Re: [Freesurfer] Found 0 unique series

[Douglas Greve]

You don't need a .dat file, it just could not create the file. It was trying to 
create it in

  /autofs/cluster/cagn/1/users/traney/Projects/FC-REVEAL-practice/DEMA65e/

do you have write permissions into that folder?



On 6/15/16 5:01 PM, Raney, Talia L. wrote:
> This is true, but in other subjects, I never had to create a .dat file while 
> running dcmunpack. It's saying there is no .dat file in the output directory 
> not the input directory.
> When I run debug, I get this:
> set filetype = `mri_probedicom --i $f --d filetype`
> set filetype = `mri_probedicom --i $f --d filetype`
> mri_probedicom --i 
> /autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071011011917795479165
>  --d filetype
> if ( $filetype == notdicom ) continue ;
> if ( notdicom == notdicom ) continue
> continue
> @ nth = $nth + 1 ;
> @ nth = 11 + 1
> set filetype = `mri_probedicom --i $f --d filetype`
> set filetype = `mri_probedicom --i $f --d filetype`
> mri_probedicom --i 
> /autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071010571512449268924
>  --d filetype
> if ( $filetype == notdicom ) continue ;
> if ( notdicom == notdicom ) continue
> continue
> @ nth = $nth + 1 ;
> @ nth = 12 + 1
> set filetype = `mri_probedicom --i $f --d filetype`
> set filetype = `mri_probedicom --i $f --d filetype`
> mri_probedicom --i 
> /autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071010583933303272479
>  --d filetype
> if ( $filetype == notdicom ) continue ;
> if ( notdicom == notdicom ) continue
> continue
> @ nth = $nth + 1 ;
> @ nth = 13 + 1
> set filetype = `mri_probedicom --i $f --d filetype`
> set filetype = `mri_probedicom --i $f --d filetype`
> mri_probedicom --i 
> /autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.201407101102248986381669
>  --d filetype
> if ( $filetype == notdicom ) continue ;
> if ( notdicom == notdicom ) continue
> continue
> @ nth = $nth + 1 ;
> @ nth = 14 + 1
> set filetype = `mri_probedicom --i $f --d filetype`
> set filetype = `mri_probedicom --i $f --d filetype`
> mri_probedicom --i 
> /autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071010594423016075195
>  --d filetype
> if ( $filetype == notdicom ) continue ;
> if ( notdicom == notdicom ) continue
> continue
> @ nth = $nth + 1 ;
> @ nth = 15 + 1
> set filetype = `mri_probedicom --i $f --d filetype`
> set filetype = `mri_probedicom --i $f --d filetype`
> mri_probedicom --i 
> /autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071010592916417774565
>  --d filetype
> if ( $filetype == notdicom ) continue ;
> if ( notdicom == notdicom ) continue
> continue
> @ nth = $nth + 1 ;
> @ nth = 16 + 1
> set filetype = `mri_probedicom --i $f --d filetype`
> set filetype = `mri_probedicom --i $f --d filetype`
> mri_probedicom --i 
> /autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071010582919491272059
>  --d filetype
> if ( $filetype == notdicom ) continue ;
> if ( notdicom == notdicom ) continue
> continue
> @ nth = $nth + 1 ;
> @ nth = 17 + 1
> set filetype = `mri_probedicom --i $f --d filetype`
> set filetype = `mri_probedicom --i $f --d filetype`
> mri_probedicom --i 
> /autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071010572916851369549
>  --d filetype
> if ( $filetype == notdicom ) continue ;
> if ( notdicom == notdicom ) continue
> continue
> @ nth = $nth + 1 ;
> @ nth = 18 + 1
> set filetype = `mri_probedicom --i $f --d filetype`
> set filetype = `mri_probedicom --i $f --d filetype`
> mri_probedicom --i 
> /autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071011010926193878749
>  --d filetype
> if ( $filetype == notdicom ) continue ;
> if ( notdicom == notdicom ) continue
> continue
> @ nth = $nth + 1 ;
> @ nth = 19 + 1
> set filetype = `mri_probedicom --i $f --d filetype`
> set filetype = `mri_probedicom --i $f --d filetype`
> mri_probedicom --i 
> /autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071011005416870778120
>  --d filetype
> if ( $filetype == notdicom ) 

[Freesurfer] wm.mgz edits

[marco mcsweeney]

Dear all,

I have a few questions regarding wm.mgz edits.

