I uploaded both subjects that I showed the snapshots for yesterday into
the FS FTP drop site.  (Do you have access to that?)

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 8/7/14 4:03 PM, "Christophe Destrieux"
 wrote:

>Hi Michael
>the limen insula explanation sounds ok, even if it's extension on the
>medial surface seem really large. would you have a snapshot to look on
>the volume to which structure this label anatomically corresponds to ?
>Also did you had a look to the results of the insula aparc with the 2009a
>atlas?
>cd
>
>--
>Christophe Destrieux,
>
>Directeur du Département Communication et Multimédia
>http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=12006511
>59612
>
>Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François
>Rabelais de Tours
>http://www.u930.tours.inserm.fr/
>
>Service de Neurochirurgie
>et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé
>37032 Tours - France
>tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07
>
>
>- Mail original -
>De: "Michael Harms" 
>À: "Freesurfer support list" 
>Cc: "Ron KILLIANY" 
>Envoyé: Jeudi 7 Août 2014 22:18:49
>Objet: Re: [Freesurfer] insula on medial surface
>
>
>I'm not itching to re-process this data so I like that explanation as
>well.  I think my main concern is that that bit of insula label seems
>somewhat arbitrary and inconsistent, in that some subjects have this bit
>of medial tissue labelled as insula, whereas others don't.  (Even within
>the same subject, it isn't consistent between the two hemispheres).
>
>I guess it is just a matter of the sulcal variability and atlas labeling
>resulting in variability in that particular region.  Presumably, Ron must
>have labelled that bit of tissue as "insula" in some subjects, but not
>others??
>
>Ron: It would be great to hear what kind of "rule" you applied when
>labeling the individual subjects in the atlas in that particular region
>when deciding whether it should be considered insula or medial/lateral
>orbitofrontal.
>
>thanks,
>-MH
>
>--
>Michael Harms, Ph.D.
>
>---
>Conte Center for the Neuroscience of Mental Disorders
>Washington University School of Medicine
>Department of Psychiatry, Box 8134
>660 South Euclid Ave.   Tel: 314-747-6173
>St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
>On 8/7/14 2:52 PM, "Bruce Fischl"  wrote:
>
>>wow, I like that answer much more than "it's a bug"! Can we go with
>>Paul's explanation?
>>
>>
>>Bruce
>>
>>On Thu, 7 Aug 2014, Paul Beach wrote:
>>
>>> I asked a neuroanatomist and insula expert on my campus about this a
>>>while
>>> back and this was his response:
>>> "This is the region of the "limen insulae" that you will remember Dr.
>>>Heimer
>>> referring to often in the brain dissection course. The insula is
>>>defined as
>>> cortex which is covered by a lid of other cortical lobes, frontal,
>>>parietal
>>> and temporal. They all fold over except at the inferior frontal end
>>>where a
>>> little bit of the surface of otherwise insular cortex is not covered,
>>>and
>>> this little corner peeks out. This is the limeninsula which neighbors
>>>the
>>> olfactory cortex on the inferior surface of the frontal lobe and the
>>>medial
>>> surface of the temporal lobe, and is olfactory cortex itself. Since it
>>>is
>>> not covered over, it technically might not be considered really
>>>"insular"
>>> but it is obviously in continuity with, and not separated by any kind
>>>of
>>> sulcus or other landmark, from the rest of the insular covered cortex.
>>>So we
>>> are left with no secure boundary line between insular cortex and
>>>inferior
>>> frontal and medial temporal cortex in this corner. It looks like
>>>Freesurfer
>>> has decided to call it all insular, and with good functional reasons."
>>>
>>>
>>> Cheers,
>>>
>>>
>>>
>>> On Thu, Aug 7, 2014 at 3:32 PM, Bruce Fischl
>>>
>>> wrote:
>>>   Hi Mike
>>>
>>>   I'm not sure - I think the insula was an additional label that
>>>   Ron Killiany added. I'll cc Ron to see if he has any insight. It
>>>   certainly looks too medial to me.
>>>
>>>   I would also check on the white surface just to make sure that
>>>   it's not a quirk of the inflation. If the aseg looks right we
>>>   could certainly put together some simple auto-editing to correct
>>>   this kind of thing
>>>
>>>   cheers
>>>   Bruce
>>>
>>>
>>>   On Thu, 7 Aug 2014, Harms, Michael wrote:
>>>
>>>
>>>   Hi,
>>>   An astute RA, while reviewing the aparc+aseg.mgz of brains
>>>   processed with FS
>>>   5.3, noticed a fair number of instances, where the insula

Re: [Freesurfer] Tool which will return the labels associated with a RAS vector ?

