Re: [Freesurfer] mri_average vs mri_concat

[Trisanna Sprung-Much]

Hi Doug

So the pixel values are 0 and 1 *in the original .mnc*. It seems that after
performing mri_vol2surf they become 0 and 255, and stay this way after
mri_surf2surf as well. So, why would mri_vol2surf be changing the values?

Trisanna



--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve 
wrote:

> What are the pixel values in the mgz file? They should be binary, ie, 1=in
> a label, 0 = out of label
>
> On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote:
>
> Overlays in .mgz format using mri_vol2surf
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve  > wrote:
>
>> what is a labeled vertex? What file format? mgz? annot?
>>
>>
>> On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
>> > the source files are labelled vertices from 20 subjects:
>> >
>> > -T1s were labelled using an MNI software
>> > -Surfaces were created in FreeSurfer and surface overlays of the
>> > labels were created using mri_vol2surf
>> > -Surface overlays were registered to fsaverage using mri_surf2surf and
>> > then averaged to create a probability map, originally using
>> "mri_average"
>> >
>> > So, essentially the overlays are binary files of my labels I believe
>> > - I can send one over if you wish.
>> >
>> > Trisanna
>> >
>> >
>> > --
>> > Ph.D. Candidate
>> > McGill University
>> > Integrated Program in Neuroscience
>> > Psychology
>> >
>> >
>> > On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve
>> > > wrote:
>> >
>> > what are the source files ("all files"). What data type, value
>> range,
>> > where did they come from?
>> >
>> >
>> > On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
>> > > Hi Doug
>> > >
>> > > So, of course now it works without --keep-filetype... :p it looks
>> > > pretty much the same was when I use --keep-filetype.
>> > >
>> > > However, the values of Min and Max are still odd (out of 256) -
>> see
>> > > snapshot
>> > >
>> > > Trisanna
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > --
>> > > Ph.D. Candidate
>> > > McGill University
>> > > Integrated Program in Neuroscience
>> > > Psychology
>> > >
>> > >
>> > > On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve
>> > > 
>> > > > >> wrote:
>> > >
>> > > Depending upon the type of the data, the --keep-datatype may
>> > mess
>> > > things
>> > > up quite a bit. What happens if you don't include that? It
>> > will not
>> > > create an annotation. maybe you mean some other file type?
>> > >
>> > >
>> > > On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote:
>> > > >
>> > > > Hi Doug
>> > > >
>> > > > I spoke with you at the Freesurfer tutorial last week
>> > about using
>> > > > mri_average to average my sulcal labels and get a
>> > probability map on
>> > > > fsaverage. You had suggested using "mri_concat" instead,
>> > which is a
>> > > > newer command. So, I performed the following command:
>> > > >
>> > > > *mri_concat all files --o output.mgz --mean --keep-datatype*
>> > > >
>> > > > I had to put --keep-datatype or else it tried to create an
>> > annot
>> > > file.
>> > > >
>> > > > This worked just fine.
>> > > >
>> > > > My question then is concerning *the min and max values
>> > *when this
>> > > > average is overlayed in Freeview. See the snapshot
>> > attached. The
>> > > > values seem to be based on 256 instead of percentage and
>> > this is
>> > > what
>> > > > happens when I used "mri_average" without specifying the
>> > "-p". Is
>> > > > there a way to illustrate the values in percentage in a
>> > similar way
>> > > > with mri_concat?
>> > > >
>> > > > Many thanks!
>> > > >
>> > > > Trisanna
>> > > >
>> > > >
>> > > > --
>> > > > Ph.D. Candidate
>> > > > McGill University
>> > > > Integrated Program in Neuroscience
>> > > > Psychology
>> > > >
>> > > >
>> > > >
>> > > > ___
>> > > > Freesurfer mailing list
>> > > > Freesurfer@nmr.mgh.harvard.edu
>> > 
>> > > > > >
>> > > >
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >  

Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

[Douglas Greve]

not yet. I'm on vacation until Wed, so it might be a while.


On 10/6/16 2:50 PM, Matthieu Vanhoutte wrote:


Hi Douglas,

Dis you have time to take a look at ?

Best regards,
Matthieu


Le 3 oct. 2016 6:25 PM, "Matthieu Vanhoutte" 
> a 
écrit :


Hi Douglas,

I have just sent it to you on Filedrop.

Best regards,
Matthieu

2016-10-03 17:45 GMT+02:00 Douglas Greve
>:

Can you tar up the FS anat analysis and BS7_PET.lps.nii.gz and
send it to me on our filedrop?


On 10/3/16 6:55 AM, Matthieu Vanhoutte wrote:

Hi Douglas,

Please find below the mri_coreg terminal output :
/
/
/$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $/
/cwd /NAS/tupac/matthieu/FS5.3/207118_M0_2014-01-29/pet/
/cmdline mri_coreg --s 207118_M0_2014-01-29 --mov
BS7_PET.lps.nii.gz --reg
Pet2T1.BS7.register.dof6.mri_coreg.lta --regdat
Pet2T1.BS7.register.dof6.mri_coreg.dat /
/sysname  Linux/
/hostname yakuza/
/machine  x86_64/
/user matthieu/
/dof6/
/nsep2/
/cras01/
/ftol0.00/
/linmintol0.001000/
/bf   1/
/bflim30.00/
/bfnsamp30/
/SmoothRef 0/
/SatPct99.99/
/MovOOB 0/
/optschema 1/
/Reading in mov BS7_PET.lps.nii.gz/
/Reading in ref
/NAS/tupac/matthieu/FS5.3//207118_M0_2014-01-29/mri/brainmask.mgz/
/Reading in and applying refmask
/NAS/tupac/matthieu/FS5.3//207118_M0_2014-01-29/mri/aparc+aseg.mgz/
/Setting cras translation parameters to align centers/
/Creating random numbers for coordinate dithering/
/Performing intensity dithering/
/Initial parameters 20.9141 11.8161 149.1538  0.  0.
 0.  1.  1.  1.  0.  0.  0. /
/Separation list (2):  4  2   min = 2/
/DoSmoothing 1/
/DoCoordDither 1/
/DoIntensityDither 1/
/nitersmax 4/
/ftol 1.000e-07/
/linmintol 1.000e-03/
/SatPct 99.99/
/Hist FWHM 7.00 7.00/
/nthreads 1/
/movsat = 10897.7666/
/mov gstd 0.8459 0.8459 0.8459/
/Smoothing mov/
/refsat = 119./
/ref gstd 0.8459 0.8459 0.8459/
/Smoothing ref/
/COREGpreproc() done/
/Testing if mov and target overlap/
/Init cost   -1.0011578057/
/nhits = 262144 out of 16777216, Percent Overlap: 100.0/
/Initial  RefRAS-to-MovRAS/
/ 1.0   0.0   0.0 20.91408;/
/ 0.0   1.0   0.0 11.81612;/
/ 0.0   0.0   1.0 149.15384;/
/ 0.0   0.0   0.0 1.0;/
/Initial  RefVox-to-MovVox/
/ 1.0   0.0   0.0 0.0;/
/ 0.0   0.0  -1.0 255.0;/
/ 0.0  -1.0   0.0 255.0;/
/ 0.0   0.0   0.0 1.0;/
/sep = 4 ---/
/COREGoptBruteForce() 30 1 30/
/Turning on MovOOB for BruteForce Search/
/#BF# sep= 4 iter=0 lim=30.0 delta=2.00   4.91408  21.81612
119.15384   2.0   0.0 0.0   -1.0078773/
/Turning  MovOOB back off after brute force search/
/
/
/
/
/-/
/Init Powel Params dof = 6/
/Starting OpenPowel2(), sep = 4/
/InitialCost  -1.0076701641 /
/#@#  4  188  4.91408 21.81612 119.15384 2.0 0.0
0.0 -1.0076702/
/fs_powell::minimize/
/  nparams 6/
/  maxfev 4/
/  ftol   0.00/
/  linmin_xtol_   0.001000/
/  powell nthiter 0: fret = -1.007670/
/#@#  4  197  4.93866 21.81612 119.15384 2.0 0.0
0.0 -1.0076704/
/#@#  4  198  4.96905 21.81612 119.15384 2.0 0.0
0.0 -1.0076705/
/#@#  4  209  4.97536 20.19808 119.15384 2.0 0.0
0.0 -1.0077189/
/#@#  4  210  4.97536 19.55424 119.15384 2.0 0.0
0.0 -1.0077529/
/#@#  4  211  4.97536 18.51247 119.15384 2.0 0.0
0.0 -1.0078081/
/#@#  4  212  4.97536 16.82685 119.15384 2.0 0.0
0.0 -1.0078434/
/#@#  4  213  4.97536 16.77889 119.15384 2.0 0.0
0.0 -1.0078460/
/#@#  4  214  4.97536 16.70129 119.15384 2.0 0.0
0.0 -1.0078515/
/#@#  4  215  4.97536 16.57572 119.15384 2.0 0.0
0.0 -1.0078617/
/#@#  4  216  4.97536 16.37254 119.15384 2.0 0.0
0.0 -1.0078768/
/#@#  4  217  4.97536 14.89926 119.15384 2.0 0.0
0.0 

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

[Martin Juneja]

Dear Dr. Greve,

Thanks a lot for your inputs on this.
In the manual-
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview,
in qdec it shows there is an option to select 'Smoothing (FWHM)' under the
step 'Design'. Could you please share your thoughts if there is any optimal
value here I can choose which does a close comparison for the two different
voxel size (1.3 vs 1) or may be if I can compare without smoothing?

Thanks.

On Wed, Oct 5, 2016 at 3:21 PM, Douglas N Greve 
wrote:

> I think the difference in voxel size (1mm vs 1.3mm) is problematic. You
> will get more smoothing with the 1.3mm (ie, partial volume effects), and
> that could easily show up in the thickness measurements
>
>
> On 10/05/2016 12:19 PM, Martin Juneja wrote:
> > Hi Dr. Greve,
> >
> > After I compare the two protocols (after using mri_info in FSL on raw
> > dicom file), I get following parameters used in both the protocols.
> > After looking at both the protocols parameters below, could you please
> > share your thoughts on whether parameters are in match enough to go
> > ahead and do the analysis i.e. patients data collected using protocol
> > 1 and controls data using protocol 2 or is it still a bad idea to
> compare.
> >
> > *Protocol 1:*
> >
> > INFO: loading series header info.
> >
> > INFO: sorting.
> >
> > RunNo = 1
> >
> > sdfiSameSlicePos() eps = 0.01
> >
> > INFO: (256 256 176), nframes = 1, ismosaic=0
> >
> > sdfi->UseSliceScaleFactor 0
> >
> > datatype = 4, short=4, float=3
> >
> > PE Dir ROW ROW
> >
> > AutoAlign matrix detected
> >
> > AutoAlign Matrix -
> >
> >  1.0 0.0   0.0   0.0;
> >
> >  0.0 1.0   0.0   0.0;
> >
> >  0.0 0.0   1.0   0.0;
> >
> >  0.0 0.0   0.0   1.0;
> >
> > Volume information for IM-0001-0001-0001.dcm
> >
> > type: siemens_dicom
> >
> > dimensions: 256 x 256 x 176
> >
> >voxel sizes: 1.00, 1.00, 1.00
> >
> > type: SHORT (4)
> >
> > fov: 256.000
> >
> > dof: 0
> >
> > xstart: -128.0, xend: 128.0
> >
> > ystart: -128.0, yend: 128.0
> >
> > zstart: -88.0, zend: 88.0
> >
> > TR: 2100.00 msec, TE: 2.30 msec, TI: 1100.00 msec, flip angle: 12.00
> > degrees
> >
> > nframes: 1
> >
> > PhEncDir: ROW
> >
> > FieldStrength: 3.00
> >
> > ras xform present
> >
> > xform info: x_r =  -0., y_r =  -0., z_r =  -1., c_r =
> > 2.5000
> >
> >   : x_a =  -1., y_a =  -0., z_a =  -0., c_a =14.
> >
> >   : x_s =   0., y_s =  -1., z_s =   0., c_s = 2.
> >
> > Orientation   : PIL
> >
> > Primary Slice Direction: sagittal
> >
> > voxel to ras transform:
> >
> >   -0.  -0.  -1.90.5000
> >
> >   -1.  -0.  -0.   142.
> >
> > 0.  -1.   0.   130.
> >
> > 0.   0.   0. 1.
> >
> > voxel-to-ras determinant -1
> >
> > ras to voxel transform:
> >
> >   -0.  -1.  -0.   142.
> >
> >   -0.  -0.  -1.   130.
> >
> >   -1.  -0.  -0.90.5000
> >
> >   -0.  -0.  -0. 1.
> >
> >
> > *Protocol 2:*
> >
> > INFO: (256 256 128), nframes = 1, ismosaic=0
> >
> > sdfi->UseSliceScaleFactor 0
> >
> > datatype = 4, short=4, float=3
> >
> > PE Dir ROW ROW
> >
> > Volume information for IM-0001-0001-0001.dcm
> >
> > type: siemens_dicom
> >
> > dimensions: 256 x 256 x 128
> >
> >voxel sizes: 1.00, 1.00, 1.33
> >
> > type: SHORT (4)
> >
> > fov: 256.000
> >
> > dof: 0
> >
> > xstart: -128.0, xend: 128.0
> >
> > ystart: -128.0, yend: 128.0
> >
> > zstart: -64.0, zend: 64.0
> >
> > TR: 2100.00 msec, TE: 2.25 msec, TI: 1100.00 msec, flip angle: 12.00
> > degrees
> >
> > nframes: 1
> >
> > PhEncDir: ROW
> >
> > FieldStrength: 3.00
> >
> > ras xform present
> >
> > xform info: x_r =  -0.0202, y_r =   0.0424, z_r =  -0.9989, c_r =
> >   -23.2439
> >
> >   : x_a =  -0.9989, y_a =  -0.0441, z_a =   0.0184, c_a =53.2183
> >
> >   : x_s =   0.0433, y_s =  -0.9981, z_s =  -0.0432, c_s =   -12.5170
> >
> > Orientation   : PIL
> >
> > Primary Slice Direction: sagittal
> >
> > voxel to ras transform:
> >
> >   -0.0202   0.0424  -1.328558.9497
> >
> >   -0.9989  -0.0441   0.0244   185.1541
> >
> > 0.0433  -0.9981  -0.0575   113.3820
> >
> > 0.   0.   0. 1.
> >
> > voxel-to-ras determinant -1.33
> >
> > ras to voxel transform:
> >
> >   -0.0202  -0.9989   0.0433   181.2290
> >
> > 0.0424  -0.0441  -0.9981   118.8377
> >
> >   -0.7511   0.0138  -0.032545.4015
> >
> >   -0.  -0.  -0. 1.
> >
> > Thanks a lot.
> >
> > On Mon, Oct 3, 2016 at 11:42 AM, Douglas N Greve
> > > wrote:
> >
> > I would still say no -- the differences could still be due to
> > differences in acquisition parameters
> >
> >
> > On 10/03/2016 02:30 PM, Martin Juneja wrote:
> > > 