I am very new to this area and have only recently started using Freesurfer so 
please excuse me if my questions appear naive or misinformed.

I have managed to make most of the necessary edits needed to fix skullstrip 
errors, intensity normalization errors and pial errors, but I am a bit stuck 
when it comes to fixing topological defects.

My question relates to what should or should not be included in the wm.mgz. 
Apart from the optic chiasm, which I have removed, is it normal to have, what 
appear to be, multiple specs included in the wm.mgz which when the aseg is 
loaded turn out to be parts of the amygdala and hippocampus. When I view the 
smoothwm.nofix these appear as jagged shard like shapes protruding out from the 
surface. In one publication I saw recently it was suggested that these should 
be removed but should this be done if they are parts of the amygdala and 
hippocampus. I am worried about this as these are the 2 main subcortical areas 
I will be focusing on.

Also, is it normal for the wm.mgz to include parts of the cerebral cortex 
(labelled as such in the aseg).

Also, most of the scans I am working with have numerous holes and handles and 
this is taking a very long time to fix. I have tried to run the automatic 
topology fixer again. This has helped a bit but the scans still require a lot 
of edits. Could this be down to the quality of the scans or could it be that I 
have edited too much - control points for example. I have followed the advice 
given and have tried not to make too many edits, but having said that it has 
taken me a very long time.

Any advice in relation to any of these questions would be very very very much 
appreciated.

Best wishes

Marco

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Re: [Freesurfer] convert from MNI152 to native space

[Leila Reddy]

Hi Doug,
Thanks for your reply.  
When I run mni152reg I get an error : ERROR: Flag --lta unrecognized
I'm using v 1.9 of this file. 

I found a post that said to download a newer version from here: 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg

but it doesn't seem to be there anymore.

Thanks,
Leila

On Wednesday, June 15, 2016 11:55 AM, Leila Reddy  wrote:
 

 Hi,
I have a binary mask from the WFU_Pickatlas. I think this mask in in the MNI152 
space (when I load_nifti in Matlab I get dimensions of [91 109 91]. I would 
like to convert this mask into the native space of each subject. I tried the 
following command but the results do not look right in Freeview:
 mri_vol2vol --mov mask_MNI152.nii --targ bold/005/f.nii.gz --o 
mask_in_Native.nii --mni152reg
The overlay of the mask on f.nii in Freeview is mostly outside the brain.

How can I go about this step?

Thanks for your help,Leila


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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] registering to fsaverage

[Trisanna Sprung-Much]

worked beautifully. Thank you!

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


On Wed, Jun 15, 2016 at 4:41 PM, Douglas N Greve 
wrote:

> Try surf2surf with --mapmethod nnf
>
> On 06/15/2016 04:25 PM, Trisanna Sprung-Much wrote:
> > Hi Doug - yes they do actually, I was quite pleased. I did some trials
> > with other subjects and the mri_vol2surf all looks good. Very similar
> > to what I had in our in-house software.
> >
> > Would things be better if I were to isolate each sulcus as a .label
> > and then try the mri_label2label? Someone suggested perhaps the
> > colours are overlapping with the overlay
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Jun 15, 2016 at 4:10 PM, Douglas N Greve
> > > wrote:
> >
> > The problem is probably that the vol2surf command did not properly
> > sample the labels onto the surface. Do the labels on subject 00350
> > surfaces look ok?
> >
> > On 06/15/2016 04:00 PM, Trisanna Sprung-Much wrote:
> > > thanks Dr. Fischl
> > >
> > > So the command seems to have worked! I have copied what ran in my
> > > terminal. When I open the test.mgz overlay on the fsaverage pial
> > > surface, things look ok but a bit funny. I am wondering if there is
> > > anything I can do to the mri_surf2surf command to improve the
> > > registration to fsaverage? *See my snapshots attached.*
> > >
> > > trisanna@kaplan:~$ mri_surf2surf --srcsubject 00350 --sval
> > > /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
> > > --trgsubject fsaverage --tval test.mgz --hemi lh
> > > srcsubject = 00350
> > > srcval =
> > /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
> > > srctype=
> > > trgsubject = fsaverage
> > > trgval = test.mgz
> > > trgtype=
> > > srcsurfreg = sphere.reg
> > > trgsurfreg = sphere.reg
> > > srchemi= lh
> > > trghemi= lh
> > > frame  = 0
> > > fwhm-in= 0
> > > fwhm-out   = 0
> > > label-src  = (null)
> > > label-trg  = (null)
> > > OKToRevFaceOrder  = 1
> > > Reading source surface reg
> > > /data-01/trisanna/freesurfer/00350/surf/lh.sphere.reg
> > > Loading source data
> > > Reading target surface reg
> > > /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg
> > > Done
> > > Mapping Source Volume onto Source Subject Surface
> > > surf2surf_nnfr: building source hash (res=16).
> > > Surf2Surf: Forward Loop (163842)
> > >
> > > surf2surf_nnfr: building target hash (res=16).
> > > Surf2Surf: Reverse Loop (166912)
> > > Reverse Loop had 41306 hits
> > > Surf2Surf: Dividing by number of hits (163842)
> > > INFO: nSrcLost = 0
> > > nTrg121 = 132490, nTrgMulti = 31352, MnTrgMultiHits = 2.31749
> > > nSrc121 = 137180, nSrcLost = 0, nSrcMulti = 29732, MnSrcMultiHits =
> > > 2.28602
> > > Saving target data
> > > Saving to test.mgz
> > >
> > > best
> > >
> > > Trisanna
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > > On Wed, Jun 15, 2016 at 12:13 PM, Bruce Fischl
> > > 
> >  > >> wrote:
> > >
> > > Hi Trisanna
> > >
> > > you would only use those options of if you were transforming
> > a surface
> > > Bruce
> > >
> > >
> > > On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
> > >
> > > thanks Dr. Fischl
> > >
> > > I assume that for surface overlays one cannot specify
> > > --sval-xyz and --tval-xyz or the command will treat the
> > input
> > > as a surface
> > > itself?
> > >
> > > best
> > >
> > > Trisanna
> > >
> > >
> > >
> > >
> > > --
> > > Ph.D. CandidateMcGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > > On Wed, Jun 15, 2016 at 11:11 AM, Bruce Fischl
> > >  > 
> > >  > >> wrote:
> > >   Hi Trisanna
> > >
> > >   you don't need to inflate the overlays. They can just
> > > use the existing surface-based (sphere.reg) registration.
> > >
> > >   cheers
> > >   Bruce
> > >   On Wed, 15 Jun 2016, Trisanna 

Re: [Freesurfer] Found 0 unique series

[Raney, Talia L.]