[Bruce Fischl]

Hi Don

you have to decide what you want! What does the "nearest surface label" 
mean? If you are outside of brain do you want to project onto the cortex 
and find that label? What if you are in the middle of caudate for example?

cheers
Bruce

On 
Fri, 8 Aug 2014, Krieger, Donald N. wrote:

> Hi Bruce,
>
> Thanks for responding so quickly.  I think it's the volume label I want 
> although honestly, I'm still not confident that I understand the language.
> The vectors for which I need the associated label(s) can be almost anywhere 
> in the volume of the head.
> And for each one, I need to get the label(s) for the nearest vector that 
> freesurfer has identified.
> It would work for my purpose if that label was for the nearest vector on a 
> surface, particularly orig, white, or pial.
>
> Don
>
> Don Krieger, Ph.D.
> Department of Neurological Surgery
> University of Pittsburgh
> (412)648-9654 Office
> (412)521-4431 Cell/Text
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Friday, August 08, 2014 11:15 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Tool which will return the labels associated with a 
>   RAS vector ?
>
> Hi Don
>
> what kind of label do you mean? Volume (aseg) or surface (annot). I guess
> you could just pick out the aparc+aseg.mgz label and get both.
>
> cheers
> Bruce
>
> On Fri, 8 Aug 2014, Krieger,
> Donald N. wrote:
>
>> Hi,
>>
>> I am almost there and now need to produce what you might call an atlas for 
>> an individual.
>> I have a large set of current source locations extracted from MEG recordings 
>> for each volunteer.
>> They are in the individual's RAS MRI coordinates so I can easily convert 
>> them to tkr or another of the coordinate systems used by freesurfer.
>> I then need to find or create a tool to which I can hand that vector and get 
>> back the labels which have been assigned to it.
>> Can you see a way to do it  with existing freesurfer tools, even if it's 
>> awkward?
>>
>> Thanks,
>>
>> Don
>>
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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>
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> at
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Re: [Freesurfer] mpr2mni305 failed error

[Francesco Deleo]

Thank you all for attention and help!
Maybe we're finding the problem: in cases I received the mpr2mni305 error
the orig.mgz is unintelligible (it is white with some black point). But my
dicoms are ok (I've checked!). I've already tried converting dicom to tiff
but I got the same error message and the same unintelligible orig.mgz (and
the tiff are ok too!).
So I think the likely problem is in the recon-all -i command!
Any idea?

It remains a mistery for me why I have this problem only in some (and not
in every one) MRI scans even if all the parameters are the same.

thanks again

Francesco


2014-08-07 17:16 GMT+02:00 Douglas N Greve :

> Have you looked in transforms/talairach_avi.log?
>
> On 08/07/2014 07:57 AM, Francesco Deleo wrote:
> > Thank you Doug!
> > but i tried it in many cases but I've always received the same error
> > message...
> > Is there something else I can try?
> >
> > Francesco
> >
> >
> > 2014-08-07 0:46 GMT+02:00 Douglas N Greve  > >:
> >
> > Try it with -notal-check
> > doug
> >
> > On 08/06/2014 04:39 PM, Francesco Deleo wrote:
> > > I all!
> > >
> > > I am a new freesurfer user.
> > > I have a problem when I perform the recon-all -all, in about 15% of
> > > MRI scans, all made with the same scanning protocol (T1 MPRAGE in a
> > > SIEMENS Avanto 1,5 T).
> > >
> > > I can't recognize any difference between those scans which work
> > > correctly and those not.
> > > I have never found the same error on 3T MRI scans.
> > >
> > > I've already tried to add these flags to the recon-all -all
> command:
> > > -use-mritotal
> > > -talairach -use-mritotal
> > > -notalairach
> > > but I've always received an error message
> > >
> > > Thank you very much
> > >
> > > ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
> > > Darwin pro-di-villani.besta.local 13.3.0 Darwin Kernel Version
> > 13.3.0:
> > > Tue Jun  3 21:27:35 PDT 2014;
> > root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64
> > >
> > > Thanks very much for your attention
> > >
> > > Francesco
> > > Milan, Italy
> > >
> > >
> > -
> > >
> > > FREESURFER_HOME: /Applications/freesurfer
> > >
> > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> > >
> > > Kernel info: Darwin 13.3.0 x86_64
> > >
> > >
> > -
> > >
> > >
> > > LAST LINES IN TALAIRACH_AVI.LOG
> > >
> > > parameters
> > > 9.0270  134.9373  110.8627  -84.3566   -7.5458  -11.3475
> > > eta,q 0.95791  3.72402
> > >   0.0485  0.0470  0.0477  0.0513  0.0470  0.0452
> > >   0.0475  0.0471  0.0478  0.0513  0.0457  0.0435
> > >   0.0472  0.0472  0.0476  0.0428  0.0434  0.0415
> > >   0.0471  0.0471  0.0476  0.0435  0.0430  0.0415
> > >   0.0470  0.0478  0.0457  0.0525  0.0415  0.0430
> > >   0.0473  0.0511  0.0430  0.0548  0.0442  0.0453
> > >   0.0486  0.0426  0.0406  0.0672  0.0431  0.0503
> > > niter,ni,del,rscale 73   12.1.2000
> > > imgrege: no voxels in register
> > > ERROR: 'imgreg_4dfp
> > > /Applications/freesurfer/average/711-2C_as_mni_average_305
> > > /Applications/freesurfer/average/711-2B_as_mni_average_305_mask
> > > talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283'
> > > failed! status=254
> > > ERROR: mpr2mni305 execution aborted
> > >
> > >
> > > ___
> > > 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
> > gr...@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  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
> > Compli

