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Today's Topics:

  1. DTI of frontostriatal tracts (Ritobrato Datta)
  2. Re: Multiple Comparison Question for surface-based analyses
     (Douglas N Greve)
  3. Re: brain mask and T1 are not the same size (Douglas N Greve)
  4. Save Overlay via Command Line (Jordan Chad)
  5. Re: MNI coordinates of all the vertices of fsaverage
     (Douglas N Greve)
  6. Retinotopy questions (Xiaomin Yue)
  7. Re: DTI of frontostriatal tracts (Anthony Dick)
  8. Re: DTI of frontostriatal tracts (Ritobrato Datta)
  9. Re: Labels to MNI152, SPM compatible (Thomas Yeo)
 10. Re: Multiple Comparison Question for surface-based analyses
     (Ajay Kurani)
 11. mapping error (Caroline Beelen)


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

Message: 1
Date: Tue, 2 Aug 2016 12:26:43 -0400 (EDT)
From: Ritobrato Datta <ridatta@mail.med.upenn.edu>
Subject: [Freesurfer] DTI of frontostriatal tracts
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<1643573287.53129960.1470155203784.JavaMail.root@zimbra.upenn.edu>
Content-Type: text/plain; charset=utf-8

Hello All,

We are studying adolescents with HIV and are interested in frontostriatal tracts (anything from frontal cortex to caudate/putamen/nucleus accumbens) and tracts connected to the amygdala.

Is anyone aware of DTI based atlases where these tracts are defined in MNI or some other standard space ?

Any suggestions will be very helpful.

Best

Ri


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

Message: 2
Date: Tue, 2 Aug 2016 12:54:01 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Multiple Comparison Question for
surface-based analyses
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <57A0D029.7020303@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

I have  been doing simulations similar to #1 (Eklund) using
surface-based analysis on both thickness and fMRI. I'll prepare a report
of the results, but the early indications are that the same effect is in
play, though it does not look like the effects are as bad as in Eklund.

For thickness analysis using applied smoothing of 5 or 10 mm FWHM, for a
voxel-wise threshold of .001, the false positives are appropriate (ie,
5%). For a voxel-wise threshold of .01, the false positives is only a
little off (about 7%); for a voxel-wise threshold of .05, the FPR is
about 13%. If the data are not smoothed at all, then the false positive
rates go way up. The reason appears to be the same as found in Eklund
(ie, the autocorrelation function has a heavier-than-Gaussian tail). I
did the analysis by randomly selecting 40 subjects from a homogeneous
data set of 809 subjects aged 18-25. I then made two groups of 20
subjects each and ran a two-group test, then found clusters significant
based on our Monte Carlo (Gaussian) simulations. I repeated this several
thousand times. Any significant clusters were interpreted as false
positives. These results are much better than Eklund, but Eklund was
analyzing fMRI data.

I'm still working on the fMRI data. It is much more complicated because
the results depend on the assumed stimulus schedule (eg, 10 sec blocks
vs 30 sec blocks) and whether a one-group or two-group anaysis is done;
nuisance variables also play a role. At very low cluster-forming
thresholds (ie, .05), the FPR is roughly 20-30%. At a threshold of .01,
the FPR is about 3-13%. At a threshold of .001 are about 1-6%. This is
all for an applied smoothing level of 5mm.

All of these results are preliminary, so don't take them as true and
established yet. As a reminder, you can always do a permutation test
using mri_glmfit-sim. Eklund found that permutation did pretty well in
most cases.

doug


On 8/2/16 12:43 AM, Ajay Kurani wrote:

Hello Freesurfer Experts,
  Recently there were two article published regarding clusterwise
simulations for volumetric fmri analyses and potential errors for
underestimating clusterwise extent thresholds.

1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes
2) biorxiv.org/content/early/2016/07/26/065862
<http://biorxiv.org/content/early/2016/07/26/065862>

One issue pointed out from these articles seems software specific,
however the second issue is determining the proper clustersize.  The
heavy-tail nature of spatial smoothness seems to be ignored and a
gaussian shape is generally assumed, leading to an underestimation of
the spatial smoothness which can affect cluster size calculations.  
The issues are highlighted in the second article above.

I created my own monte carlo simulation in Freesurfer for a specific
brain template and I wanted to find out if these concerns also apply
to my surface based simulations?  I am not sure if it does since the
monte carlo tool is a GRF simulation as opposed to an analytic
equation, however given that these articles were highlighted very
recently, I wanted to ensure I am running things appropriately for
surface based cortical thickness/dti analyses.

