Sorry, I did not see that one of the volumes was 256x256x255. I cannot replicate here on your data using 5.3 under linux. Can you say exactly what you do in freeview? Also, what version of FS are you using? And what platform?
On 08/03/2016 06:50 AM, Isabelle Deschamps wrote:
I had the problem before and was told the the output of mri_info should be 256 x 256 x 256 for the dimensions of the brainmask and T1. When I run mri_info on the brainmask.mgz that I modified I have 256 x 256 x 255 but the T1 I have 256 x 256 x 256. The zstart and zend are also different between the brainmask and T1. Could that be the source of the problem?
*Modified brainmask:* mri_info /Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S14_FS/mri/brainmask.mgz
Volume information for /Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S14_FS/mri/brainmask.mgz type: MGH dimensions: 256 x 256 x 255 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -127.5, zend: 127.5
*T1:* mri_info /Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S14_FS/mri/T1.mgz Volume information for /Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S14_FS/mri/T1.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0
*Non-modified brain mask:* mri_info /Users/Isabelle/Desktop/S14/brainmask_orig.mgz Volume information for /Users/Isabelle/Desktop/S14/brainmask_orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0
I am not sure why I get this error and why the change in dimensions, zstart and zend between the brainmask and T1. For all other participants that do not have an error the information of mri_info for dimensions, zstart and zend is the same for the brainmask and T1. So I am very confuse as to why these 4 participants are exiting with the same error. I am not sure what I am doing wrong in this case.
Thanks,
Isabelle
On 3 Aug 2016, at 06:00, freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu wrote:
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Today's Topics:
- DTI of frontostriatal tracts (Ritobrato Datta)
- Re: Multiple Comparison Question for surface-based analyses (Douglas N Greve)
- Re: brain mask and T1 are not the same size (Douglas N Greve)
- Save Overlay via Command Line (Jordan Chad)
- Re: MNI coordinates of all the vertices of fsaverage (Douglas N Greve)
- Retinotopy questions (Xiaomin Yue)
- Re: DTI of frontostriatal tracts (Anthony Dick)
- Re: DTI of frontostriatal tracts (Ritobrato Datta)
- Re: Labels to MNI152, SPM compatible (Thomas Yeo)
- Re: Multiple Comparison Question for surface-basedanalyses (Ajay Kurani)
- mapping error (Caroline Beelen)
Message: 1 Date: Tue, 2 Aug 2016 12:26:43 -0400 (EDT) From: Ritobrato Datta <ridatta@mail.med.upenn.edu mailto:ridatta@mail.med.upenn.edu> Subject: [Freesurfer] DTI of frontostriatal tracts To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <1643573287.53129960.1470155203784.JavaMail.root@zimbra.upenn.edu mailto: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 mailto:greve@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Multiple Comparison Question for surface-based analyses To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <57A0D029.7020303@nmr.mgh.harvard.edu http://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.
- http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes
- biorxiv.org/content/early/2016/07/26/065862
http://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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Message: 3 Date: Tue, 2 Aug 2016 13:18:09 -0400 From: Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] brain mask and T1 are not the same size To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <57A0D5D1.20301@nmr.mgh.harvard.edu http://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 mailto:freesurfer-request@nmr.mgh.harvard.edu wrote:
Re: [Freesurfer] brain mask and T1 are not the same size
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-- 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: 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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Isabelle Deschamps