Re: [Freesurfer] mpr2mni305 failed error

[Bruce Fischl]

what does the rawavg.mgz look like? If it is ok, can you email it to us?
On 
Fri, 8 Aug 2014, Francesco Deleo wrote:



Thank you all for attention and help!
Maybe we're finding the problem: in cases I received the mpr2mni305 error
the orig.mgz is unintelligible (it is white with some black point). But my
dicoms are ok (I've checked!). I've already tried converting dicom to tiff
but I got the same error message and the same unintelligible orig.mgz (and
the tiff are ok too!).
So I think the likely problem is in the recon-all -i command!
Any idea?

It remains a mistery for me why I have this problem only in some (and not in
every one) MRI scans even if all the parameters are the same.

thanks again

Francesco


2014-08-07 17:16 GMT+02:00 Douglas N Greve :
  Have you looked in transforms/talairach_avi.log?

  On 08/07/2014 07:57 AM, Francesco Deleo wrote:
  > Thank you Doug!
  > but i tried it in many cases but I've always received the same
  error
  > message...
  > Is there something else I can try?
  >
  > Francesco
  >
  >
  > 2014-08-07 0:46 GMT+02:00 Douglas N Greve
   >:
>
>     Try it with -notal-check
>     doug
>
>     On 08/06/2014 04:39 PM, Francesco Deleo wrote:
>     > I all!
>     >
>     > I am a new freesurfer user.
>     > I have a problem when I perform the recon-all -all, in about
15% of
>     > MRI scans, all made with the same scanning protocol (T1 MPRAGE
in a
>     > SIEMENS Avanto 1,5 T).
>     >
>     > I can't recognize any difference between those scans which
work
>     > correctly and those not.
>     > I have never found the same error on 3T MRI scans.
>     >
>     > I've already tried to add these flags to the recon-all -all
command:
>     > -use-mritotal
>     > -talairach -use-mritotal
>     > -notalairach
>     > but I've always received an error message
>     >
>     > Thank you very much
>     >
>     > ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
>     > Darwin pro-di-villani.besta.local 13.3.0 Darwin Kernel Version
>     13.3.0:
>     > Tue Jun  3 21:27:35 PDT 2014;
>     root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64
>     >
>     > Thanks very much for your attention
>     >
>     > Francesco
>     > Milan, Italy
>     >
>     >
>    
-
>     >
>     > FREESURFER_HOME: /Applications/freesurfer
>     >
>     > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>     >
>     > Kernel info: Darwin 13.3.0 x86_64
>     >
>     >
>    
-
>     >
>     >
>     > LAST LINES IN TALAIRACH_AVI.LOG
>     >
>     > parameters
>     >     9.0270  134.9373  110.8627  -84.3566   -7.5458  -11.3475
>     > eta,q 0.95791  3.72402
>     >   0.0485  0.0470  0.0477  0.0513  0.0470  0.0452
>     >   0.0475  0.0471  0.0478  0.0513  0.0457  0.0435
>     >   0.0472  0.0472  0.0476  0.0428  0.0434  0.0415
>     >   0.0471  0.0471  0.0476  0.0435  0.0430  0.0415
>     >   0.0470  0.0478  0.0457  0.0525  0.0415  0.0430
>     >   0.0473  0.0511  0.0430  0.0548  0.0442  0.0453
>     >   0.0486  0.0426  0.0406  0.0672  0.0431  0.0503
>     > niter,ni,del,rscale     7    3   12.    1.2000
>     > imgrege: no voxels in register
>     > ERROR: 'imgreg_4dfp
>     > /Applications/freesurfer/average/711-2C_as_mni_average_305
>     >
/Applications/freesurfer/average/711-2B_as_mni_average_305_mask
>     > talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4
1283'
>     > failed! status=254
>     > ERROR: mpr2mni305 execution aborted
>     >
>     >
>     > ___
>     > 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
>     gr...@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:

Re: [Freesurfer] Tool which will return the labels associated with a RAS vector ?