Re: [Freesurfer] Question about Cortical Thickness

[Bruce Fischl]

yes, that's true
On Thu, 6 Oct 2016, Funk, Quentin wrote:

> I have a few questions regarding the instructions at:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
>
>
> The instructions assume that there is an ROI in the same space as the
> T1.mgz map. Then they do the following:
>
> 1) Register the T1 to fsaverage
> 2) resample the ROI to the cortical surface of fsaverage
> 3) map the thickness data of the subject to fsaverage
> 4) measure the thickness data
>
> Why is the registering to fsaverage helpful? It seems as if this
> computation could be done in the native space. Why couldn't one make the
> following changes:
>
> 1) in mri_vol2surf, the reg option could be replaced with regheader MYSUB.
> 2) Then the surf2surf command becomes unnecessary.
>
>
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[Freesurfer] Question about Cortical Thickness

[Funk, Quentin]

I have a few questions regarding the instructions at:

https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness


The instructions assume that there is an ROI in the same space as the 
T1.mgz map. Then they do the following:

1) Register the T1 to fsaverage
2) resample the ROI to the cortical surface of fsaverage
3) map the thickness data of the subject to fsaverage
4) measure the thickness data

Why is the registering to fsaverage helpful? It seems as if this 
computation could be done in the native space. Why couldn't one make the 
following changes:

1) in mri_vol2surf, the reg option could be replaced with regheader MYSUB.
2) Then the surf2surf command becomes unnecessary.

-- 

Quentin Funk, PhD
Houston Methodist Research Institute
713-363-9003

Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
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Re: [Freesurfer] mris_divide_parcellation

[Mamashli, Fahimeh]

Dear Bruce,
Many thanks for quick reply. Actually, I meant doing the same thing as you 
explained with mris_make_face_parcellation command . 

with mris_divide_parcellation, I have done what you told me but the problem is 
that it only divide the labels perpendicular to the axis of the label which 
does not look nice. I prefer 
to use mris_make_face_parcellation and do for a certain label like superior 
temporal. Is that possible?

Thanks,
Fahimeh

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, October 06, 2016 4:13 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_divide_parcellation

Hi Fahimeh

you can also give mris_divide_parcellation a "splitfile" :

rst, a splitfile can be specified as the fourth argument. The
splitfile is a text file with two columns. The first column is the
name of the label in the source annotation, and the second column is
the number of units that label should be divided into. The names of
the labels depends upon the source parcellation.  For aparc.annot and
aparc.a2005.annot, the names can be found in
$FREESURFER_HOME/FreeSurferColorLUT.txt.  For aparc.annot, the labels
are between the ranges of 1000-1034.  For aparc.a2005s.annot, the
labels are between the ranges of 1100-1181.  The name for the label is
the name of the segmentation without the 'ctx-lh'. Note that the name
included in the splitfile does not indicate the hemisphere. For
example, 1023 is 'ctx-lh-posteriorcingulate'.  You should put
'posteriorcingulate' in the splitfile. Eg, to divide it into three
segments, the following line should appear in the splitfile:

posteriorcingulate 3

Only labels that should be split need be specified in the splitfile.


cheers
Bruce
On
Thu,
6
Oct
2016, Mamashli, Fahimeh wrote:

>
> Hi,
> Thanks for your help. I tried and it worked. However, the problem is that 
> this is doing for all brain and it is very hard to find out which label 
> belongs to which parcellation in the brain.
> For example, I am interested only to superior temporal area of the brain and 
> I don't need rest of the brain. How can I figure out which of these labels 
> belong to superior temporal?
> is there any way to do this for a certain parcellation like lh.aparc.annot ?
>
> Thank you,
> Fahimeh
>
> 
> 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, September 16, 2016 6:31 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mris_divide_parcellation
>
> how would you like them divided? You can also use
> mris_make_face_parcellation to make units of approximately equal area
> (either in the individual or in the group)
> On Fri, 16 Sep 2016, Mamashli,
> Fahimeh wrote:
>
>> Dear Freesurfer group,
>> I am going to divide a brain parcellation into divisions using
>> mris_divide_parcellation. As far as I know from the help comment, this
>> function "divides one or more parcellations into divisions perpendicular to
>> the long axis of the label". Is there any other program that does not make
>> the divisions perpendicular to the long axis?
>>
>> Thank you,
>> Fahimeh
>>
>>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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>
>
>
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Re: [Freesurfer] mris_divide_parcellation

