Re: [Freesurfer] Gamma / Histogram

[Anders Hougaard]

Excellent, thanks!

2016-10-12 20:27 GMT+02:00 Douglas N Greve :

>
>
> On 10/08/2016 02:43 AM, Anders Hougaard wrote:
> > Dear Freesurfers,
> >
> > Please see the attached image.
> > It shows inflated fsaverage surface with gamma.mgh overlaid.
> > Gamma.mgh is from one contrast of a standard group analysis of
> > cortical thickness (two groups A and B, two contrasts A>B and B>A).
> >
> > 1) Is it correct to interpret the gamma values as between-group
> > difference of cortical thickness in mm?
> It depends on how you set up the contrast. If it is a simple A vs B,
> then yes, mm is correct.
> >
> > 2) I would like to reproduce the histogram in another software. Is it
> > possible to extract the gamma values for each vertex for this purpose?
> You can do it in matlab easily enough, eg,
> gamma = MRIread('gamma.mgh');
> gamma.vol will be the pixel values
> >
> > All the best,
> > Anders
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Cortical Thickness Zero Values

[Taha Abdullah]

Hello All,

Quick question, I ran recon-all with the qcache option and after converting
the ?.thickness.fsaverage.mgh to an ascii text file via mri_convert I am
noticing some vertices have 0mm thickness and it varies, for example, one
subject had 53 vertices labeled as zeros while another had over 9,000
vertices. Is there a method I can use to have a thickness value for each of
the 163000+ vertices? I am not sure if this is a possible registration
issue to mni305.

Thanks in advance,
Taha
-- 
*Taha Abdullah*
*Department of Physiology,*

*Northwestern University Feinberg School of Medicine*
*MS in Physiology and Biophysics, Georgetown University 2015*
*Work Cell: (312)-451-8468*
___
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.

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

[Douglas N Greve]

you need to go back to the source data. At some point someone set or 
changed the voxel size to the wrong thing. This can sometimes happen in 
PET as reconstruction into volumes is not all that standardizeed


On 10/12/2016 06:12 PM, Matthieu Vanhoutte wrote:
>
> Thank you for your diagnosis Douglas. How could I get the voxel sizes 
> right from input nifti pet and mri data ?
>
> Best regards,
> Matthieu
>
>
> Le 12 oct. 2016 10:05 PM, "Douglas N Greve"  > a écrit :
>
> The problem appears to be that the PET or the MRI (or both) have
> incorrect voxel sizes (about 15%). You need to fix the problem.
> You can
> get a decent registration using something like
>
> mri_coreg --mov BS7_PET.lps.nii.gz --s 207118_FS_Filedrop --reg
> dof9.wb.lta --dof 9 --no-ref-mask --ref mri/orig.mgz
>
> with 9 DOF instead of 6 to account for the scaling (voxel size error).
> But it is *much* better to get the voxel sizes right and use 6 dof
>
>
> On 10/06/2016 02:50 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;/
>

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

[Matthieu Vanhoutte]

Thank you for your diagnosis Douglas. How could I get the voxel sizes right
from input nifti pet and mri data ?

Best regards,
Matthieu

Le 12 oct. 2016 10:05 PM, "Douglas N Greve"  a
écrit :

> The problem appears to be that the PET or the MRI (or both) have
> incorrect voxel sizes (about 15%). You need to fix the problem. You can
> get a decent registration using something like
>
> mri_coreg --mov BS7_PET.lps.nii.gz --s 207118_FS_Filedrop --reg
> dof9.wb.lta --dof 9 --no-ref-mask --ref mri/orig.mgz
>
> with 9 DOF instead of 6 to account for the scaling (voxel size error).
> But it is *much* better to get the voxel sizes right and use 6 dof
>
>
> On 10/06/2016 02:50 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/
> >> /  

[Freesurfer] Error long_mris_slopes

[tom parker]

Dear FreeSurfers,

I've been trying to run a longitudinal cortical thickness analysis in
FreeSurfer but unfortunately, so far, it has not worked.

After preprocessing the data following the instructions from the tutorial,
I tried running:
*long_mris_slopes --qdec /Volumes/WD/Long/qdec/long.qdec.table.dat --meas
thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack
--do-label --time years --qcache fsaverage --sd /Volumes/WD/Long/*

And the following error came out:

*Parsing the qdec table: /Volumes/WD/Long/qdec/long.qdec.table.datERROR:
qdec table /Volumes/WD/Long/qdec/long.qdec.table.dat not found or empty?*

The path is correct and there are no empty lines in the file.

When I ran:
*mris_preproc --debug --qdec-long qdec/long.qdec.table.dat*

This comes out:




























*set echo = 1 ;set debug = 1 ;set debug = 1breakswbreakswendendwhile (
$#argv != 0 )while ( 2 != 0 )set flag = $argv[1] ; shift ;set flag =
--qdec-longshiftswitch ( $flag )switch ( --qdec-long )if ( $#argv == 0 )
goto arg1err ;if ( 1 == 0 ) goto arg1errset fsgdf = $argv[1] ; shift ;set
fsgdf = qdec/long.qdec.table.datshiftif ( ! -e $fsgdf ) thenif ( ! -e
qdec/long.qdec.table.dat ) thenecho "ERROR: cannot find $fsgdf" ;echo
ERROR: cannot find qdec/long.qdec.table.datERROR: cannot find
qdec/long.qdec.table.datexit 1 ;exit 1*

Do you have any idea why this is happening?

Thank you so much!
___
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.

Re: [Freesurfer] Remapping Volume

[Crawford, Anna]

That seems to have worked and the regions are solid now.

Thank you!

Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, October 12, 2016 2:53 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Remapping Volume