[Krieger, Donald N.]

I think I'm up against my ignorance here.
But it seems fairly clear that what I need is to pass the vector to the tool in 
a form where the tool will come back with label(s) for that precise location or 
return something like "unknown."
So if it's outside the head ... "unknown"
If it's in the caudate ... "caudate"
If it's in Right V1 gray ... rh.V1.orig.
If it's in Right V1 white ... rh.V1.white.

Does that make sense?  Honestly I'm not quite sure because I haven't fooled 
around with the different labelled vectors enough to figure out when to expect 
something on a surface vs something in the volume.  I'm happy to try for both 
if that's needed depending on the region since there do not appear to be volume 
labels for many regions in aseg.mgz .
I apologize for being slow on the  uptake here but there are several things 
about freesurfer that I still don't get.

Don



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, August 08, 2014 11:38 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tool which will return the labels associated with a   
RAS vector ?

Hi Don

you have to decide what you want! What does the "nearest surface label"
mean? If you are outside of brain do you want to project onto the cortex
and find that label? What if you are in the middle of caudate for example?

cheers
Bruce

On
Fri, 8 Aug 2014, Krieger, Donald N. wrote:

> Hi Bruce,
>
> Thanks for responding so quickly.  I think it's the volume label I want 
> although honestly, I'm still not confident that I understand the language.
> The vectors for which I need the associated label(s) can be almost anywhere 
> in the volume of the head.
> And for each one, I need to get the label(s) for the nearest vector that 
> freesurfer has identified.
> It would work for my purpose if that label was for the nearest vector on a 
> surface, particularly orig, white, or pial.
>
> Don
>
> Don Krieger, Ph.D.
> Department of Neurological Surgery
> University of Pittsburgh
> (412)648-9654 Office
> (412)521-4431 Cell/Text
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Friday, August 08, 2014 11:15 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Tool which will return the labels associated with a 
>   RAS vector ?
>
> Hi Don
>
> what kind of label do you mean? Volume (aseg) or surface (annot). I guess
> you could just pick out the aparc+aseg.mgz label and get both.
>
> cheers
> Bruce
>
> On Fri, 8 Aug 2014, Krieger,
> Donald N. wrote:
>
>> Hi,
>>
>> I am almost there and now need to produce what you might call an atlas for 
>> an individual.
>> I have a large set of current source locations extracted from MEG recordings 
>> for each volunteer.
>> They are in the individual's RAS MRI coordinates so I can easily convert 
>> them to tkr or another of the coordinate systems used by freesurfer.
>> I then need to find or create a tool to which I can hand that vector and get 
>> back the labels which have been assigned to it.
>> Can you see a way to do it  with existing freesurfer tools, even if it's 
>> awkward?
>>
>> Thanks,
>>
>> Don
>>
>>
>> ___
>> 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
>
>
> 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.
>
>
> ___
> 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

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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] insula on medial surface

[Harms, Michael]

Hi,
In response to Christophe's question, I looked at the two other whole
brain parcellation schemes -- DKTatlas40 and a2009s.  In those two
subjects at least, that medial region which is labelled "insula" in the
aparc.annot is labelled (mostly) as medial/lateral orbitofrontal (with
some even as rostralanteriorcingulate) in aparc.DKTatlas40.annot, and as
G_subcallosal in aparc.a2009s.annot.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 8/8/14 10:30 AM, "Harms, Michael"  wrote:

>
>Hi Christophe,
>I uploaded both subjects that I showed the snapshots for yesterday into
>the FS FTP drop site.  (Do you have access to that?)
>
>cheers,
>-MH
>
>--
>Michael Harms, Ph.D.
>
>---
>Conte Center for the Neuroscience of Mental Disorders
>Washington University School of Medicine
>Department of Psychiatry, Box 8134
>660 South Euclid Ave.  Tel: 314-747-6173
>St. Louis, MO  63110   Email: mha...@wustl.edu
>
>
>
>
>On 8/7/14 4:03 PM, "Christophe Destrieux"
> wrote:
>
>>Hi Michael
>>the limen insula explanation sounds ok, even if it's extension on the
>>medial surface seem really large. would you have a snapshot to look on
>>the volume to which structure this label anatomically corresponds to ?
>>Also did you had a look to the results of the insula aparc with the 2009a
>>atlas?
>>cd
>>
>>--
>>Christophe Destrieux,
>>
>>Directeur du Département Communication et Multimédia
>>http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651
>>1
>>59612
>>
>>Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François
>>Rabelais de Tours
>>http://www.u930.tours.inserm.fr/
>>
>>Service de Neurochirurgie
>>et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé
>>37032 Tours - France
>>tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07
>>
>>
>>- Mail original -
>>De: "Michael Harms" 
>>À: "Freesurfer support list" 
>>Cc: "Ron KILLIANY" 
>>Envoyé: Jeudi 7 Août 2014 22:18:49
>>Objet: Re: [Freesurfer] insula on medial surface
>>
>>
>>I'm not itching to re-process this data so I like that explanation as
>>well.  I think my main concern is that that bit of insula label seems
>>somewhat arbitrary and inconsistent, in that some subjects have this bit
>>of medial tissue labelled as insula, whereas others don't.  (Even within
>>the same subject, it isn't consistent between the two hemispheres).
>>
>>I guess it is just a matter of the sulcal variability and atlas labeling
>>resulting in variability in that particular region.  Presumably, Ron must
>>have labelled that bit of tissue as "insula" in some subjects, but not
>>others??
>>
>>Ron: It would be great to hear what kind of "rule" you applied when
>>labeling the individual subjects in the atlas in that particular region
>>when deciding whether it should be considered insula or medial/lateral
>>orbitofrontal.
>>
>>thanks,
>>-MH
>>
>>--
>>Michael Harms, Ph.D.
>>
>>---
>>Conte Center for the Neuroscience of Mental Disorders
>>Washington University School of Medicine
>>Department of Psychiatry, Box 8134
>>660 South Euclid Ave.   Tel: 314-747-6173
>>St. Louis, MO  63110Email: mha...@wustl.edu
>>
>>
>>
>>
>>On 8/7/14 2:52 PM, "Bruce Fischl"  wrote:
>>
>>>wow, I like that answer much more than "it's a bug"! Can we go with
>>>Paul's explanation?
>>>
>>>
>>>Bruce
>>>
>>>On Thu, 7 Aug 2014, Paul Beach wrote:
>>>
 I asked a neuroanatomist and insula expert on my campus about this a
while
 back and this was his response:
 "This is the region of the "limen insulae" that you will remember Dr.
Heimer
 referring to often in the brain dissection course. The insula is
defined as
 cortex which is covered by a lid of other cortical lobes, frontal,
parietal
 and temporal. They all fold over except at the inferior frontal end
where a
 little bit of the surface of otherwise insular cortex is not covered,
and
 this little corner peeks out. This is the limeninsula which neighbors
the
 olfactory cortex on the inferior surface of the frontal lobe and the
medial
 surface of the temporal lobe, and is olfactory cortex itself. Since it
is
 not covered over, it technically might not be considered really
"insular"
 but it is obviously in continuity with, and not separated by any kind
of
 sulcus or other landmark, from the rest of the insular covered cortex.
So we
 are left with no secure boundary line between insular cortex and
inferior
 frontal and medial temporal cortex in this corner. It looks like
Freesurfer
 

[Freesurfer] Fwd: mpr2mni305 failed error

[Francesco Deleo]

-- Forwarded message --
From: Francesco Deleo 
Date: 2014-08-08 18:06 GMT+02:00
Subject: Re: [Freesurfer] mpr2mni305 failed error
To: freesurfer 


It is not ok...

It seems to have a contrast problem... I can send a snapshot, or if you
want I can send the rawavg.mgz

Francesco


2014-08-08 17:53 GMT+02:00 Bruce Fischl :