[Bruce Fischl]

Hi Fahimeh

you can also give mris_divide_parcellation a "splitfile" :

rst, a splitfile can be specified as the fourth argument. The
splitfile is a text file with two columns. The first column is the
name of the label in the source annotation, and the second column is
the number of units that label should be divided into. The names of
the labels depends upon the source parcellation.  For aparc.annot and
aparc.a2005.annot, the names can be found in
$FREESURFER_HOME/FreeSurferColorLUT.txt.  For aparc.annot, the labels
are between the ranges of 1000-1034.  For aparc.a2005s.annot, the
labels are between the ranges of 1100-1181.  The name for the label is
the name of the segmentation without the 'ctx-lh'. Note that the name
included in the splitfile does not indicate the hemisphere. For
example, 1023 is 'ctx-lh-posteriorcingulate'.  You should put
'posteriorcingulate' in the splitfile. Eg, to divide it into three
segments, the following line should appear in the splitfile:

posteriorcingulate 3

Only labels that should be split need be specified in the splitfile.


cheers
Bruce
On 
Thu, 
6 
Oct 
2016, Mamashli, Fahimeh wrote:

>
> Hi,
> Thanks for your help. I tried and it worked. However, the problem is that 
> this is doing for all brain and it is very hard to find out which label 
> belongs to which parcellation in the brain.
> For example, I am interested only to superior temporal area of the brain and 
> I don't need rest of the brain. How can I figure out which of these labels 
> belong to superior temporal?
> is there any way to do this for a certain parcellation like lh.aparc.annot ?
>
> Thank you,
> Fahimeh
>
> 
> 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, September 16, 2016 6:31 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mris_divide_parcellation
>
> how would you like them divided? You can also use
> mris_make_face_parcellation to make units of approximately equal area
> (either in the individual or in the group)
> On Fri, 16 Sep 2016, Mamashli,
> Fahimeh wrote:
>
>> Dear Freesurfer group,
>> I am going to divide a brain parcellation into divisions using
>> mris_divide_parcellation. As far as I know from the help comment, this
>> function "divides one or more parcellations into divisions perpendicular to
>> the long axis of the label". Is there any other program that does not make
>> the divisions perpendicular to the long axis?
>>
>> Thank you,
>> Fahimeh
>>
>>
>
> ___
> Freesurfer mailing list
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>
>
>
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Re: [Freesurfer] mris_divide_parcellation

[Mamashli, Fahimeh]

Hi,
Thanks for your help. I tried and it worked. However, the problem is that this 
is doing for all brain and it is very hard to find out which label belongs to 
which parcellation in the brain. 
For example, I am interested only to superior temporal area of the brain and I 
don't need rest of the brain. How can I figure out which of these labels belong 
to superior temporal?
is there any way to do this for a certain parcellation like lh.aparc.annot ?

Thank you,
Fahimeh


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, September 16, 2016 6:31 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_divide_parcellation

how would you like them divided? You can also use
mris_make_face_parcellation to make units of approximately equal area
(either in the individual or in the group)
On Fri, 16 Sep 2016, Mamashli,
Fahimeh wrote:

> Dear Freesurfer group,
> I am going to divide a brain parcellation into divisions using
> mris_divide_parcellation. As far as I know from the help comment, this
> function "divides one or more parcellations into divisions perpendicular to
> the long axis of the label". Is there any other program that does not make
> the divisions perpendicular to the long axis?
>
> Thank you,
> Fahimeh
>
>

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Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

[Matthieu Vanhoutte]

Hi Douglas,

Dis you have time to take a look at ?

Best regards,
Matthieu

Le 3 oct. 2016 6:25 PM, "Matthieu Vanhoutte" 
a écrit :

