Re: [Freesurfer] DTI of frontostriatal tracts

[Ritobrato Datta]

Many thanks. 

Best

Ri

- Original Message -
From: Anthony Dick 
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
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Neuroscience
Department of Psychology
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Re: [Freesurfer] DTI of frontostriatal tracts

[Anthony Dick]

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
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>> 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: ad...@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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[Freesurfer] Retinotopy questions

[Xiaomin Yue]

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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Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

[Douglas N Greve]

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 
> > 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
>> > 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  --sum  --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.
>>
>>
>
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[Freesurfer] Save Overlay via Command Line

[Jordan Chad]

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

[Douglas N Greve]

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-requ...@nmr.mgh.harvard.edu 
>  wrote:
>
>> Re: [Freesurfer] brain mask and T1 are not the same size
>
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] Multiple Comparison Question for surface-based analyses

[Douglas N Greve]

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 
> 
>
> 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] DTI of frontostriatal tracts

[Ritobrato Datta]

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
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Re: [Freesurfer] Labels to MNI152, SPM compatible

[Matyáš Kuhn]

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, Matyáš 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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>>
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[Freesurfer] FreeSurfer Course Registration now open!

[Allison Stevens]

The Freesurfer group is offering a four-day Freesurfer Tutorial and Workshop 
September 26th to 29th, 2016 at the Martinos Center in Charlestown, MA. You can 
register for the course on our course website: 
https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription

Details about the content of the course, the location, registration fees, 
accepted payment types, and nearby hotels is currently on the website above. 
Please read the above page in its entirety before registering and before 
sending questions.

If you are not one of the first 50 to register, you will be put on a waiting 
list and will be notified if a spot becomes available. *Do not submit a payment 
or make travel arrangements until you have received an email confirmation that 
you successfully secured a seat in the course.


Allison Stevens
> Lab Manager
> FreeSurfer Development Team
> Laboratory for Computational Neuroimaging
> Massachusetts General Hospital
> Athinoula A. Martinos Center for Biomedical Imaging
> Bldg. 149, 13th Street, CNY 2301
> Charlestown, MA 02129


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

[Isabelle Deschamps]

Yes, of course. The upload is now active.


Thank you again for your help,


Isabelle

On 2 Aug 2016, at 08:55, 
freesurfer-requ...@nmr.mgh.harvard.edu wrote:

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





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Re: [Freesurfer] Labels to MNI152, SPM compatible

[Douglas Greve]

 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, Matyáš 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
> (http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011)
> 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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>

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[Freesurfer] Labels to MNI152, SPM compatible

[Matyáš Kuhn]

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 
(http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011) 
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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