 what does the rawavg.mgz look like? If it is ok, can you email it to us?
>
> On Fri, 8 Aug 2014, Francesco Deleo wrote:
>
>  Thank you all for attention and help!
>> Maybe we're finding the problem: in cases I received the mpr2mni305 error
>> the orig.mgz is unintelligible (it is white with some black point). But my
>> dicoms are ok (I've checked!). I've already tried converting dicom to tiff
>> but I got the same error message and the same unintelligible orig.mgz (and
>> the tiff are ok too!).
>> So I think the likely problem is in the recon-all -i command!
>> Any idea?
>>
>> It remains a mistery for me why I have this problem only in some (and not
>> in
>> every one) MRI scans even if all the parameters are the same.
>>
>> thanks again
>>
>> Francesco
>>
>>
>> 2014-08-07 17:16 GMT+02:00 Douglas N Greve :
>>   Have you looked in transforms/talairach_avi.log?
>>
>>   On 08/07/2014 07:57 AM, Francesco Deleo wrote:
>>   > Thank you Doug!
>>   > but i tried it in many cases but I've always received the same
>>   error
>>   > message...
>>   > Is there something else I can try?
>>   >
>>   > Francesco
>>   >
>>   >
>>   > 2014-08-07 0:46 GMT+02:00 Douglas N Greve
>>   > > >:
>> >
>> > Try it with -notal-check
>> > doug
>> >
>> > On 08/06/2014 04:39 PM, Francesco Deleo wrote:
>> > > I all!
>> > >
>> > > I am a new freesurfer user.
>> > > I have a problem when I perform the recon-all -all, in about
>> 15% of
>> > > MRI scans, all made with the same scanning protocol (T1 MPRAGE
>> in a
>> > > SIEMENS Avanto 1,5 T).
>> > >
>> > > I can't recognize any difference between those scans which
>> work
>> > > correctly and those not.
>> > > I have never found the same error on 3T MRI scans.
>> > >
>> > > I've already tried to add these flags to the recon-all -all
>> command:
>> > > -use-mritotal
>> > > -talairach -use-mritotal
>> > > -notalairach
>> > > but I've always received an error message
>> > >
>> > > Thank you very much
>> > >
>> > > ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
>> > > Darwin pro-di-villani.besta.local 13.3.0 Darwin Kernel Version
>> > 13.3.0:
>> > > Tue Jun  3 21:27:35 PDT 2014;
>> > root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64
>> > >
>> > > Thanks very much for your attention
>> > >
>> > > Francesco
>> > > Milan, Italy
>> > >
>> > >
>> >
>> -
>> > >
>> > > FREESURFER_HOME: /Applications/freesurfer
>> > >
>> > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>> > >
>> > > Kernel info: Darwin 13.3.0 x86_64
>> > >
>> > >
>> >
>> -
>> > >
>> > >
>> > > LAST LINES IN TALAIRACH_AVI.LOG
>> > >
>> > > parameters
>> > > 9.0270  134.9373  110.8627  -84.3566   -7.5458  -11.3475
>> > > eta,q 0.95791  3.72402
>> > >   0.0485  0.0470  0.0477  0.0513  0.0470  0.0452
>> > >   0.0475  0.0471  0.0478  0.0513  0.0457  0.0435
>> > >   0.0472  0.0472  0.0476  0.0428  0.0434  0.0415
>> > >   0.0471  0.0471  0.0476  0.0435  0.0430  0.0415
>> > >   0.0470  0.0478  0.0457  0.0525  0.0415  0.0430
>> > >   0.0473  0.0511  0.0430  0.0548  0.0442  0.0453
>> > >   0.0486  0.0426  0.0406  0.0672  0.0431  0.0503
>> > > niter,ni,del,rscale 73   12.1.2000
>> > > imgrege: no voxels in register
>> > > ERROR: 'imgreg_4dfp
>> > > /Applications/freesurfer/average/711-2C_as_mni_average_305
>> > >
>> /Applications/freesurfer/average/711-2B_as_mni_average_305_mask
>> > > talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4
>> 1283'
>> > > failed! status=254
>> > > ERROR: mpr2mni305 execution aborted
>> > >
>> > >
>> > > ___
>> > > 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
>> > gr...@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.

Re: [Freesurfer] Cortical Thickness Correction Factor

[David Tate]

FreeSurfer Gurus,
I would like to pose this question again to the group if possible.  We are 
working with data that comes from two different scanners.  Our experimental 
group was collected on one scanner and then control data was acquired on 
another scanner.  Not the optimal situation I realize but unavoidable.  We were 
fortunate to be able to acquire imaging for a subsample of patients on both 
scanners in the same day.  Preliminary results suggest that one site measures 
cortical thickness and subcortical volumes in a non-significant (statistically) 
but consistent direction with one scanner producing larger volume and thickness 
measures.  

My question is whether or not it is possible to mathematically account for 
these differences in any analysis that we are doing using FreeSurfer and if so 
where can I find those procedures for practically implementing the correction?

Thanks in advance for any help with this.

David


On Apr 17, 2014, at 11:07 AM, David Tate  wrote:

> We are working on a study that includes data from multiple scanners and 
> initial indication suggest that there may be small differences in cortical 
> thickness measures that are scanner related (human and other phantom data 
> were acquired at both sites).
> 
> Is it possible to include a correction factor adjusting for the scanner 
> differences when using glmfit or qdec?
> 
> Thanks,
> 
> David
> 
> David F. Tate, Ph.D.
> Research Neuropsychologist
> Defense and Veterans Brain Injury Center
> Contractor, General Dynamics Information Technology
> Brooke Army Medical Center MCHE MDU (DVBIC)
> 3551 Roger Brooke Drive
> JSBA Ft. Sam Houston, TX 78234-4504
> 
> Office (210) 916-8090
> 
> 
> 

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[Freesurfer] recon-all change for lgi affects NuCorrect

[Kathy L. Pearson]

When I follow the advice to prevent lgi problems with MATLAB 2013 using this 
update to 5.3 recon-all:
For Version 5.3 change the line 6148 in recon-all from
if ( ! $found_tpNid  ) then
to
if ( ! $found_tpNid  && ! $DoAddTp ) then

11 new subjects that I tested running from scratch fail in NuCorrect.  When 
reverting to the original recon-all, the same subjects all ran to completion 
without error.  Any suggestions on this?  I am running on Redhat Linux 6.3 with 
MATLAB 2013a.