> Hi Douglas,
>
> I have just sent it to you on Filedrop.
>
> Best regards,
> Matthieu
>
> 2016-10-03 17:45 GMT+02:00 Douglas Greve :
>
>> Can you tar up the FS anat analysis and BS7_PET.lps.nii.gz and send it to
>> me on our filedrop?
>>
>> On 10/3/16 6:55 AM, Matthieu Vanhoutte wrote:
>>
>> Hi Douglas,
>>
>> Please find below the mri_coreg terminal output :
>>
>> *$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $*
>> *cwd /NAS/tupac/matthieu/FS5.3/207118_M0_2014-01-29/pet*
>> *cmdline mri_coreg --s 207118_M0_2014-01-29 --mov BS7_PET.lps.nii.gz
>> --reg Pet2T1.BS7.register.dof6.mri_coreg.lta --regdat
>> Pet2T1.BS7.register.dof6.mri_coreg.dat *
>> *sysname  Linux*
>> *hostname yakuza*
>> *machine  x86_64*
>> *user matthieu*
>> *dof6*
>> *nsep2*
>> *cras01*
>> *ftol0.00*
>> *linmintol0.001000*
>> *bf   1*
>> *bflim30.00*
>> *bfnsamp30*
>> *SmoothRef 0*
>> *SatPct99.99*
>> *MovOOB 0*
>> *optschema 1*
>> *Reading in mov BS7_PET.lps.nii.gz*
>> *Reading in ref
>> /NAS/tupac/matthieu/FS5.3//207118_M0_2014-01-29/mri/brainmask.mgz*
>> *Reading in and applying refmask
>> /NAS/tupac/matthieu/FS5.3//207118_M0_2014-01-29/mri/aparc+aseg.mgz*
>> *Setting cras translation parameters to align centers*
>> *Creating random numbers for coordinate dithering*
>> *Performing intensity dithering*
>> *Initial parameters 20.9141 11.8161 149.1538  0.  0.  0.
>>  1.  1.  1.  0.  0.  0. *
>> *Separation list (2):  4  2   min = 2*
>> *DoSmoothing 1*
>> *DoCoordDither 1*
>> *DoIntensityDither 1*
>> *nitersmax 4*
>> *ftol 1.000e-07*
>> *linmintol 1.000e-03*
>> *SatPct 99.99*
>> *Hist FWHM 7.00 7.00*
>> *nthreads 1*
>> *movsat = 10897.7666*
>> *mov gstd 0.8459 0.8459 0.8459*
>> *Smoothing mov*
>> *refsat = 119.*
>> *ref gstd 0.8459 0.8459 0.8459*
>> *Smoothing ref*
>> *COREGpreproc() done*
>> *Testing if mov and target overlap*
>> *Init cost   -1.0011578057*
>> *nhits = 262144 out of 16777216, Percent Overlap: 100.0*
>> *Initial  RefRAS-to-MovRAS*
>> * 1.0   0.0   0.0   20.91408;*
>> * 0.0   1.0   0.0   11.81612;*
>> * 0.0   0.0   1.0   149.15384;*
>> * 0.0   0.0   0.0   1.0;*
>> *Initial  RefVox-to-MovVox*
>> * 1.0   0.0   0.0   0.0;*
>> * 0.0   0.0  -1.0   255.0;*
>> * 0.0  -1.0   0.0   255.0;*
>> * 0.0   0.0   0.0   1.0;*
>> *sep = 4 ---*
>> *COREGoptBruteForce() 30 1 30*
>> *Turning on MovOOB for BruteForce Search*
>> *#BF# sep= 4 iter=0 lim=30.0 delta=2.00   4.91408  21.81612 119.15384
>> 2.0   0.0   0.0   -1.0078773*
>> *Turning  MovOOB back off after brute force search*
>>
>>
>> *-*
>> *Init Powel Params dof = 6*
>> *Starting OpenPowel2(), sep = 4*
>> *InitialCost-1.0076701641 *
>> *#@#  4  188  4.91408 21.81612 119.15384 2.0 0.0 0.0
>> -1.0076702*
>> *fs_powell::minimize*
>> *  nparams 6*
>> *  maxfev 4*
>> *  ftol   0.00*
>> *  linmin_xtol_   0.001000*
>> *  powell nthiter 0: fret = -1.007670*
>> *#@#  4  197  4.93866 21.81612 119.15384 2.0 0.0 0.0
>> -1.0076704*
>> *#@#  4  198  4.96905 21.81612 119.15384 2.0 0.0 0.0
>> -1.0076705*
>> *#@#  4  209  4.97536 20.19808 119.15384 2.0 0.0 0.0
>> -1.0077189*
>> *#@#  4  210  4.97536 19.55424 119.15384 2.0 0.0 0.0
>> -1.0077529*
>> *#@#  4  211  4.97536 18.51247 119.15384 2.0 0.0 0.0
>> -1.0078081*
>> *#@#  4  212  4.97536 16.82685 119.15384 2.0 0.0 0.0
>> -1.0078434*
>> *#@#  4  213  4.97536 16.77889 119.15384 2.0 0.0 0.0
>> -1.0078460*
>> *#@#  4  214  4.97536 16.70129 119.15384 2.0 0.0 0.0
>> -1.0078515*
>> *#@#  4  215  4.97536 16.57572 119.15384 2.0 0.0 0.0
>> -1.0078617*
>> *#@#  4  216  4.97536 16.37254 119.15384 2.0 0.0 0.0
>> -1.0078768*
>> *#@#  4  217  4.97536 14.89926 119.15384 2.0 0.0 0.0
>> -1.0079292*
>> *#@#  4  218  4.97536 14.85724 119.15384 2.0 0.0 0.0
>> -1.0079303*
>> *#@#  4  219  4.97536 12.95773 119.15384 2.0 0.0 0.0
>> -1.0079467*
>> *#@#  4  220  4.97536 13.40911 119.15384 2.0 0.0 0.0
>> -1.0079498*
>> *#@#  4  223  4.97536 13.62039 119.15384 2.0 0.0 0.0
>> -1.0079516*
>> *#@#  4  229  4.97536 13.61634 117.53580 2.0 0.0 0.0
>> -1.0086172*
>> *#@#  4  230  4.97536 13.61634 80.23408 2.0 0.0 0.0
>> -1.0266197*
>> *#@#  4  235  4.97536 13.61634 69.09492 2.0 0.0 0.0
>> -1.0285894*
>> *#@#  4  236  4.97536 13.61634 69.00322 2.0 0.0 0.0
>> -1.0285913*
>> *#@#  4  237  4.97536 13.61634 68.30045 2.0 0.0 0.0
>> -1.0285933*
>> 

Re: [Freesurfer] Extracting thickness values using labels

[Douglas Greve]

The easiest way to to re-run mris_preproc without the --paired-diff to 
get a stack of all your data, then run


mri_segstats --i stackwithalldata.smoothed.mgh --seg ocn.mgh --excludeid 
0 --avgwf ocn.dat


ocn.mgh is the ocn file (output cluster number), and ocn.dat will be a 
table with each input from diff.fsgd on the rows and each cluster on the 
columns



On 10/6/16 2:23 AM, Anders Hougaard wrote:

Dear Freesurfers,

This is probably a very basic question, but I was unable to find an 
answer in the mailing list:


I did a paired cortical thickness group analysis:

mris_preproc --fsgd /home/paired.fsgd --target fsaverage --hemi lh 
--meas thickness --out lh.paired.00.mgh --paired-diff


(smoothing)

mri_glmfit --y lh.paired.05.mgh --fsgd diff.fsgd --osgm --surf 
fsaverage lh --cortex --glmdir lh.05_diff.glmdir


I found an area of difference in cortical thickness and I would like 
to know the thickness values of this area for all of the input in 
paired.fsgd, not just the differences I get from the y.ocn.dat file.


How do I extract thickness values from the lh.paired.00.mgh file using 
the label file of the significant cluster?


All the best,
Anders



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Re: [Freesurfer] mri_average vs mri_concat

[Douglas Greve]

What are the pixel values in the mgz file? They should be binary, ie, 
1=in a label, 0 = out of label



On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote:

Overlays in .mgz format using mri_vol2surf

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve 
> wrote:


what is a labeled vertex? What file format? mgz? annot?