Try adding --projfrac 0.5


On 10/12/2016 11:29 AM, Crawford, Anna wrote:
> I did:
>
> mri_vol2surf --src 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+asegRMnn.mgz
>  --out 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegRMnnS.mgh
>  --regheader segfs --hemi lh --surf white --out_type mgh --fixtkreg
>
> which resulted in the same type of surface. I looked at the volume and it 
> seemed as though things were labeled correctly. The images are attached.
>
> Thanks,
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, October 12, 2016 10:47 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Remapping Volume
>
> that seems ok, as I think the default is nearest neighbor. Can you
> visualize the volume you created and see if the incorrect labels are in
> it?
>
> On Wed, 12 Oct 2016, Crawford, Anna wrote:
>
>> I used:
>>
>> --src 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+asegRMpostcent2.mgz
>>  --out 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegRMpostcent2S.mgh
>>  --regheader segfs --hemi lh --surf white --out_type mgh
>>
>>>  From the help file online, it looks like --fixtkreg would be used for the 
>>> nearest neighbor. What is the proper flag to set it to use nearest neighbor 
>>> interpolation?
>> Thanks,
>> Anna
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, October 11, 2016 10:29 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Remapping Volume
>>
>> what was your vol2surf command line? Make sure that it is using nearest
>> neighbor interpolation
>> On Tue, 11 Oct 2016, Crawford, Anna wrote:
>>
>>> Hi,
>>>
>>> I am trying to remap a volume. I am using aparc+aseg.mgz volume. I loaded it
>>> into Matlab using load_mgh. In Matlab I remap the volume to different
>>> values. For example, all original values of 1022 will become 200 and all
>>> 1030 values will become 150. (This is just an example, not necessarily these
>>> numbers.) I save a new aparc+asegNew.mgz file using save_mgh. I use the same
>>> M and mr_parms that I got when I loaded in the original file. I'm not sure
>>> what these mean or if I need to change them. Then I use mri_vol2surf to
>>> create a new surface overlay onto the inflated hemisphere. When I do this,
>>> each region such as post central gyrus is 2 colors spotted together instead
>>> of a solid color like in the original. I have attached pictures as an
>>> example of what the original and remapped looked like. I didn't change the
>>> location of values, just simple gave each value a new one. Why is the one
>>> value speckled throughout?
>>>
>>> Thank you,
>>> Anna
>>>
>>> ===
>>>
>>> Please consider the environment before printing this e-mail
>>>
>>> Cleveland Clinic is ranked as one of the top hospitals in America by
>>> U.S.News & World Report (2015). Visit us online at
>>> http://www.clevelandclinic.org for a complete listing of our services, staff
>>> and locations. Confidentiality Note: This message is intended for use only
>>> by the individual or entity to which it is addressed and may contain
>>> information that is privileged, confidential, and exempt from disclosure
>>> under applicable law. If the reader of this message is not the intended
>>> recipient or the employee or agent responsible for delivering the message to
>>> the intended recipient, you are hereby notified that any dissemination,
>>> distribution or copying of this communication is strictly prohibited. If you
>>> have received this communication in error, please contact the sender
>>> immediately and destroy the material in its entirety, whether electronic or
>>> hard copy. Thank you.
>>>
>>>
>> ___
>> 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 

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

[Douglas N Greve]

The problem appears to be that the PET or the MRI (or both) have 
incorrect voxel sizes (about 15%). You need to fix the problem. You can  
get a decent registration using something like

mri_coreg --mov BS7_PET.lps.nii.gz --s 207118_FS_Filedrop --reg 
dof9.wb.lta --dof 9 --no-ref-mask --ref mri/orig.mgz

with 9 DOF instead of 6 to account for the scaling (voxel size error). 
But it is *much* better to get the voxel sizes right and use 6 dof


On 10/06/2016 02:50 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  

[Freesurfer] Checking Longitudinal Runs

[Tamara Tavares]

Hello Experts,

I have a question regarding the outputs to the longitudinal processing
stream.

I ran my two participant's scans through the Cross, then created a Base and
two longitudinal runs. I am primarily interested in looking at ventricular
change over time. Other than the aseg output overlaid on the brainmask,
should I look at any other outputs to ensure the longitudinal process ran
correctly?

Thank you in advance for your help,
Tamara
___
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.

Re: [Freesurfer] Fdr correction using command line

[neuroimage analyst]

Thank you for that clarification,Doug.

VM

On Oct 12, 2016 12:09 PM, "Douglas N Greve" 
wrote:

> The sign depends on how you set up the contrast. If you are using an
> FSGD file and have two classes A and B and a contrast [+1 -1], then
> positive indicates A>B. The F.mgh is the map of F values which are
> unsigned. The gamma.mgh file will have the contrast values themselves
> including sign. The sig.mgh will be the -log10(p) signed by the sign of
> gamma.mgh at that vertex
>
>
> On 10/12/2016 02:23 PM, neuroimage analyst wrote:
> > Thanks, Doug for the binary.
> >
> >  A quick follow-up: what does the sign in either
> > mri_glmfit-sim/mri_fdr indicate? When I open F.mgh, the values are
> > only positive and p-values obtained from them has sign of +/-. My
> > understanding is + indicates where mean_A>mean_B and vice versa.
> >
> > If for example, I am interested in mean_A>mean_B then should I pass
> > --pos (mri_fdr) or --cache 2.30101 pos (mri_glmfit-sim for uncorrected
> > cluster defining threshold of p<0.005)  in the contrast that was
> > designed for that test?
> >
> > Regards
> >
> > MV
> >
> > On Wed, Oct 12, 2016 at 10:27 AM, Douglas N Greve
> > > wrote:
> >
> > try this binary
> >
> > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr
> > 
> >
> >
> >
> > On 10/07/2016 04:11 PM, neuroimage analyst wrote:
> > >
> > > Hi,
> > >
> > > I was wondering if there is a way to perform fdr correction using
> > > command line in freesurfer without using matlab as
> > mri_glmfit-sim only
> > > does bonferroni ?
> > >
> > > Thanks
> > > Regards
> > > MV
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > 
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > 
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> >
> >
> > The information in this e-mail is intended only for the person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in error and
> > the e-mail
> > contains patient information, please contact the Partners
> > Compliance HelpLine at
> > http://www.partners.org/complianceline
> >  . If the e-mail was sent
> > to you in error
> > but does not contain patient information, please contact the
> > sender and properly
> > dispose of the e-mail.
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
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 

Re: [Freesurfer] Fdr correction using command line

[Douglas N Greve]

The sign depends on how you set up the contrast. If you are using an 
FSGD file and have two classes A and B and a contrast [+1 -1], then 
positive indicates A>B. The F.mgh is the map of F values which are 
unsigned. The gamma.mgh file will have the contrast values themselves 
including sign. The sig.mgh will be the -log10(p) signed by the sign of 
gamma.mgh at that vertex


On 10/12/2016 02:23 PM, neuroimage analyst wrote:
> Thanks, Doug for the binary.
>
>  A quick follow-up: what does the sign in either 
> mri_glmfit-sim/mri_fdr indicate? When I open F.mgh, the values are 
> only positive and p-values obtained from them has sign of +/-. My 
> understanding is + indicates where mean_A>mean_B and vice versa.
>
> If for example, I am interested in mean_A>mean_B then should I pass 
> --pos (mri_fdr) or --cache 2.30101 pos (mri_glmfit-sim for uncorrected 
> cluster defining threshold of p<0.005)  in the contrast that was 
> designed for that test?
>
> Regards
>
> MV
>
> On Wed, Oct 12, 2016 at 10:27 AM, Douglas N Greve 
> > wrote:
>
> try this binary
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr
> 
>
>
>
> On 10/07/2016 04:11 PM, neuroimage analyst wrote:
> >
> > Hi,
> >
> > I was wondering if there is a way to perform fdr correction using
> > command line in freesurfer without using matlab as
> mri_glmfit-sim only
> > does bonferroni ?
> >
> > Thanks
> > Regards
> > MV
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> 
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline
>  . If the e-mail was sent
> to you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