Thanks,

Kathy Pearson

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Re: [Freesurfer] Fwd: mpr2mni305 failed error

[Bruce Fischl]

can you tar and gzip the dicoms and send them to us? Is there a high 
background level in them as well? Is this the average of more than one 
run? You should check the mri/orig/00?.mgz volume(s) as well
On Fri, 8 Aug 
2014, Francesco Deleo wrote:




-- Forwarded message --
From: Francesco Deleo 
Date: 2014-08-08 18:06 GMT+02:00
Subject: Re: [Freesurfer] mpr2mni305 failed error
To: freesurfer 


It is not ok...

It seems to have a contrast problem... I can send a snapshot, or if you want
I can send the rawavg.mgz

Francesco


2014-08-08 17:53 GMT+02:00 Bruce Fischl :
  what does the rawavg.mgz look like? If it is ok, can you email
  it to us?
  On Fri, 8 Aug 2014, Francesco Deleo wrote:

Thank you all for attention and help!
Maybe we're finding the problem: in cases I received
the mpr2mni305 error
the orig.mgz is unintelligible (it is white with
some black point). But my
dicoms are ok (I've checked!). I've already tried
converting dicom to tiff
but I got the same error message and the same
unintelligible orig.mgz (and
the tiff are ok too!).
So I think the likely problem is in the recon-all -i
command!
Any idea?

It remains a mistery for me why I have this problem
only in some (and not in
every one) MRI scans even if all the parameters are
the same.

thanks again

Francesco


2014-08-07 17:16 GMT+02:00 Douglas N Greve
:
      Have you looked in
transforms/talairach_avi.log?

      On 08/07/2014 07:57 AM, Francesco Deleo wrote:
      > Thank you Doug!
      > but i tried it in many cases but I've always
received the same
      error
      > message...
      > Is there something else I can try?
      >
      > Francesco
      >
      >
      > 2014-08-07 0:46 GMT+02:00 Douglas N Greve
       >:
>
>     Try it with -notal-check
>     doug
>
>     On 08/06/2014 04:39 PM, Francesco Deleo wrote:
>     > I all!
>     >
>     > I am a new freesurfer user.
>     > I have a problem when I perform the
recon-all -all, in about
15% of
>     > MRI scans, all made with the same scanning
protocol (T1 MPRAGE
in a
>     > SIEMENS Avanto 1,5 T).
>     >
>     > I can't recognize any difference between
those scans which
work
>     > correctly and those not.
>     > I have never found the same error on 3T MRI
scans.
>     >
>     > I've already tried to add these flags to the
recon-all -all
command:
>     > -use-mritotal
>     > -talairach -use-mritotal
>     > -notalairach
>     > but I've always received an error message
>     >
>     > Thank you very much
>     >
>     > ERROR: mpr2mni305 failed, see
transforms/talairach_avi.log
>     > Darwin pro-di-villani.besta.local 13.3.0
Darwin Kernel Version
>     13.3.0:
>     > Tue Jun  3 21:27:35 PDT 2014;
>     root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64
>     >
>     > Thanks very much for your attention
>     >
>     > Francesco
>     > Milan, Italy
>     >
>     >
>    

-
>     >
>     > FREESURFER_HOME: /Applications/freesurfer
>     >
>     > Build stamp:
freesurfer-Darwin-lion-stable-pub-v5.3.0
>     >
>     > Kernel info: Darwin 13.3.0 x86_64
>     >
>     >
>    

-
>     >
>     >
>     > LAST LINES IN TALAIRACH_AVI.LOG
>     >
>     > parameters
>     >     9.0270  134.9373  110.8627  -84.3566  
-7.5458  -11.3475
>     > eta,q 0.95791  3.72402
>     >   0.0485  0.0470  0.0477  0.0513  0.0470
 0.0452
>     >   0.0475  0.0471  0.0478  0.0513  0.0457
 0.0435
>     >   0.0472  0.0472  0.0476  0.0428  0.0434
 0.0415
>     >   0.0471  0.0471  0.0476  0.0435  0.0430
 

[Freesurfer] Update to Tracula longitudinal?