On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
> the source files are labelled vertices from 20 subjects:
>
> -T1s were labelled using an MNI software
> -Surfaces were created in FreeSurfer and surface overlays of the
> labels were created using mri_vol2surf
> -Surface overlays were registered to fsaverage using
mri_surf2surf and
> then averaged to create a probability map, originally using
"mri_average"
>
> So, essentially the overlays are binary files of my labels I believe
> - I can send one over if you wish.
>
> Trisanna
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve
> 
>> wrote:
>
> what are the source files ("all files"). What data type,
value range,
> where did they come from?
>
>
> On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
> > Hi Doug
> >
> > So, of course now it works without --keep-filetype... :p
it looks
> > pretty much the same was when I use --keep-filetype.
> >
> > However, the values of Min and Max are still odd (out of
256) - see
> > snapshot
> >
> > Trisanna
> >
> >
> >
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve
> > 
>
> 
>  >
> > Depending upon the type of the data, the
--keep-datatype may
> mess
> > things
> > up quite a bit. What happens if you don't include that? It
> will not
> > create an annotation. maybe you mean some other file type?
> >
> >
> > On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote:
> > >
> > > Hi Doug
> > >
> > > I spoke with you at the Freesurfer tutorial last week
> about using
> > > mri_average to average my sulcal labels and get a
> probability map on
> > > fsaverage. You had suggested using "mri_concat" instead,
> which is a
> > > newer command. So, I performed the following command:
> > >
> > > *mri_concat all files --o output.mgz --mean
--keep-datatype*
> > >
> > > I had to put --keep-datatype or else it tried to
create an
> annot
> > file.
> > >
> > > This worked just fine.
> > >
> > > My question then is concerning *the min and max values
> *when this
> > > average is overlayed in Freeview. See the snapshot
> attached. The
> > > values seem to be based on 256 instead of percentage and
> this is
> > what
> > > happens when I used "mri_average" without specifying the
> "-p". Is
> > > there a way to illustrate the values in percentage in a
> similar way
> > > with mri_concat?
> > >
> > > Many thanks!
> > >
> > > Trisanna
> > >
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu

> >
> > 
> 

Re: [Freesurfer] mri_average vs mri_concat

[Trisanna Sprung-Much]

Overlays in .mgz format using mri_vol2surf

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve 
wrote:

> what is a labeled vertex? What file format? mgz? annot?
>
>
> On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
> > the source files are labelled vertices from 20 subjects:
> >
> > -T1s were labelled using an MNI software
> > -Surfaces were created in FreeSurfer and surface overlays of the
> > labels were created using mri_vol2surf
> > -Surface overlays were registered to fsaverage using mri_surf2surf and
> > then averaged to create a probability map, originally using "mri_average"
> >
> > So, essentially the overlays are binary files of my labels I believe
> > - I can send one over if you wish.
> >
> > Trisanna
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve
> > > wrote:
> >
> > what are the source files ("all files"). What data type, value range,
> > where did they come from?
> >
> >
> > On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
> > > Hi Doug
> > >
> > > So, of course now it works without --keep-filetype... :p it looks
> > > pretty much the same was when I use --keep-filetype.
> > >
> > > However, the values of Min and Max are still odd (out of 256) - see
> > > snapshot
> > >
> > > Trisanna
> > >
> > >
> > >
> > >
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > > On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve
> > > 
> >  > >> wrote:
> > >
> > > Depending upon the type of the data, the --keep-datatype may
> > mess
> > > things
> > > up quite a bit. What happens if you don't include that? It
> > will not
> > > create an annotation. maybe you mean some other file type?
> > >
> > >
> > > On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote:
> > > >
> > > > Hi Doug
> > > >
> > > > I spoke with you at the Freesurfer tutorial last week
> > about using
> > > > mri_average to average my sulcal labels and get a
> > probability map on
> > > > fsaverage. You had suggested using "mri_concat" instead,
> > which is a
> > > > newer command. So, I performed the following command:
> > > >
> > > > *mri_concat all files --o output.mgz --mean --keep-datatype*
> > > >
> > > > I had to put --keep-datatype or else it tried to create an
> > annot
> > > file.
> > > >
> > > > This worked just fine.
> > > >
> > > > My question then is concerning *the min and max values
> > *when this
> > > > average is overlayed in Freeview. See the snapshot
> > attached. The
> > > > values seem to be based on 256 instead of percentage and
> > this is
> > > what
> > > > happens when I used "mri_average" without specifying the
> > "-p". Is
> > > > there a way to illustrate the values in percentage in a
> > similar way
> > > > with mri_concat?
> > > >
> > > > Many thanks!
> > > >
> > > > Trisanna
> > > >
> > > >
> > > > --
> > > > Ph.D. Candidate
> > > > McGill University
> > > > Integrated Program in Neuroscience
> > > > Psychology
> > > >
> > > >
> > > >
> > > > ___
> > > > 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
> > 
> > > 

Re: [Freesurfer] Processing 7T data

[Bruce Fischl]

Hi Damein

6.0 beta will handle this *much* better if you can wait.

cheers
Bruce
On Thu, 6 Oct 2016, 
Damien MARIE wrote:

> Dear experts,
>
> I plan to process some MRI 7T data, 0.6 mm^3 isotropic voxel size. The aim is 
> to look a R1 maps.
>
> I was wondering what was your opinion concerning the downsampling to 1 mm^3 
> (performed by the current FreeSurfer version if I am correct). What do you 
> think would be the best: FreeSurfer 5.3 , FreeSurfer 5.3-HCP or FreeSurfer 
> beta 6.0?
>
> Thank You and Best,
>
> Damien
>
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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[Freesurfer] Job opening: AFNI group (NIMH, NIH, USA)

[P Taylor]

 There is a job opening in the AFNI group at NIHM, NIH, USA.

Please see this link if you or someone you know is a scientific programmer:
https://kelly.secure.force.com/CandidateExperience/CandExpJobDetails?id=a7V8000PChaEAG=true

Applications are made directly through the Kelly Services company (not
through the AFNI group itself).

If you have questions, please feel free to email:
Robert W Cox, PhD
Director, Scientific and Statistical Computing Core (AKA the AFNI group)
NIMH & NIH
email: robert...@mail.nih.gov
http://afni.nimh.nih.gov
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Re: [Freesurfer] Processing 7T data

[Falk Lüsebrink]

Hi Damien,

depending on what you want to do you are forced to use the stable release. The 
developmental version of FreeSurfer should be used for testing only, not 
publishing results.

Following the notes of the HiResRecon 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon) you should be able to 
process your data with version 5.1 and above at native resolution. However, 
this affects the surfaces based processing only as the aseg.mgz is simply 
upsampled from previously downsampled data. There are also a few methods to 
make use of the native resolution which I haven't tested in recent past, e.g. 
using the surface of the downsampled data on the native data. Otherwise you 
will have to downsample you data to 1mm using v5.3.