Thanks,
Ajay


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Freesurfer mailing list
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------------------------------

Message: 3
Date: Tue, 2 Aug 2016 13:18:09 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] brain mask and T1 are not the same size
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <57A0D5D1.20301@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

The voxel size and dimensions of all three volumes are the same: 256^3
and 1mm^3.  Why do you think they are not?

On 08/02/2016 09:17 AM, Isabelle Deschamps wrote:

Yes, of course. The upload is now active.

Thank you again for your help,

Isabelle
On 2 Aug 2016, at 08:55, freesurfer-request@nmr.mgh.harvard.edu
<mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:

Re: [Freesurfer] brain mask and T1 are not the same size

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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--
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: 4
Date: Tue, 2 Aug 2016 14:17:28 -0400
From: Jordan Chad <jchad@research.baycrest.org>
Subject: [Freesurfer] Save Overlay via Command Line
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CA+FdjQX9T0cr50M4awGdW0YJHM3n32FrFcQ9AvGM_+=vMB1JPQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hello,

I am trying to perform between-subject statistics on cortical DTI data in
certain ROIs.

I can do this by overlaying the DTI data on the surfaces on tksurfer, load
and mask the label with the ROI, and then go to File -> Save Overlay. After
doing this for all subjects I can perform statistics on the output files.

However, it is not practical to do this for all >200 subjects for each ROI.
Is there a way to go about this process on the command line?

Thank You,
Jordan Chad
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Message: 5
Date: Tue, 2 Aug 2016 15:40:33 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MNI coordinates of all the vertices of
fsaverage
To: Sabin Khadka <mr.sabinkhadka@gmail.com>,
"Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu>
Message-ID: <57A0F731.9050108@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=utf-8; format=flowed

By default they are in talairach. But you can get mni305 by adding
--nofixmni to the surfcluster command line

On 08/02/2016 03:36 PM, Sabin Khadka wrote:

Hi Doug, Thanks. Are these coordinates in talairach or MNI space? From
previous post you mentioned these are in mni305 space but if I look at
the log file it say TalX, TalY, TalZ. I am a little confused.

And how can I convert these coordinates to MNI152 space?

thanks for your help.

Cheers,
Sabin Khadka

On Mon, Aug 1, 2016 at 9:24 PM, Douglas Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

   ps. you can always just load the xyz in the label into matlab and
   compute the centroid


   On 8/1/16 10:23 AM, Sabin Khadka wrote:

   Anyone?

   Cheers,
   Sabin Khadka

   On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka
   <mr.sabinkhadka@gmail.com <mailto:mr.sabinkhadka@gmail.com>> wrote:

       Hi Doug, I tried to pick up from the thread below to get MNI
       coordinates of each destrieux parcellation region.


       https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html

       I created label files from
       mri_annotation2label --subject fsaverage --hemi lh(/rh)
       --annotation aparc.a2009s --outdir label_destrieux   # which
       works fine

       And I tried to get the coordinates of each labels using

       mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness
       --clabel <label file> --sum <output file> --centroid --thmin
       0 --hemi lh --subject fsaverage

       But, all left labels would produce the same coordinates and
       so does right labels. (I've attached few example files here
       with). Also, it says TalX, TalY, TalZ are these coordinates
       in MNI or Talairach?

       Thanks for help.

   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.

--
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: 6
Date: Tue, 2 Aug 2016 21:55:38 +0000
From: Xiaomin Yue <yuexm@hotmail.com>
Subject: [Freesurfer] Retinotopy questions
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <BLU406-EAS159BDB45B45CE0F30358A01B3050@phx.gbl>
Content-Type: text/plain; charset="utf-8"

Hi,
I am running a retinotopy analysis using fsfast 5.3. ?The design has 15 TR blank before and after wedge presented for 30 TR with 7 repeats, and ring presented ?for 24 TR with 7 repeats. ?Here is my analysis:?mkanalysis -s vz -a rtoy.self.rh -fsd bold -fwhm 2 -nskip 15 -TR 1.5 -retinotopy 48 -paradigm rtopy.par.
The data doesn't look right. ?I assume that the analysis does require the stimuli presentation as a full circle, which means that the last 15 TR blank was accounted as the stimuli presentation time. If I am correct, ?is there simple way to take care of it in mkanalysis-sess? Second, the ring and wedge were presented in different frequency. It seems that the anslysis-sess does not take this into account in the current configration. Is there a way to specify this??
Thanks very much for the help.?
Xiaomin?