Re: [Freesurfer] question about Unpaired T-test group analysis

[Douglas N Greve]

On 10/11/2016 11:41 AM, kinson li wrote:
> /Hello, /
> /
> /
> /Question 1: I would like to conduct an Unpaired T-test group 
> analysis, I have two group of people, Group A8 age is 8 and Group A9 
> age is 9, and I to test the/ change in thickness with age. But I am 
> little confusion about the matirx and FSGD design. I am appreciated if 
> you can take a look at my FSGD file and Matrix file. Please correct me 
> if I am wrong,
that looks right. The contrast will comppute A9-A8
>
> Question2 : I am using tksurfer to analysis the brain thickness, and I 
> have a question about setting threshold, for I am not so sure about 
> the relation between threshold and Min.
> is the equation  Min = -log10(threshold) 
> correct?(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) 
>
> For example, if I want the threshold to be 0.05, and the Min will be 
> set to 1.3
> Please see the image attached in this email, and correct me if I am 
> wrong.
You are correct
>
> Thank you!
>
> Jincheng
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://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.

Re: [Freesurfer] Using caudate as a seed

[Douglas N Greve]

11 and 50

11  Left-Caudate122 186 220 0

50  Right-Caudate   122 186 220 0



On 10/11/2016 10:56 AM, Raney, Talia L. wrote:
> Hi,
> Is there any way in FSFAST to use caudate as a seed for connectivity 
> analysis? I was checking to see if it had a seg id for which I could run 
> fc-seed-config, but it only had ids for caudate intensity abnormalities.
> Thank you!
> Best,
> Talia
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://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.

Re: [Freesurfer] Remapping Volume

[Douglas N Greve]

Try adding --projfrac 0.5


On 10/12/2016 11:29 AM, Crawford, Anna wrote:
> I did:
>
> mri_vol2surf --src 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+asegRMnn.mgz
>  --out 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegRMnnS.mgh
>  --regheader segfs --hemi lh --surf white --out_type mgh --fixtkreg
>
> which resulted in the same type of surface. I looked at the volume and it 
> seemed as though things were labeled correctly. The images are attached.
>
> Thanks,
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, October 12, 2016 10:47 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Remapping Volume
>
> that seems ok, as I think the default is nearest neighbor. Can you
> visualize the volume you created and see if the incorrect labels are in
> it?
>
> On Wed, 12 Oct 2016, Crawford, Anna wrote:
>
>> I used:
>>
>> --src 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+asegRMpostcent2.mgz
>>  --out 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegRMpostcent2S.mgh
>>  --regheader segfs --hemi lh --surf white --out_type mgh
>>
>>>  From the help file online, it looks like --fixtkreg would be used for the 
>>> nearest neighbor. What is the proper flag to set it to use nearest neighbor 
>>> interpolation?
>> Thanks,
>> Anna
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, October 11, 2016 10:29 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Remapping Volume
>>
>> what was your vol2surf command line? Make sure that it is using nearest
>> neighbor interpolation
>> On Tue, 11 Oct 2016, Crawford, Anna wrote:
>>
>>> Hi,
>>>
>>> I am trying to remap a volume. I am using aparc+aseg.mgz volume. I loaded it
>>> into Matlab using load_mgh. In Matlab I remap the volume to different
>>> values. For example, all original values of 1022 will become 200 and all
>>> 1030 values will become 150. (This is just an example, not necessarily these
>>> numbers.) I save a new aparc+asegNew.mgz file using save_mgh. I use the same
>>> M and mr_parms that I got when I loaded in the original file. I'm not sure
>>> what these mean or if I need to change them. Then I use mri_vol2surf to
>>> create a new surface overlay onto the inflated hemisphere. When I do this,
>>> each region such as post central gyrus is 2 colors spotted together instead
>>> of a solid color like in the original. I have attached pictures as an
>>> example of what the original and remapped looked like. I didn't change the
>>> location of values, just simple gave each value a new one. Why is the one
>>> value speckled throughout?
>>>
>>> Thank you,
>>> Anna
>>>
>>> ===
>>>
>>> Please consider the environment before printing this e-mail
>>>
>>> Cleveland Clinic is ranked as one of the top hospitals in America by
>>> U.S.News & World Report (2015). Visit us online at
>>> http://www.clevelandclinic.org for a complete listing of our services, staff
>>> and locations. Confidentiality Note: This message is intended for use only
>>> by the individual or entity to which it is addressed and may contain
>>> information that is privileged, confidential, and exempt from disclosure
>>> under applicable law. If the reader of this message is not the intended
>>> recipient or the employee or agent responsible for delivering the message to
>>> the intended recipient, you are hereby notified that any dissemination,
>>> distribution or copying of this communication is strictly prohibited. If you
>>> have received this communication in error, please contact the sender
>>> immediately and destroy the material in its entirety, whether electronic or
>>> hard copy. Thank you.
>>>
>>>
>> ___
>> 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.
>>
>>
>> ===
>>
>>
>> Please consider the environment before printing this e-mail
>>
>> Cleveland Clinic is ranked as one of the top hospitals in America by 
>> U.S.News & World Report (2015).
>> Visit us online at http://www.clevelandclinic.org for a complete listing 

Re: [Freesurfer] Should I use no-adjust in mri_surfcluster

[Mishra, Virendra]

Thank you, Doug.



Regards



Virendra



-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Wednesday, October 12, 2016 11:45 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Should I use no-adjust in mri_surfcluster



If all you want to do is fdr correction you can use this program:



https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr





On 10/10/2016 07:31 PM, Mishra, Virendra wrote:

>

> Hi, FreeSurfer Users.

>

> I am comparing cortical thickness of 2 groups controlled for certain

> variables of no interest.

>

> My contrast matrix is

>

> 1 -1 0 0 0 0 0 0 0 0 0 0  to check for group 1 thickness > group 2

> thickness

>

> I get my sig.mgh and I want to run mri_surfcluster command to correct

> for FDR.

>

> I am confused as to whether I should use -no-adjust in

> mri_surfcluster. According to the help mri_surfcluster

> (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surfcluster) :

>

> I have to use -no-adjust if my sig.mgh is not a log(10) map and

> sig.mgh was created using a one-tailed test.

>

> Since my contrast is group1>group2 ; I am thinking my sig.mgh is a

> log(10) but a one-tailed. Hence I have to use -no-adjust.

>

> But then again, mri_glmfit

> (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit) says if #of

> rows in Contrast matrix is 1 (which is true in my case), then the

> F-test reduces to a two-tailed t-test which means I should not use

> -no-adjust.