Version 6 will be able to handle high resolution data at native resolution 
using the -hires flag, making the workaround of the HiResRecon obsolete. Having 
tested the developmental version (from mid September) on several high 
resolution 7T datasets it seems to work nicely and is less laborious than 
before. I haven't compared results between v5.3 and v6 though.

Best,
Falk

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Damien MARIE
Gesendet: Donnerstag, 6. Oktober 2016 14:01
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Processing 7T data

Dear experts,

I plan to process some MRI 7T data, 0.6 mm^3 isotropic voxel size. The aim is 
to look a R1 maps.

I was wondering what was your opinion concerning the downsampling to 1 mm^3 
(performed by the current FreeSurfer version if I am correct). What do you 
think would be the best: FreeSurfer 5.3 , FreeSurfer 5.3-HCP or FreeSurfer beta 
6.0?

Thank You and Best,

Damien

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[Freesurfer] Postdoctoral Fellowship at the Martinos Center

[Baran, Bengi]

We believe this posting may be of interest for some members of the group:


Postdoctoral Fellowship at the Martinos Center for Biomedical Imaging and the 
Psychiatric Neuroimaging.
Division of the Psychiatry Department at Massachusetts General Hospital, 
Charlestown, MA.
Project: Multimodal neuroimaging studies of sleep and memory
PI: Dara S. Manoach, Ph.D.


The position will involve investigating the role of sleep in memory 
consolidation, how these processes go awry in schizophrenia and autism, and the 
efficacy of pharmacological and other interventions. Our work has linked 
cognitive deficits to a specific heritable mechanism (sleep spindles) and we 
are seeking effective interventions. In collaboration with Dr. Robert 
Stickgold’s lab at Beth Israel Deaconess Medical Center, we are extending and 
expanding this basic and clinical research program using state-of-the art tools 
including high density EEG (polysomnography), MEG, DTI, functional connectivity 
MRI, fMRI, and behavioral studies. We are seeking someone to participate in 
these foundation and NIMH-funded investigations who is familiar with MEG/EEG 
methodology and data analysis, comfortable with methodological innovation, and 
is interested in optimizing and developing analysis streams tailored to the 
study aims and populations. New approaches and ideas are encouraged, as are 
independent projects that dovetail with current studies. The position requires 
working closely with the PI, as well as with Dr. Stickgold, other Martinos 
Center investigators, particularly Dr. Matti Hamalainen, Director of the MEG 
Core Lab, and lab mates to design studies, acquire data, and develop, explore, 
improve and apply data analytic techniques. Training in clinical research and 
in the acquisition, analysis, and interpretation of neuroimaging data will be 
provided.

Requirements: PhD or MD Experience with MEG/EEG data analysis/methodology 
and/or other signal processing. Background in cognitive neuroscience, 
experimental psychology, and an interest in clinical applications are a plus.

Position available immediately. Interested applicants should email: (a) CV, (b) 
statement of post-doctoral and career goals, (c) writing sample (e.g., a 
published manuscript), and (d) letters and/or contact information for three 
references to Dara Manoach 
dara.mano...@mgh.harvard.edu
Stipend levels are in line with experience and NIH. A two-year commitment is 
required.



Best,




Bengi Baran, Ph.D.
Post-Doctoral Fellow
Martinos Center for Biomedical Imaging
Harvard Medical School
Massachusetts General Hospital
149 13th Street
Charlestown Navy Yard
Charlestown, MA 02129
email: bba...@mgh.harvard.edu
phone: 617-643-7964
fax: 617-726-4078
https://sleep.med.harvard.edu/people/trainees/1598/Bengi+Baran+MA+PhD



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Re: [Freesurfer] Postdoctoral Fellowship at the Martinos Center

[Smaragdi A.]

For you xx

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Baran, Bengi 
[bba...@mgh.harvard.edu]
Sent: 06 October 2016 14:35
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Postdoctoral Fellowship at the Martinos Center

We believe this posting may be of interest for some members of the group:


Postdoctoral Fellowship at the Martinos Center for Biomedical Imaging and the 
Psychiatric Neuroimaging.
Division of the Psychiatry Department at Massachusetts General Hospital, 
Charlestown, MA.
Project: Multimodal neuroimaging studies of sleep and memory
PI: Dara S. Manoach, Ph.D.


The position will involve investigating the role of sleep in memory 
consolidation, how these processes go awry in schizophrenia and autism, and the 
efficacy of pharmacological and other interventions. Our work has linked 
cognitive deficits to a specific heritable mechanism (sleep spindles) and we 
are seeking effective interventions. In collaboration with Dr. Robert 
Stickgold’s lab at Beth Israel Deaconess Medical Center, we are extending and 
expanding this basic and clinical research program using state-of-the art tools 
including high density EEG (polysomnography), MEG, DTI, functional connectivity 
MRI, fMRI, and behavioral studies. We are seeking someone to participate in 
these foundation and NIMH-funded investigations who is familiar with MEG/EEG 
methodology and data analysis, comfortable with methodological innovation, and 
is interested in optimizing and developing analysis streams tailored to the 
study aims and populations. New approaches and ideas are encouraged, as are 
independent projects that dovetail with current studies. The position requires 
working closely with the PI, as well as with Dr. Stickgold, other Martinos 
Center investigators, particularly Dr. Matti Hamalainen, Director of the MEG 
Core Lab, and lab mates to design studies, acquire data, and develop, explore, 
improve and apply data analytic techniques. Training in clinical research and 
in the acquisition, analysis, and interpretation of neuroimaging data will be 
provided.

Requirements: PhD or MD Experience with MEG/EEG data analysis/methodology 
and/or other signal processing. Background in cognitive neuroscience, 
experimental psychology, and an interest in clinical applications are a plus.

Position available immediately. Interested applicants should email: (a) CV, (b) 
statement of post-doctoral and career goals, (c) writing sample (e.g., a 
published manuscript), and (d) letters and/or contact information for three 
references to Dara Manoach 
dara.mano...@mgh.harvard.edu
Stipend levels are in line with experience and NIH. A two-year commitment is 
required.