This is true, but in other subjects, I never had to create a .dat file while 
running dcmunpack. It's saying there is no .dat file in the output directory 
not the input directory.
When I run debug, I get this:
set filetype = `mri_probedicom --i $f --d filetype`
set filetype = `mri_probedicom --i $f --d filetype`
mri_probedicom --i 
/autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071011011917795479165
 --d filetype
if ( $filetype == notdicom ) continue ;
if ( notdicom == notdicom ) continue
continue
@ nth = $nth + 1 ;
@ nth = 11 + 1
set filetype = `mri_probedicom --i $f --d filetype`
set filetype = `mri_probedicom --i $f --d filetype`
mri_probedicom --i 
/autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071010571512449268924
 --d filetype
if ( $filetype == notdicom ) continue ;
if ( notdicom == notdicom ) continue
continue
@ nth = $nth + 1 ;
@ nth = 12 + 1
set filetype = `mri_probedicom --i $f --d filetype`
set filetype = `mri_probedicom --i $f --d filetype`
mri_probedicom --i 
/autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071010583933303272479
 --d filetype
if ( $filetype == notdicom ) continue ;
if ( notdicom == notdicom ) continue
continue
@ nth = $nth + 1 ;
@ nth = 13 + 1
set filetype = `mri_probedicom --i $f --d filetype`
set filetype = `mri_probedicom --i $f --d filetype`
mri_probedicom --i 
/autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.201407101102248986381669
 --d filetype
if ( $filetype == notdicom ) continue ;
if ( notdicom == notdicom ) continue
continue
@ nth = $nth + 1 ;
@ nth = 14 + 1
set filetype = `mri_probedicom --i $f --d filetype`
set filetype = `mri_probedicom --i $f --d filetype`
mri_probedicom --i 
/autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071010594423016075195
 --d filetype
if ( $filetype == notdicom ) continue ;
if ( notdicom == notdicom ) continue
continue
@ nth = $nth + 1 ;
@ nth = 15 + 1
set filetype = `mri_probedicom --i $f --d filetype`
set filetype = `mri_probedicom --i $f --d filetype`
mri_probedicom --i 
/autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071010592916417774565
 --d filetype
if ( $filetype == notdicom ) continue ;
if ( notdicom == notdicom ) continue
continue
@ nth = $nth + 1 ;
@ nth = 16 + 1
set filetype = `mri_probedicom --i $f --d filetype`
set filetype = `mri_probedicom --i $f --d filetype`
mri_probedicom --i 
/autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071010582919491272059
 --d filetype
if ( $filetype == notdicom ) continue ;
if ( notdicom == notdicom ) continue
continue
@ nth = $nth + 1 ;
@ nth = 17 + 1
set filetype = `mri_probedicom --i $f --d filetype`
set filetype = `mri_probedicom --i $f --d filetype`
mri_probedicom --i 
/autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071010572916851369549
 --d filetype
if ( $filetype == notdicom ) continue ;
if ( notdicom == notdicom ) continue
continue
@ nth = $nth + 1 ;
@ nth = 18 + 1
set filetype = `mri_probedicom --i $f --d filetype`
set filetype = `mri_probedicom --i $f --d filetype`
mri_probedicom --i 
/autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071011010926193878749
 --d filetype
if ( $filetype == notdicom ) continue ;
if ( notdicom == notdicom ) continue
continue
@ nth = $nth + 1 ;
@ nth = 19 + 1
set filetype = `mri_probedicom --i $f --d filetype`
set filetype = `mri_probedicom --i $f --d filetype`
mri_probedicom --i 
/autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071011005416870778120
 --d filetype
if ( $filetype == notdicom ) continue ;
if ( notdicom == notdicom ) continue
continue
@ nth = $nth + 1 ;
@ nth = 20 + 1
set filetype = `mri_probedicom --i $f --d filetype`
set filetype = `mri_probedicom --i $f --d filetype`
mri_probedicom --i 
/autofs/cluster/cagn/1/users/dcm/DEMA65e/cdrom/DICOM_ScanDirs/024_ge_functionals_128_32ch/TrioTim-35162-20140710-100150-451000_MR.1.3.12.2.1107.5.2.32.35162.2014071010575424717370596
 --d filetype
if ( $filetype == notdicom ) continue ;
if ( notdicom == 

Re: [Freesurfer] selxavg3-sess error

[Francesca Strappini]

Thank you, I'll try!