>

> I would appreciate any response regarding this.

>

> Thanks

>

>

> Regards

>

> Virendra

>

> ===

>

> Please consider the environment before printing this e-mail

>

> Cleveland Clinic is ranked as one of the top hospitals in America by

> U.S.News & World Report (2015). Visit us online at

> http://www.clevelandclinic.org for a complete listing of our services,

> staff and locations. Confidentiality Note: This message is intended

> for use only by the individual or entity to which it is addressed and

> may contain information that is privileged, confidential, and exempt

> from disclosure under applicable law. If the reader of this message is

> not the intended recipient or the employee or agent responsible for

> delivering the message to the intended recipient, you are hereby

> notified that any dissemination, distribution or copying of this

> communication is strictly prohibited. If you have received this

> communication in error, please contact the sender immediately and

> destroy the material in its entirety, whether electronic or hard copy.

> Thank you.

>

>

> ___

> Freesurfer mailing list

> Freesurfer@nmr.mgh.harvard.edu

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



--

Douglas N. Greve, Ph.D.

MGH-NMR Center

gr...@nmr.mgh.harvard.edu

Phone Number: 617-724-2358

Fax: 617-726-7422



Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2

www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

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





The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Partners Compliance HelpLine 
at http://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.



===


 Please consider the environment before printing this e-mail

Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & 
World Report (2015).  
Visit us online at http://www.clevelandclinic.org for a complete listing of our 
services, staff and locations.


Confidentiality Note:  This message is intended for use only by the individual 
or entity to which it is addressed and may contain information that is 
privileged, confidential, and exempt from disclosure under applicable law.  If 
the reader of this message is not the intended recipient or the employee or 
agent responsible for delivering the message to the intended recipient, you are 
hereby notified that any dissemination, distribution or copying of this 
communication is strictly prohibited.  If you have received this communication 
in error,  please contact the sender immediately and destroy the material in 
its entirety, whether electronic or hard copy.  

Thank you.

Re: [Freesurfer] Should I use no-adjust in mri_surfcluster

[Douglas N Greve]

If all you want to do is fdr correction you can use this program:

https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr


On 10/10/2016 07:31 PM, Mishra, Virendra wrote:
>
> Hi, FreeSurfer Users.
>
> I am comparing cortical thickness of 2 groups controlled for certain 
> variables of no interest.
>
> My contrast matrix is
>
> 1 -1 0 0 0 0 0 0 0 0 0 0  to check for group 1 thickness > group 2 
> thickness
>
> I get my sig.mgh and I want to run mri_surfcluster command to correct 
> for FDR.
>
> I am confused as to whether I should use –no-adjust in 
> mri_surfcluster. According to the help mri_surfcluster 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surfcluster) :
>
> I have to use –no-adjust if my sig.mgh is not a log(10) map and 
> sig.mgh was created using a one-tailed test.
>
> Since my contrast is group1>group2 ; I am thinking my sig.mgh is a 
> log(10) but a one-tailed. Hence I have to use –no-adjust.
>
> But then again, mri_glmfit 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit) says if #of 
> rows in Contrast matrix is 1 (which is true in my case), then the 
> F-test reduces to a two-tailed t-test which means I should not use 
> –no-adjust.
>
> I would appreciate any response regarding this.
>
> Thanks
>
>
> Regards
>
> Virendra
>
> ===
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is ranked as one of the top hospitals in America by 
> U.S.News & World Report (2015). Visit us online at 
> http://www.clevelandclinic.org for a complete listing of our services, 
> staff and locations. Confidentiality Note: This message is intended 
> for use only by the individual or entity to which it is addressed and 
> may contain information that is privileged, confidential, and exempt 
> from disclosure under applicable law. If the reader of this message is 
> not the intended recipient or the employee or agent responsible for 
> delivering the message to the intended recipient, you are hereby 
> notified that any dissemination, distribution or copying of this 
> communication is strictly prohibited. If you have received this 
> communication in error, please contact the sender immediately and 
> destroy the material in its entirety, whether electronic or hard copy. 
> Thank you.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://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.

Re: [Freesurfer] smoothing kernel inconsistency

[Douglas N Greve]

On 10/10/2016 08:20 AM, Qi Ting wrote:
> Dear Freesurfer experts,
>
> I am trying to do the group analysis, before this I tried to smooth the data 
> with the different smoothing kernel. However, when I checked the output dir, 
> it turned out that data were smoothed with a larger smoothing kernel than I 
> expected. For example, images intended to be smoothed with 5mm were actually 
> smoothed with 8mm. So does anyone know why?
The 8mm is the measured smoothing level, not the level you applied. Real 
data have  endogenous smoothness that adds to the smoothness you applied 
to give you a final level of smoothness that is greater than both.
>
> Another thing is about the surface area in the analysis. I am a little 
> confused which surface does the default cmd or the area in qdec indicate? 
> Does it mean the area I got is white surface? If so, can I also get a pial 
> surface? Technically, is the middle between the white surface and the pial 
> surface the more reasonable one?
The one that is just "area" is the area of the white surface. I think 
there is a option called  "area.pial". In general we like to use the 
area of the white surface because that will be independent of changes in 
thickness.
> Thank you in advance.
>
> Best regards,
> Ting
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://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.

Re: [Freesurfer] how to exact the result of the stats filedir

[Douglas N Greve]

We use mris_anatomical_stats. Is that what you mean?


On 10/08/2016 05:33 AM, zhang yue wrote:
>
> Hello FreeSurfer Developers,
>
> I’m attempting to exact the result of ‘stats’filedir, such as file 
> ‘lh.aparc.stats’, I want to know you guys how to do this work. Your 
> kind reply would be appreciated.
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://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.

Re: [Freesurfer] Gamma / Histogram

[Douglas N Greve]

On 10/08/2016 02:43 AM, Anders Hougaard wrote:
> Dear Freesurfers,
>
> Please see the attached image.
> It shows inflated fsaverage surface with gamma.mgh overlaid.
> Gamma.mgh is from one contrast of a standard group analysis of 
> cortical thickness (two groups A and B, two contrasts A>B and B>A).
>
> 1) Is it correct to interpret the gamma values as between-group 
> difference of cortical thickness in mm?
It depends on how you set up the contrast. If it is a simple A vs B, 
then yes, mm is correct.
>
> 2) I would like to reproduce the histogram in another software. Is it 
> possible to extract the gamma values for each vertex for this purpose?
You can do it in matlab easily enough, eg,
gamma = MRIread('gamma.mgh');
gamma.vol will be the pixel values
>
> All the best,
> Anders
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://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.

Re: [Freesurfer] Fdr correction using command line

[neuroimage analyst]

Thanks, Doug for the binary.