Best,




Bengi Baran, Ph.D.
Post-Doctoral Fellow
Martinos Center for Biomedical Imaging
Harvard Medical School
Massachusetts General Hospital
149 13th Street
Charlestown Navy Yard
Charlestown, MA 02129
email: bba...@mgh.harvard.edu
phone: 617-643-7964
fax: 617-726-4078
https://sleep.med.harvard.edu/people/trainees/1598/Bengi+Baran+MA+PhD




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Re: [Freesurfer] Processing 7T data

[Kevin Aquino]

Hi Damien,

I have tested using the HighResRecon vs Freesurfer beta on 0.7 mm^3 data
and have preferred the segmentations on the beta version.

Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
www.physics.usyd.edu.au/~aquino/

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

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Please think of our environment and only print this e-mail if necessary.


On Thu, Oct 6, 2016 at 1:01 PM, Damien MARIE  wrote:

> Dear experts,
>
> I plan to process some MRI 7T data, 0.6 mm^3 isotropic voxel size. The aim
> is to look a R1 maps.
>
> I was wondering what was your opinion concerning the downsampling to 1
> mm^3 (performed by the current FreeSurfer version if I am correct). What do
> you think would be the best: FreeSurfer 5.3 , FreeSurfer 5.3-HCP or
> FreeSurfer beta 6.0?
>
> Thank You and Best,
>
> Damien
>
> ___
> 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.
>
>
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[Freesurfer] Processing 7T data

[Damien MARIE]

Dear experts,

I plan to process some MRI 7T data, 0.6 mm^3 isotropic voxel size. The aim is 
to look a R1 maps.

I was wondering what was your opinion concerning the downsampling to 1 mm^3 
(performed by the current FreeSurfer version if I am correct). What do you 
think would be the best: FreeSurfer 5.3 , FreeSurfer 5.3-HCP or FreeSurfer beta 
6.0?

Thank You and Best,

Damien

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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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Re: [Freesurfer] ERROR: QdecGlmDesign::Create: bad factor!

[Nabin Koirala]

The problem is solved. There was an error in table format.

Thank you.

Regards,
Nabin

On Wed, Oct 5, 2016 at 6:56 PM, Nabin Koirala 
wrote:

> Dear freesurfer team,
>
> I was trying to run QDEC with two discrete factors but I got this error
> and could not quite figure out what is wrong. Your suggestion would be
> highly appreciated. The table and the error is as shown below:
>
>
> Data table /Applications/freesurfer/subjects/qdec/qdec.table.dat loaded.
> Verifying subject 
> dataSubject
> verification complete.
> Input table: /Applications/freesurfer/subjects/qdec/qdec.table.dat
> Subj#, SubjID, Data...
> 1 SubBSF0_01 Pre BSF
> 2 SubBSF0_02 Pre BSF
> 3 SubBSF0_03 Pre BSF
> 4 SubBSF0_04 Pre BSF
> 5 SubBSF0_05 Pre BSF
> 6 SubBSF0_06 Pre BSF
> 7 SubBSF0_07 Pre BSF
> 8 SubBSF0_08 Pre BSF
> 9 SubBSF0_09 Pre BSF
>10 SubBSF0_10 Pre BSF
>11 SubBSF0_11 Pre BSF
>12 SubBSF0_12 Pre BSF
>13 SubBSF0_13 Pre BSF
>14 SubBSF0_14 Pre HFS
>15 SubBSF0_15 Pre HFS
>16 SubBSF0_16 Pre HFS
>17 SubBSF0_17 Pre HFS
>18 SubBSF0_18 Pre HFS
>19 SubBSF0_19 Pre HFS
>20 SubBSF0_20 Pre HFS
>21 SubBSF0_21 Pre HFS
>22 SubBSF0_22 Pre HFS
>23 SubBSF0_23 Pre HFS
>24 SubBSF0_24 Pre HFS
>25 SubBSF0_25 Pre HFS
>26 SubBSF0_26 Pre HFS
>27 SubBSF1_01 Post BSF
>28 SubBSF1_02 Post BSF
>29 SubBSF1_03 Post BSF
>30 SubBSF1_04 Post BSF
>31 SubBSF1_05 Post BSF
>32 SubBSF1_06 Post BSF
>33 SubBSF1_07 Post BSF
>34 SubBSF1_08 Post BSF
>35 SubBSF1_09 Post BSF
>36 SubBSF1_10 Post BSF
>37 SubBSF1_11 Post BSF
>38 SubBSF1_12 Post BSF
>39 SubBSF1_13 Post BSF
>40 SubBSF1_14 Post HFS
>41 SubBSF1_15 Post HFS
>42 SubBSF1_16 Post HFS
>43 SubBSF1_17 Post HFS
>44 SubBSF1_18 Post HFS
>45 SubBSF1_19 Post HFS
>46 SubBSF1_20 Post HFS
>47 SubBSF1_21 Post HFS
>48 SubBSF1_22 Post HFS
>49 SubBSF1_23 Post HFS
>50 SubBSF1_24 Post HFS
>51 SubBSF1_25 Post HFS
>52 SubBSF1_26 Post HFS
> 1  Time  discrete 2
> 1  Pre
> 2  Post
> 2  Group  discrete 2
> 1  BSF
> 2  HFS
> Continuous Factors: Mean:   StdDev:
> --- -   ---
>
> Number of subjects:   52
> Number of factors:2 (2 discrete, 0 continuous)
> Number of classes:4
> Number of regressors: 4
> 
> Data table loading completed successfully.
> SUBJECTS_DIR is '/Applications/freesurfer/subjects'
> ERROR: QdecDataTable::GetFactor: '' is not in datatable!
> ERROR: QdecGlmDesign::Create: bad factor!
>
> Thank you.
>
> Regards,
> Nabin
>
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[Freesurfer] Extracting thickness values using labels

[Anders Hougaard]

Dear Freesurfers,

This is probably a very basic question, but I was unable to find an answer
in the mailing list:

I did a paired cortical thickness group analysis:

mris_preproc --fsgd /home/paired.fsgd --target fsaverage --hemi lh --meas
thickness --out lh.paired.00.mgh --paired-diff

(smoothing)

mri_glmfit --y lh.paired.05.mgh --fsgd diff.fsgd --osgm --surf fsaverage lh
--cortex --glmdir lh.05_diff.glmdir

I found an area of difference in cortical thickness and I would like to
know the thickness values of this area for all of the input in paired.fsgd,
not just the differences I get from the y.ocn.dat file.

How do I extract thickness values from the lh.paired.00.mgh file using the
label file of the significant cluster?

All the best,
Anders
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