Best
Francesca

On Wednesday, June 15, 2016, Douglas N Greve 
wrote:

> Sorry for the delay. Do you have polar angle data? Unfortunately, FSFAST
> needs both. If you don't have polar, just copy the eccen data and call
> it polar. for what you want to do it won't make much difference.
>
> On 06/08/2016 09:55 AM, Francesca Strappini wrote:
> > I have only something similar in the temporal dynamics to the
> > eccentricity data. I attached the Xtmp.mat file.
> > Thank you!
> >
> > Francesca
> >
> > 2016-06-08 15:44 GMT+02:00 Douglas Greve  
> > >>:
> >
> > Do you have both polar and eccen data? If so, can you send the
> > Xtmp.mat file?
> >
> >
> > On 6/8/16 6:08 AM, Francesca Strappini wrote:
> >> Hi Freesurfer experts,
> >>
> >> I'm re-posting this message because I think it got lost.
> >>
> >> I'm trying to analyze some phase-encoded data with the eccentricity
> >> protocol for retinotopic data and I'm having troubles with
> >> selxavg3-sess.
> >>
> >> I run the following commands:
> >>
> >> mkanalysis-sess -analysis OrderDisorder.idsubj.lh -surface idsubj
> >> lh -TR 2
> >> -retinotopy 24 -paradigm rtopy.par -fwhm 0 -per-run -nskip 5 -fsd
> >> bold
> >>
> >> selxavg3-sess -a OrderDisorder.idsubj.lh -s
> >> idsubj_OrderDisorder_continous
> >>
> >> and I got this error message:
> >>
> >> Found 122573/130829 (93.7) voxels in mask
> >> Creating Design Matrix
> >>  ... creation time =  0.019 sec
> >> DoMCFit = 1
> >> ntptot = 875, nX = 80, DOF = 795
> >> Saving X matrix to
> >>
>  
> /usr/local/freesurfer/fsfast/OrderDisorder_new/MK_OrderDisorder_continous/bold/OrderDisorder.MishaK.lh/Xtmp.mat
> >> Error using svd
> >> Input to SVD must not contain NaN or Inf.
> >>
> >> Error in cond (line 35)
> >> s = svd(A);
> >>
> >> Error in fast_selxavg3 (line 279)
> >>   XCond = cond(XtX);
> >>
> >> Thanks!
> >> Best
> >> Francesca
> >>
> >>
> >>
> >> --
> >> Francesca Strappini, Ph.D.
> >> Neurobiology Department
> >> Weizmann Institute of Science
> >> 234 Herzl Street, Rehovot 7610001 Israel
> >> Tel.: +972 58 444 2584 
> >> E-mail: francesca.strapp...@weizmann.ac.il 
> >> >
> >>
> >>
> >> ___
> >> 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   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.
> >
> >
> >
> >
> > --
> > Francesca Strappini, Ph.D.
> > Neurobiology Department
> > Weizmann Institute of Science
> > 234 Herzl Street, Rehovot 7610001 Israel
> > Tel.: +972 58 444 2584
> > E-mail: francesca.strapp...@weizmann.ac.il 
> > >
> >
> >
> > ___
> > 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
>


-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
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Re: [Freesurfer] Fwd: Getting the pial surface to cover the entire medial temporal lobe structures

[dgw]

I would try Bruce's idea first, but another option would be to run
mri_tesselate on the aseg volume you had loaded in those images.

hth
d

On Wed, Jun 15, 2016 at 4:46 PM, Bruce Fischl
 wrote:
> Hi David
>
> we don't have anything that does this by default, sorry. If you don't care
> about the location of the white surface you could try setting all the voxels
> in the wm.mgz that are left or right hippo/amygdala in the aseg to 255 then
> running from autorecon2-wm forward.
>
> cheers
> Bruce
>
>
>
> On Wed, 15 Jun 2016, David Groppe wrote:
>
>>
>> Dear Free Surfers,
>>  I am using FreeSurfer's pial surface to map ECoG electrodes onto the
>> FreeSurfer average brain for group analyses via these two methods:
>>
>> Dykstra, A. R., Chan, A. M., Quinn, B. T., Zepeda, R., Keller, C. J.,
>> Cormier, J., et al. (2011). Individualized localization and cortical
>> surface-based registration of intracranial electrodes. NeuroImage, 1–42.
>> http://doi.org/10.1016/j.neuroimage.2011.11.046
>>
>>
>> Yang, A. I., Wang, X., Doyle, W. K., Halgren, E., Carlson, C., Belcher, T.
>> L., et al. (2012). Localization of dense intracranial electrode arrays
>> using
>> magnetic resonance imaging. NeuroImage, 63(1), 157–165.
>> http://doi.org/10.1016/j.neuroimage.2012.06.039
>>
>>
>> The methods work great. However, we've noticed that the pial surface
>> typically underestimates the extent of the amygdala and hippocampus (see
>> attached example images from FreeSurfer's demo Bert subject) where we
>> often
>> have electrodes. I understand that FreeSurfer does this by design, since
>> the
>> amygdala and hippocampus are not neocortex. However, is there a way to
>> force
>> the pial surface to include those medial temporal lobe structures for our
>> purposes? I tried "mris_make_surfaces -fix_mtl" but that did the opposite
>> of
>> what we need (i.e., it withdrew the pial surface so that it included none
>> of
>> the amygdala or hippocampus).
>>  much appreciated,
>> -David
>>
>> P.S. Thanks for creating and maintaining such an amazing suite of
>> freeware.
>>
>>
>>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>