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The information in this e-mail is intended only for the person to whom it is
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------------------------------

Message: 7
Date: Tue, 2 Aug 2016 18:34:53 -0400
From: Anthony Dick <adick@fiu.edu>
Subject: Re: [Freesurfer] DTI of frontostriatal tracts
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <ef9ff21a-e069-a7b7-74e8-04ab84e11840@fiu.edu>
Content-Type: text/plain; charset="windows-1252"; format=flowed

Hello,

See the paper at this link: http://www.ncbi.nlm.nih.gov/pubmed/25086832

Anthony

On 8/2/16 12:26 PM, Ritobrato Datta wrote:

Hello All,

We are studying adolescents with HIV and are interested in
frontostriatal tracts (anything from frontal cortex to
caudate/putamen/nucleus accumbens) and tracts connected to the amygdala.

Is anyone aware of DTI based atlases where these tracts are defined
in MNI or some other standard space ?

Any suggestions will be very helpful.

Best

Ri
_______________________________________________
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.

--
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: adick@fiu.edu
Webpage: http://myweb.fiu.edu/adick
Join the Society for the Study of Human Development: http://www.sshdonline.org



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

Message: 8
Date: Tue, 2 Aug 2016 19:41:51 -0400 (EDT)
From: Ritobrato Datta <ridatta@mail.med.upenn.edu>
Subject: Re: [Freesurfer] DTI of frontostriatal tracts
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<1403815860.53391808.1470181311536.JavaMail.root@zimbra.upenn.edu>
Content-Type: text/plain; charset=utf-8

Many thanks.

Best

Ri

----- Original Message -----
From: Anthony Dick <adick@fiu.edu>
To: freesurfer@nmr.mgh.harvard.edu
Sent: Tue, 02 Aug 2016 18:34:53 -0400 (EDT)
Subject: Re: [Freesurfer] DTI of frontostriatal tracts

Hello,

See the paper at this link: http://www.ncbi.nlm.nih.gov/pubmed/25086832

Anthony

On 8/2/16 12:26 PM, Ritobrato Datta wrote:

Hello All,

We are studying adolescents with HIV and are interested in
frontostriatal tracts (anything from frontal cortex to
caudate/putamen/nucleus accumbens) and tracts connected to the amygdala.

Is anyone aware of DTI based atlases where these tracts are defined
in MNI or some other standard space ?

Any suggestions will be very helpful.

Best

Ri
_______________________________________________
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.

--
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: adick@fiu.edu
Webpage: http://myweb.fiu.edu/adick
Join the Society for the Study of Human Development: http://www.sshdonline.org

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

Message: 9
Date: Wed, 3 Aug 2016 10:43:40 +0800
From: Thomas Yeo <ythomas@csail.mit.edu>
Subject: Re: [Freesurfer] Labels to MNI152, SPM compatible
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CANZVnTaW8ja0F7NpK9ErqSQpcBHcGxRRvNm7T3WFTQTNyN4Ovw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Matyas,

In freeview, looks fine to me. See attached.

Can you send us your screenshot?

Regards,
Thomas

On Tue, Aug 2, 2016 at 9:39 PM, Maty?? Kuhn <matyas.kuhn@gmail.com> wrote:

The Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz
comes from
http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011,
and the description says it is the FSL MNI152 1mm template interpolated
and intensity normalized into a 256 x 256 x 256 1mm-isotropic volume
(obtained by putting the FSL MNI152 1mm template through recon-all ). So
I supposed it is in MNI305 after it was processed with freesurfer. When
I overlap the
Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz and
Template_T1_IXI555_MNI152.nii it is really shifted so I think it is not
in MNI152.

When I add the --invertmtx then the result is still the same, empty image.

I uploaded those images here:
https://dl.dropboxusercontent.com/u/70539709/Freesurfer_question.zip ,
if you want to try yourself.


Thank you,

Matyas



Dne 2.8.2016 v 14:55 Douglas Greve napsal(a):

 From the names, it looks like both the seg vol and the template vol are both in mni152. Where did Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz come from? One thing you can try is to invert the registration by adding --invertmtx to the command line.


On 8/2/16 8:18 AM, Maty?? Kuhn wrote:

Hi Freesurfer experts,

I just started to use Freesurfer and I was wondering how can I convert
images from MNI305 which uses Freesurfer to MNI152 which is used by SPM.
We would like to get MNI152 template of Yeo parcelation
(    )
so we can overlay with our results from SPM fMRI analysis.