 A quick follow-up: what does the sign in either mri_glmfit-sim/mri_fdr
indicate? When I open F.mgh, the values are only positive and p-values
obtained from them has sign of +/-. My understanding is + indicates where
mean_A>mean_B and vice versa.

If for example, I am interested in mean_A>mean_B then should I pass --pos
(mri_fdr) or --cache 2.30101 pos (mri_glmfit-sim for uncorrected cluster
defining threshold of p<0.005)  in the contrast that was designed for that
test?

Regards

MV

On Wed, Oct 12, 2016 at 10:27 AM, Douglas N Greve  wrote:

> try this binary
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr
>
>
>
> On 10/07/2016 04:11 PM, neuroimage analyst wrote:
> >
> > Hi,
> >
> > I was wondering if there is a way to perform fdr correction using
> > command line in freesurfer without using matlab as mri_glmfit-sim only
> > does bonferroni ?
> >
> > Thanks
> > Regards
> > MV
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] mri_average vs mri_concat

[Douglas N Greve]

Hmmm, I don't know what could be going on. Can you send the command line 
and all terminal output?


On 10/06/2016 10:37 PM, Trisanna Sprung-Much wrote:
> 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
>> > > > 
>> > >
>> > > 
>> >> > > >
>> > > 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 

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

[Douglas N Greve]

That is surface-based smoothing. the voxel size differences create 
differences in volume-based smoothing (a partial volume effect). I don't 
know of a good way to simulate volume-based PVC. This cannot be done in qdec


On 10/06/2016 06:36 PM, Martin Juneja wrote:
> 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 =   

Re: [Freesurfer] Cortical Thickness Overlay Slice by Slice

[Bruce Fischl]

Hi Sancgeetha

you can use mri_surf2vol to sample the thickness into the volume if you 
want. The thickness file itself does not contain any topological 
information - that is stored in the surface files (e.g. lh.pial)


cheers
Bruce
On Wed, 12 
Oct 2016, Sancgeetha Kulaseharan wrote:



Hello Freesurfer Experts,

I am using Freeview to visualize cortical thickness with the command
freeview -v mri/T1.mgz \ -f surf/lh.pial:overlay=lh.thickness

While the cortical thickness overlay is visible in the 3-Dimensional
display, I was wondering if it was possible to also view the cortical
thickness map on a slice-by-slice case?

Also where can I find topological information on ?h.thickness files?

Thank you,
Sancgeetha

 

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Cortical Thickness Overlay Slice by Slice

[Sancgeetha Kulaseharan]

Hello Freesurfer Experts,

I am using Freeview to visualize cortical thickness with the command
freeview -v mri/T1.mgz \ -f surf/lh.pial:overlay=lh.thickness

While the cortical thickness overlay is visible in the 3-Dimensional
display, I was wondering if it was possible to also view the cortical
thickness map on a slice-by-slice case?

Also where can I find topological information on ?h.thickness files?

Thank you,
Sancgeetha
___
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.

Re: [Freesurfer] Fdr correction using command line

[Douglas N Greve]

try this binary

https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr



On 10/07/2016 04:11 PM, neuroimage analyst wrote:
>
> Hi,
>
> I was wondering if there is a way to perform fdr correction using 
> command line in freesurfer without using matlab as mri_glmfit-sim only 
> does bonferroni ?
>
> Thanks
> Regards
> MV
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://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.

Re: [Freesurfer] group analysis

[charles laidi]

Dear Douglas and Trisanna,

Thank you very much for your explanations.

I just would like to be sure of what I am doing since there is no example
on the wiki as complex as mine.

If I have the following classes :

Diagnosis : Patient or Control
Gender : Male or Female
Site : Site1 or Site2 or Site3

NregressorsDODS = Nclasses*(Nvariables+1) = 6*(0+1) = 2*2*3*(1+1) = 24
Regressor1: ones for PatientMaleSite1 subjects, 0 otherwise. Codes
intercept for Group 1
Regressor2: ones for PatientMaleSite2 subjects, 0 otherwise. Codes
intercept for Group 2
Regressor2: ones for PatientMaleSite3 subjects, 0 otherwise. Codes
intercept for Group 3

Regressor12: ones for ControlFemaleSite3 subjects, 0 otherwise. Codes
intercept for Group 12
Regressor13: age for PatientMaleSite1 subjects, 0 otherwise. Codes age
slope for Group 1
Regressor14: age for PatientMaleSite2 subjects, 0 otherwise. Codes age
slope for Group 2
...
Regressor24: age for ControlFemaleSite3 subjects, 0 otherwise. Codes age
slope for Group 12

*I assume my FSGDF file should look like : *

GroupDescriptorFile 1
Title analysis
Class PatientMaleSite1
Class PatientMaleSite2
Class PatientMaleSite3
Class PatientFemaleSite1
Class PatientFemaleSite2
Class PatientFemaleSite3
Class ControlMaleSite1
Class ControlMaleSite2
Class ControlMaleSite3
Class ControlFemaleSite1
Class ControlFemaleSite2
Class ControlFemaleSite3
Variables Age
Input subject1 PatientMaleSite1 30
Input subject2 PatientFemaleSite2 45
Input subject3 PatientFemaleSite3 85
Input subject4 PatientFemaleSite4 75
...

As for the contrast analysis :

If my question is : *is there a difference between Patient and Controls age
slope regressing out the effects of gender and site? *

*Contrast1 patient-control.slope.mtx*

0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 -0.5
-0.5

with all regressor1 to regressor12 equal to *0*
with regressor13 to 18 equal to *0.5  *(regressor with Patient in it)
with regressor19 to 24 equal to *- 0.5* (regressor with Controls in it)

If my question is :* is there a difference between cortical thickness in
patients and controls, regressing out the effects of age, gender and site ?
*

*Contrast2 patient-controls.mtx*

0.5 0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0
0

with all regressor1 to regressor6 equal to
*0.5*with all regressor7 to regressor12 equal to -*0.5*
with all regressor13 to regressor24 equal to *0*

Thank you very much in advance for your help and sorry for taking your
time.