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Re: [Freesurfer] Fwd: Getting the pial surface to cover the entire medial temporal lobe structures

[Bruce Fischl]

Hi David

we don't have anything that does this by default, sorry. If you don't 
care about the location of the white surface you could try setting all 
the voxels in the wm.mgz that are left or right hippo/amygdala in the aseg 
to 255 then running from autorecon2-wm forward.


cheers
Bruce


On Wed, 15 
Jun 2016, David Groppe wrote:




Dear Free Surfers,
 I am using FreeSurfer's pial surface to map ECoG electrodes onto the
FreeSurfer average brain for group analyses via these two methods:

Dykstra, A. R., Chan, A. M., Quinn, B. T., Zepeda, R., Keller, C. J.,
Cormier, J., et al. (2011). Individualized localization and cortical
surface-based registration of intracranial electrodes. NeuroImage, 1–42.
http://doi.org/10.1016/j.neuroimage.2011.11.046


Yang, A. I., Wang, X., Doyle, W. K., Halgren, E., Carlson, C., Belcher, T.
L., et al. (2012). Localization of dense intracranial electrode arrays using
magnetic resonance imaging. NeuroImage, 63(1), 157–165.
http://doi.org/10.1016/j.neuroimage.2012.06.039


The methods work great. However, we've noticed that the pial surface
typically underestimates the extent of the amygdala and hippocampus (see
attached example images from FreeSurfer's demo Bert subject) where we often
have electrodes. I understand that FreeSurfer does this by design, since the
amygdala and hippocampus are not neocortex. However, is there a way to force
the pial surface to include those medial temporal lobe structures for our
purposes? I tried "mris_make_surfaces -fix_mtl" but that did the opposite of
what we need (i.e., it withdrew the pial surface so that it included none of
the amygdala or hippocampus).
 much appreciated,
    -David

P.S. Thanks for creating and maintaining such an amazing suite of freeware.



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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Found 0 unique series

[Douglas N Greve]

The problem appears to be

cat: /imagelist.dat: No such file or directory


Not sure what is going on there. Make sure you're not in / when running 
it or that the output points to /. Try running it with -debug as the 
first argument and sending the output.

On 06/15/2016 04:36 PM, Raney, Talia L. wrote:
> My command line is dcmunpack -src $dcmdir -targ $homedir/$subj -fsfast -run 
> $run_num restingstate nii.gz f.nii.gz  and the output is
> ---
>1 24 restingstate f 0 0
> ---
> Searching for matching files
> Wed Jun 15 16:34:27 EDT 2016
> Wed Jun 15 16:34:27 EDT 2016
> Found 65 total files.
> cat: /imagelist.dat: No such file or directory
> Found 0 unique series:
> Patient: Undefined variable.
>
> 
> 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, June 15, 2016 4:08 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Found 0 unique series
>
> what is your command line and what is the full terminal output
>
> On 06/15/2016 04:06 PM, Raney, Talia L. wrote:
>> Hi FreeSurfer users,
>> I've been running dcmunpack and I get an error that said Found 0 unique 
>> series, even though it has dicom files. What does this mean and what could I 
>> do to fix the problem?
>> 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
> ___
> 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/