[Chung, Yoonho]

Dear Freesurfer Experts
We decided to reprocess our T1 and DTI data with the latest stream v.5.3 – we
would like to give TRACULA longitudinal stream a try. Before we go ahead and
reprocess our recons and DTI data with FS v 5.3 we were wondering if you plan
to release a new version of the TRACULA DTI longitudinal stream anytime soon.
I think I saw somewhere in the email chain that this is likely to happen soon
with additional features and bug fixes. If so, I think it would be worth a wait.

Thank you!

Yoon


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Re: [Freesurfer] Cortical Thickness Correction Factor

[Chris Watson]

In your FSGD you'll have to add a covariate for "scanner"

On 08/08/2014 12:34 PM, David Tate wrote:

FreeSurfer Gurus,
I would like to pose this question again to the group if possible.  We 
are working with data that comes from two different scanners.  Our 
experimental group was collected on one scanner and then control data 
was acquired on another scanner.  Not the optimal situation I realize 
but unavoidable.  We were fortunate to be able to acquire imaging for 
a subsample of patients on both scanners in the same day.  Preliminary 
results suggest that one site measures cortical thickness and 
subcortical volumes in a non-significant (statistically) but 
consistent direction with one scanner producing larger volume and 
thickness measures.


My question is whether or not it is possible to mathematically account 
for these differences in any analysis that we are doing using 
FreeSurfer and if so where can I find those procedures for practically 
implementing the correction?


Thanks in advance for any help with this.

David


On Apr 17, 2014, at 11:07 AM, David Tate > wrote:


We are working on a study that includes data from multiple scanners 
and initial indication suggest that there may be small differences in 
cortical thickness measures that are scanner related (human and other 
phantom data were acquired at both sites).


Is it possible to include a correction factor adjusting for the 
scanner differences when using glmfit or qdec?


Thanks,

David

David F. Tate, Ph.D.
Research Neuropsychologist
Defense and Veterans Brain Injury Center
Contractor, General Dynamics Information Technology
Brooke Army Medical Center MCHE MDU (DVBIC)
3551 Roger Brooke Drive
JSBA Ft. Sam Houston, TX 78234-4504

Office (210) 916-8090







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Re: [Freesurfer] Cortical Thickness Correction Factor

[Harms, Michael]

How many subjects are in each group, and how large is the "subsample" of patients which you scanned on both scanner on the same day?  The issue at hand is whether that subsample is large enough to get an accurate and meaningful estimate of the "scanner"
 effect to use as a covariate.  Unless that subsample is reasonably large, you are stuck with a situation where "scanner" is rather hopelessly confounded with "group".  


Stated differently, as you know, you ideally want scanner and group to be orthogonal (i.e., balanced design).  Depending on the N of the subsample, I suspect that they are probably actually highly co-linear in your case, which means that inclusion of a
 scanner covariate is probably going to account for most of whatever variability you have that may be an actual group effect (if one exists), which means that your odds of seeing any group difference are rather low.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: Chris Watson 
Reply-To: Freesurfer support list 
Date: Friday, August 8, 2014 1:21 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Cortical Thickness Correction Factor




In your FSGD you'll have to add a covariate for "scanner"


On 08/08/2014 12:34 PM, David Tate wrote:

FreeSurfer Gurus,


I would like to pose this question again to the group if possible.  We are working with data that comes from two different scanners.  Our experimental group was collected on one scanner and then control data was acquired on another scanner.  Not the optimal
 situation I realize but unavoidable.  We were fortunate to be able to acquire imaging for a subsample of patients on both scanners in the same day.  Preliminary results suggest that one site measures cortical thickness and subcortical volumes in a non-significant
 (statistically) but consistent direction with one scanner producing larger volume and thickness measures.  




My question is whether or not it is possible to mathematically account for these differences in any analysis that we are doing using FreeSurfer and if so where can I find those procedures for practically implementing the correction?




Thanks in advance for any help with this.




David






On Apr 17, 2014, at 11:07 AM, David Tate  wrote:



We are working on a study that includes data from multiple scanners and initial indication suggest that there may be small differences in cortical thickness measures that are scanner related (human and other phantom data were acquired at both sites).


Is it possible to include a correction factor adjusting for the scanner differences when using glmfit or qdec?


Thanks,


David




David F. Tate, Ph.D.

Research Neuropsychologist

Defense and Veterans Brain Injury Center
Contractor, General Dynamics Information Technology
Brooke Army Medical Center MCHE MDU (DVBIC)
3551 Roger Brooke Drive
JSBA Ft. Sam Houston, TX 78234-4504


Office (210) 916-8090













 
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