I tried this:
mri_label2vol --seg
/path_to_analysis/Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz
\
                           --temp
/path_to_analysis/Template_T1_IXI555_MNI152.nii \
                           --reg
$FREESURFER_HOME/average/mni152.register.dat \
                           --o /path_to_analysis/output_mni152.nii

which resulted in image full of zeros (so maybe problem with
registration?). The "Template_T1_IXI555_MNI152.nii" is the MNI152
template which is used by Computational anatomical toolbox 12 for SPM
from Christian Gaser and his group.

Thanks in advance for any suggestions,

Matyas
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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
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Message: 10
Date: Wed, 3 Aug 2016 02:45:47 -0500
From: Ajay Kurani <dr.ajay.kurani@gmail.com>
Subject: Re: [Freesurfer] Multiple Comparison Question for
surface-based analyses
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CA+uskrDgnhv2SaRJHGHUQQVJseuEKQC6ov-=f7N0DYrTsgeLTg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Doug,
  Thank you very much for your update regarding this issue.

1)Just curious, will LGI be included in this report as this is another
analysis of interest?

2)As for the cortical thickness I originally used 15mm in the analysis so
based on your email I think using 5-10mm may be more prudent in order to
minimize FPR.  From your email, I understand that mris_surf2surf (command I
use to convert individual subject to fsaverage or template and smooth to
10-15mm) assumes an ACF estimation of smoothness which DOES NOT take into
account the long tail distribution.  Does this mean that when using
mri_mcsim on my own template, the cluster extents for a given smoothness
will be undersampled due to the fact that the "true" smoothness is more
than what is estimated in the simulation, correct?  For instance, when I
select 15mm in qdec, it would point to the 21mm folder (fwhm.dat=20.8mm
estimate), and I would select a given cluster extent for p=0.05.  However,
in this case, 15mm may translate to a larger FWHM than the estimated 21mm,
correct?

3)You mentioned that I can use mri_glmfit-sim which is permutation testing
based.  I am struggling a bit in understanding how this differs from the
simulation ran with mri_mcsim/qdec?  Does qdec monte carlo simulation
option run mri_glmfit-sim in the background to estimate the smoothness
which looks up the cluster extent within the mri_mcsim based on the
estimated FWHM?  If so, is this estimate incorrect due to the fact that the
long tails are not taken into account?


Thanks,
Ajay

On Mon, Aug 1, 2016 at 11:43 PM, Ajay Kurani <dr.ajay.kurani@gmail.com>
wrote:

Hello Freesurfer Experts,
  Recently there were two article published regarding clusterwise
simulations for volumetric fmri analyses and potential errors for
underestimating clusterwise extent thresholds.

1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes
2) biorxiv.org/content/early/2016/07/26/065862

One issue pointed out from these articles seems software specific, however
the second issue is determining the proper clustersize.  The heavy-tail
nature of spatial smoothness seems to be ignored and a gaussian shape is
generally assumed, leading to an underestimation of the spatial smoothness
which can affect cluster size calculations.  The issues are highlighted in
the second article above.

I created my own monte carlo simulation in Freesurfer for a specific brain
template and I wanted to find out if these concerns also apply to my
surface based simulations?  I am not sure if it does since the monte carlo
tool is a GRF simulation as opposed to an analytic equation, however given
that these articles were highlighted very recently, I wanted to ensure I am
running things appropriately for surface based cortical thickness/dti
analyses.

Thanks,
Ajay

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Message: 11
Date: Wed, 3 Aug 2016 10:00:18 +0000
From: Caroline Beelen <caroline.beelen@kuleuven.be>
Subject: [Freesurfer] mapping error
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<40b86b2ee4c24b96b8d585eb822a02cd@ICTS-S-EXMBX26.luna.kuleuven.be>
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Dear FS,

An aparc.annot ctab file was created but I got the following error:
Colortable:aparc.annot.ctab
Annotname: myaparc
Nhitsfile nhits.mgh
Nlabels 6
Labeltresh 0 0.00000
Loading freesurfer/fsaverage/surf/lh.orig
1 -1 not found
2 -1 not found
3 -1 not found
Etc...
Mapping unhit to unknown
Found 132101 unhit vertices
Writing annot to freesurfer/fsaverage/lh.myaparc.annot

I guess my ctab file is incorrect? I included an example of a label with it.

Thanks again for your help.

Caroline
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End of Freesurfer Digest, Vol 150, Issue 5
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