Best,

Charles










2016-10-05 17:44 GMT+02:00 Douglas N Greve :

> This is a straightforward extension to the FSGD examples. You have 3
> discrete factors (2 diagnosis, 2 gender, 6 centers), this yields
> 2*2*6=24 classes. With one covariate, you would have 24 covariate
> regressors (one for each class) for a total of 48. You would then need
> to create a contrast matrix that tests for an interaction between
> diagnosis and age which is also a straight-forward extension to the
> examples.
>
> Having said that, I think that 48 regressors is a lot unless you have
> about 500 subjects. It is also possible to have a less agressive model
> and just have two regressors, one for each diagnosis. But you'd have to
> create the design matrix yourself as this is outside of the FSGD
> specification.
>
>
> On 10/05/2016 09:22 AM, charles laidi wrote:
> > Dear FreeSurfers,
> >
> > I would like to study the interaction between age and cortical
> > thickness in patients and controls.
> > My hypothesis is that there is an interaction and that cortical
> > thickness is decreasing faster with age in patients than in controls.
> > I have both Male and Female included in 6 different centers.
> > I would like to consider also Gender and Site (6 centers) as confounds.
> >
> > My understanding is that I should perform a surface based group
> > analysis with freesurfer.
> >
> > I am not able to find an example for my problem in the documentation
> > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V
> >
> > Would anyone had some tips to build the Fsgd file and the contrast file ?
> >
> > Thank you very much in advance.
> >
> > Best,
> >
> > Charles
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the 

Re: [Freesurfer] [Dev Build] Processing very high resolution dataset

[Bruce Fischl]

Hi Falk

you are almost certainly running into a problem with some MAX number of 
defects/faces or something. If you upload the subject dir I'll fix it


cheers
Bruce
On 
Wed, 12 Oct 2016, Falk Lüsebrink wrote:




Dear all,

 

using mris_topo_fixer instead of mris_fix_topology also results in a
segmentation fault. The command line used was: 

mris_topo_fixer -mgz -warning -seed 1234  lh

 

INFO: assuming .mgz format
setting seed for random number genererator to 1234
reading input surface /surf/lh.orig...
Before topology correction, eno=-2042 (nv=2743306, nf=5490696, ne=8236044,
g=1022)
Surface Diagnostics:   
   eno=-2042 (nv=2743306, nf=5490696, ne=8236044)
   # of border vertices [ #v ~ #f ] 0
   # of edges with single face  0
   # of edges with more than 2 faces    0
   # of corner configurations   0
   The original surface is a valid manifold
   Counting the number of connected components
   The original surface has one component
   The original surface does not self-intersect

The surface has 1022 loops (X=-2042)

Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 15 iterations
identify defects...
marking ambiguous vertices...
1475515 ambiguous faces found in tessellation
segmenting defects...
Segmentation fault

 

Any suggestions or tips are highly appreciated.

 

Best,

Falk

 

Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Falk
Lüsebrink
Gesendet: Donnerstag, 6. Oktober 2016 17:51
An: Freesurfer support list
Betreff: [Freesurfer] [Dev Build] Processing very high resolution dataset

 

Dear all,


I am currently trying to process a MPRAGE with an isotropic resolution of
250 µm acquired in vivo. Downsampling the data to .5 and 1 mm resulted in no
errors and surfaces look good.

However, while processing the data at native resolution I receive a
segmentation fault during topology fixation. May this be related to the
number of vertices / faces? Surfaces look okay and not totally corrupted.
Memory and disk space are available plentiful.

INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781 2016/06/13 21:20:50 fischl Exp $
before topology correction, eno=-2042 (nv=2743306, nf=5490696, ne=8236044,
g=1022)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
marking ambiguous vertices...
1461809 ambiguous faces found in tessellation
segmenting defects...
Segmentation fault

 

Uploading of the dataset is currently not possible.

 

Best,

Falk


___
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.

Re: [Freesurfer] Issues processing brain hemispherectomized patients

[Bruce Fischl]

Hi Hinke

mri_em_register, mri_ca_label, mri_ca_register and mri_ca_normalize all 
take -lh and -rh commands to indicate that only one hemisphere exists. Try 
including them and see if it fixes things (you should be able to use expert 
options for this). We have only used it for ex vivo analysis in the past, 
but hopefully it will do the trick for you


cheers
Bruce


On Wed, 12 Oct 2016, Halbertsma, 
HN (ohk) wrote:



Dear all,
I’m having troubles getting a good Freesurfer output from a
hemispherectomised brain using recon-all. I was wondering whether there’s
someone that has experience with running Freesurfer on such an unusual
brain?

The first couple of issues I bumped into were failures regarding the
talaraich alignment which I solved using registration matrices from FSL. 

The issue I’m having now regards the labeling of subcortical structures.
Apparently Freesurfer cannot deal with the fact that there’s just one
hemisphere, and the fact that there is no clear corpus callosum. It looks
like it’s trying to divide one hemisphere into two, which obviously messes
up the subcortical labelling.
Any ideas on how to work around this issues? 

Is there maybe a way to mirror the intact hemisphere pretending to form a
full brain? Or are there any flags I can use to make sure the subcortical
labelling works fine? 

Thanks in advance

Hinke N. Halbertsma, MSc

PhD Student
University Medical Center Groningen (UMCG)
Department of Ophthalmology
NeuroImaging Center (Antonius Deusinglaan 2,  9713 AW Groningen), room 124
T. (+31) 050 363 4431
E. h.n.halbert...@umcg.nl








De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de
geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken
van dit bericht, het niet openbaar maken of op enige wijze verspreiden of
vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een
incomplete aankomst of vertraging van dit verzonden bericht.

The contents of this message are confidential and only intended for the eyes
of the addressee(s). Others than the addressee(s) are not allowed to use
this message, to make it public or to distribute or multiply this message in
any way. The UMCG cannot be held responsible for incomplete reception or
delay of this transferred message.
___
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.

Re: [Freesurfer] Remapping Volume

[Bruce Fischl]

that seems ok, as I think the default is nearest neighbor. Can you 
visualize the volume you created and see if the incorrect labels are in 
it?

On Wed, 12 Oct 2016, Crawford, Anna wrote:

> I used:
>
> --src 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+asegRMpostcent2.mgz
>  --out 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegRMpostcent2S.mgh
>  --regheader segfs --hemi lh --surf white --out_type mgh
>
>> From the help file online, it looks like --fixtkreg would be used for the 
>> nearest neighbor. What is the proper flag to set it to use nearest neighbor 
>> interpolation?
>
> Thanks,
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Tuesday, October 11, 2016 10:29 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Remapping Volume
>
> what was your vol2surf command line? Make sure that it is using nearest
> neighbor interpolation
> On Tue, 11 Oct 2016, Crawford, Anna wrote:
>
>> Hi,
>>
>> I am trying to remap a volume. I am using aparc+aseg.mgz volume. I loaded it
>> into Matlab using load_mgh. In Matlab I remap the volume to different
>> values. For example, all original values of 1022 will become 200 and all
>> 1030 values will become 150. (This is just an example, not necessarily these
>> numbers.) I save a new aparc+asegNew.mgz file using save_mgh. I use the same
>> M and mr_parms that I got when I loaded in the original file. I'm not sure
>> what these mean or if I need to change them. Then I use mri_vol2surf to
>> create a new surface overlay onto the inflated hemisphere. When I do this,
>> each region such as post central gyrus is 2 colors spotted together instead
>> of a solid color like in the original. I have attached pictures as an
>> example of what the original and remapped looked like. I didn't change the
>> location of values, just simple gave each value a new one. Why is the one
>> value speckled throughout?
>>
>> Thank you,
>> Anna
>>
>> ===
>>
>> Please consider the environment before printing this e-mail
>>
>> Cleveland Clinic is ranked as one of the top hospitals in America by
>> U.S.News & World Report (2015). Visit us online at
>> http://www.clevelandclinic.org for a complete listing of our services, staff
>> and locations. Confidentiality Note: This message is intended for use only
>> by the individual or entity to which it is addressed and may contain
>> information that is privileged, confidential, and exempt from disclosure
>> under applicable law. If the reader of this message is not the intended
>> recipient or the employee or agent responsible for delivering the message to
>> the intended recipient, you are hereby notified that any dissemination,
>> distribution or copying of this communication is strictly prohibited. If you
>> have received this communication in error, please contact the sender
>> immediately and destroy the material in its entirety, whether electronic or
>> hard copy. Thank you.
>>
>>
> ___
> 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.
>
>
> ===
>
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News 
> & World Report (2015).
> Visit us online at http://www.clevelandclinic.org for a complete listing of 
> our services, staff and locations.
>
>
> Confidentiality Note:  This message is intended for use only by the 
> individual or entity to which it is addressed and may contain information 
> that is privileged, confidential, and exempt from disclosure under applicable 
> law.  If the reader of this message is not the intended recipient or the 
> employee or agent responsible for delivering the message to the intended 
> recipient, you are hereby notified that any dissemination, distribution or 
> copying of this communication is strictly prohibited.  If you have received 
> this communication in error,  please contact the sender immediately and 
> destroy the material in its entirety, whether electronic or hard copy.
>
> Thank you.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

Re: [Freesurfer] Hippocampal subfield analysis in FS 6.0

[Bruce Fischl]

Hi Synne

we are (hopefully!) in the final stages of alpha testing and will release 
a beta soon


cheers
Bruce


On Wed, 12 Oct 2016, Synne Aanes wrote:



Hello,


I am about to start my project on hippocampal subfield analysis and realise
that this function is highly improved in FS version 6.0. I have run my data
in FS 5.3 before this came to my knowledge, and I am now wondering
when version 6.0 will be released to the public so I can run them again?


Sincerely,


Synne Aanes




___
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.

Re: [Freesurfer] [Dev Build] Processing very high resolution dataset

[Falk Lüsebrink]

Dear all,

using mris_topo_fixer instead of mris_fix_topology also results in a 
segmentation fault. The command line used was:
mris_topo_fixer -mgz -warning -seed 1234  lh

INFO: assuming .mgz format
setting seed for random number genererator to 1234
reading input surface /surf/lh.orig...
Before topology correction, eno=-2042 (nv=2743306, nf=5490696, ne=8236044, 
g=1022)
Surface Diagnostics:
   eno=-2042 (nv=2743306, nf=5490696, ne=8236044)
   # of border vertices [ #v ~ #f ] 0
   # of edges with single face  0
   # of edges with more than 2 faces0
   # of corner configurations   0
   The original surface is a valid manifold
   Counting the number of connected components
   The original surface has one component
   The original surface does not self-intersect

The surface has 1022 loops (X=-2042)

Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 15 iterations
identify defects...
marking ambiguous vertices...
1475515 ambiguous faces found in tessellation
segmenting defects...
Segmentation fault

Any suggestions or tips are highly appreciated.

Best,
Falk

Von: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Falk Lüsebrink
Gesendet: Donnerstag, 6. Oktober 2016 17:51
An: Freesurfer support list
Betreff: [Freesurfer] [Dev Build] Processing very high resolution dataset

Dear all,

I am currently trying to process a MPRAGE with an isotropic resolution of 250 
µm acquired in vivo. Downsampling the data to .5 and 1 mm resulted in no errors 
and surfaces look good.

However, while processing the data at native resolution I receive a 
segmentation fault during topology fixation. May this be related to the number 
of vertices / faces? Surfaces look okay and not totally corrupted. Memory and 
disk space are available plentiful.

INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781 2016/06/13 21:20:50 fischl Exp $
before topology correction, eno=-2042 (nv=2743306, nf=5490696, ne=8236044, 
g=1022)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
marking ambiguous vertices...
1461809 ambiguous faces found in tessellation
segmenting defects...
Segmentation fault

Uploading of the dataset is currently not possible.

Best,
Falk
___
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.

Re: [Freesurfer] Quantifying volumes

[Josue Luiz Dalboni Da Rocha]

Dear Doug,

Thank you very much for your advice!
We get to extract results for the volumes from a ".curv file encoded ROI" using 
your recommended command lines (mri_binarize and mri_segstats ), but 
unfortunately the results are much smaller (around 3 times) than when we 
extract total gray matter volumes from a respective ".label file encoded ROI" 
using mris_anatomical_stats .

Example:
Volumes from a ".curv file encoded ROI" using your recommended command lines 
(mri_binarize and mri_segstats):
Subject1 = 1090
Subject2 = 1181
Subject3 = 713
Subject4 = 1230
Volumes from a respective ".label file encoded ROI" (mris_anatomical_stats):
Subject1 = 3497
Subject2 = 3786
Subject3 = 2268
Subject4 = 3491

Are the volumes extracted from a ".curv file encoded ROI" (using mri_binarize 
and mri_segstats) an estimation of the total gray matter volumes?
Why these values are differing that much?

Thank you very much,
Josue Dalboni

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N Greve 

Sent: Wednesday, October 5, 2016 5:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Quantifying volumes

I would binarize the curv file with

mri_binarize --i lh.yourcurvfile --abs --min .001 --o
lh.yourcurvfilebin.mgh

Then compute the volume with

mri_segstats --seg lh.yourcurvfilebin.mgh --id 1 --i lh.volume
--accumulate --sum lh.vol.yourcurv.sum


On 10/05/2016 09:09 AM, Josue Luiz Dalboni Da Rocha wrote:
> Dear Douglas,
>
> I have a ".curv" file that contains the curvature information inside an 
> automatically delineated ROI and 0 everywhere else.
> I would like to calculate the volume of this ROI,
>
> Can I extract statistics directly from the ".curv" file?
>
> Best regards,
> Josue
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Tuesday, October 4, 2016 9:41 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Quantifying volumes
>
> What is the nature of the segmentation? Is it just a binary (1=in,
> 0=out) segmentation? And what file format? In general we don't use .w
> anymore, but it can be converted into something else.
>
> doug
>
>
> On 10/03/2016 12:35 PM, Josue Luiz Dalboni Da Rocha wrote:
>> Dear Douglas,
>>
>>
>> I have a segmented gyrus curvature file (.curv or .w) and I would like
>> to calculate the volume (and other statistics) of this gyrus.
>>
>>
>> I currently only know mris_anatomical_stats to perform that, but
>> requiring a '.label' file.
>>
>>
>> Can I extract statistics directly from the ".curv" file?
>>
>>
>> Or can I convert directly from .curv to .label in order to extract
>> these statistics?
>>
>>
>> As another option, is it feasible to convert the '.curv' file to nifti
>> volume (mri_surf2vol), binarize it (mri_binarize), and then convert to
>> label (mri_cor2label)?
>>
>>
>> What does the output nifti file from 'mri_surf2vol' contain? Does it
>> contain the complete volume behind the surface? Or does it only
>> contain the surface over the 3D space?
>>
>>
>> Thank you very much in advance for your help!
>>
>>
>> Best regards,
>>
>> Josue
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: 

Re: [Freesurfer] Segmentation editing

[Bruce Fischl]

if the surfaces are fine probably not, but you will want to recreate the 
stats tables


cheers
Bruce


On Tue, 11 Oct 2016, firet...@web.de wrote:


Dear experts
 
after editing aseg the Segmentations wiki says one:

" could recreate the final surfaces with the command:

recon-all -autorecon2-noaseg -subjid  "
Is there any need to run this specific command? The surfaces look just fine.
Only left pallidum wasn't outlined correctly and needed manual edit.
 
Appreciate your help!

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Issues processing brain hemispherectomized patients

[Halbertsma, HN (ohk)]

Dear all,

I’m having troubles getting a good Freesurfer output from a hemispherectomised 
brain using recon-all. I was wondering whether there’s someone that has 
experience with running Freesurfer on such an unusual brain?

The first couple of issues I bumped into were failures regarding the talaraich 
alignment which I solved using registration matrices from FSL.

The issue I’m having now regards the labeling of subcortical structures. 
Apparently Freesurfer cannot deal with the fact that there’s just one 
hemisphere, and the fact that there is no clear corpus callosum. It looks like 
it’s trying to divide one hemisphere into two, which obviously messes up the 
subcortical labelling.
Any ideas on how to work around this issues?

Is there maybe a way to mirror the intact hemisphere pretending to form a full 
brain? Or are there any flags I can use to make sure the subcortical labelling 
works fine?

Thanks in advance

Hinke N. Halbertsma, MSc

PhD Student
University Medical Center Groningen (UMCG)
Department of Ophthalmology
NeuroImaging Center (Antonius Deusinglaan 2,  9713 AW Groningen), room 124
T. (+31) 050 363 4431
E. h.n.halbert...@umcg.nl








De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de 
geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van 
dit bericht, het niet openbaar maken of op enige wijze verspreiden of 
vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een 
incomplete aankomst of vertraging van dit verzonden bericht.

The contents of this message are confidential and only intended for the eyes of 
the addressee(s). Others than the addressee(s) are not allowed to use this 
message, to make it public or to distribute or multiply this message in any 
way. The UMCG cannot be held responsible for incomplete reception or delay of 
this transferred message.
___
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.

Re: [Freesurfer] Remapping Volume

[Crawford, Anna]

I used:

--src 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+asegRMpostcent2.mgz
 --out 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegRMpostcent2S.mgh
 --regheader segfs --hemi lh --surf white --out_type mgh

>From the help file online, it looks like --fixtkreg would be used for the 
>nearest neighbor. What is the proper flag to set it to use nearest neighbor 
>interpolation?

Thanks,
Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, October 11, 2016 10:29 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Remapping Volume

what was your vol2surf command line? Make sure that it is using nearest
neighbor interpolation
On Tue, 11 Oct 2016, Crawford, Anna wrote:

> Hi,
>
> I am trying to remap a volume. I am using aparc+aseg.mgz volume. I loaded it
> into Matlab using load_mgh. In Matlab I remap the volume to different
> values. For example, all original values of 1022 will become 200 and all
> 1030 values will become 150. (This is just an example, not necessarily these
> numbers.) I save a new aparc+asegNew.mgz file using save_mgh. I use the same
> M and mr_parms that I got when I loaded in the original file. I'm not sure
> what these mean or if I need to change them. Then I use mri_vol2surf to
> create a new surface overlay onto the inflated hemisphere. When I do this,
> each region such as post central gyrus is 2 colors spotted together instead
> of a solid color like in the original. I have attached pictures as an
> example of what the original and remapped looked like. I didn't change the
> location of values, just simple gave each value a new one. Why is the one
> value speckled throughout?
>
> Thank you,
> Anna
>
> ===
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is ranked as one of the top hospitals in America by
> U.S.News & World Report (2015). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services, staff
> and locations. Confidentiality Note: This message is intended for use only
> by the individual or entity to which it is addressed and may contain
> information that is privileged, confidential, and exempt from disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the message to
> the intended recipient, you are hereby notified that any dissemination,
> distribution or copying of this communication is strictly prohibited. If you
> have received this communication in error, please contact the sender
> immediately and destroy the material in its entirety, whether electronic or
> hard copy. Thank you.
>
>
___
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.


===


 Please consider the environment before printing this e-mail

Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & 
World Report (2015).  
Visit us online at http://www.clevelandclinic.org for a complete listing of our 
services, staff and locations.


Confidentiality Note:  This message is intended for use only by the individual 
or entity to which it is addressed and may contain information that is 
privileged, confidential, and exempt from disclosure under applicable law.  If 
the reader of this message is not the intended recipient or the employee or 
agent responsible for delivering the message to the intended recipient, you are 
hereby notified that any dissemination, distribution or copying of this 
communication is strictly prohibited.  If you have received this communication 
in error,  please contact the sender immediately and destroy the material in 
its entirety, whether electronic or hard copy.  

Thank you.

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

Re: [Freesurfer] Hippocampal subfield analysis in FS 6.0

[Iglesias Gonzalez, Eugenio]

Dear Synne,
There will hopefully be a beta release of 6.0 some time soon, but it’s hard to 
tell exactly when (please see recent messages on the list by Bruce Fischl and 
Zeke Kaufman about this topic).
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 12 Oct 2016, at 11:41, Synne Aanes 
> wrote:

Hello,

I am about to start my project on hippocampal subfield analysis and realise 
that this function is highly improved in FS version 6.0. I have run my data in 
FS 5.3 before this came to my knowledge, and I am now wondering when version 
6.0 will be released to the public so I can run them again?

Sincerely,

Synne Aanes


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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Hippocampal subfield analysis in FS 6.0

[Synne Aanes]

Hello,


I am about to start my project on hippocampal subfield analysis and realise 
that this function is highly improved in FS version 6.0. I have run my data in 
FS 5.3 before this came to my knowledge, and I am now wondering when version 
6.0 will be released to the public so I can run them again?


Sincerely,


Synne Aanes


___
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.