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] registering to fsaverage

[Douglas N Greve]

Try surf2surf with --mapmethod nnf

On 06/15/2016 04:25 PM, Trisanna Sprung-Much wrote:
> Hi Doug - yes they do actually, I was quite pleased. I did some trials 
> with other subjects and the mri_vol2surf all looks good. Very similar 
> to what I had in our in-house software.
>
> Would things be better if I were to isolate each sulcus as a .label 
> and then try the mri_label2label? Someone suggested perhaps the 
> colours are overlapping with the overlay
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Jun 15, 2016 at 4:10 PM, Douglas N Greve 
> > wrote:
>
> The problem is probably that the vol2surf command did not properly
> sample the labels onto the surface. Do the labels on subject 00350
> surfaces look ok?
>
> On 06/15/2016 04:00 PM, Trisanna Sprung-Much wrote:
> > thanks Dr. Fischl
> >
> > So the command seems to have worked! I have copied what ran in my
> > terminal. When I open the test.mgz overlay on the fsaverage pial
> > surface, things look ok but a bit funny. I am wondering if there is
> > anything I can do to the mri_surf2surf command to improve the
> > registration to fsaverage? *See my snapshots attached.*
> >
> > trisanna@kaplan:~$ mri_surf2surf --srcsubject 00350 --sval
> > /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
> > --trgsubject fsaverage --tval test.mgz --hemi lh
> > srcsubject = 00350
> > srcval =
> /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
> > srctype=
> > trgsubject = fsaverage
> > trgval = test.mgz
> > trgtype=
> > srcsurfreg = sphere.reg
> > trgsurfreg = sphere.reg
> > srchemi= lh
> > trghemi= lh
> > frame  = 0
> > fwhm-in= 0
> > fwhm-out   = 0
> > label-src  = (null)
> > label-trg  = (null)
> > OKToRevFaceOrder  = 1
> > Reading source surface reg
> > /data-01/trisanna/freesurfer/00350/surf/lh.sphere.reg
> > Loading source data
> > Reading target surface reg
> > /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg
> > Done
> > Mapping Source Volume onto Source Subject Surface
> > surf2surf_nnfr: building source hash (res=16).
> > Surf2Surf: Forward Loop (163842)
> >
> > surf2surf_nnfr: building target hash (res=16).
> > Surf2Surf: Reverse Loop (166912)
> > Reverse Loop had 41306 hits
> > Surf2Surf: Dividing by number of hits (163842)
> > INFO: nSrcLost = 0
> > nTrg121 = 132490, nTrgMulti = 31352, MnTrgMultiHits = 2.31749
> > nSrc121 = 137180, nSrcLost = 0, nSrcMulti = 29732, MnSrcMultiHits =
> > 2.28602
> > Saving target data
> > Saving to test.mgz
> >
> > best
> >
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Jun 15, 2016 at 12:13 PM, Bruce Fischl
> > 
>  >> wrote:
> >
> > Hi Trisanna
> >
> > you would only use those options of if you were transforming
> a surface
> > Bruce
> >
> >
> > On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
> >
> > thanks Dr. Fischl
> >
> > I assume that for surface overlays one cannot specify
> > --sval-xyz and --tval-xyz or the command will treat the
> input
> > as a surface
> > itself?
> >
> > best
> >
> > Trisanna
> >
> >
> >
> >
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Jun 15, 2016 at 11:11 AM, Bruce Fischl
> >  
> >  >> wrote:
> >   Hi Trisanna
> >
> >   you don't need to inflate the overlays. They can just
> > use the existing surface-based (sphere.reg) registration.
> >
> >   cheers
> >   Bruce
> >   On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
> >
> > Hi there
> > So I have sulcal labels from another software
> > (.mnc format) from which I am trying to generate some
> > probability maps. I was able
> > to convert the .mnc to .mgz surface overlay
> using
> > mri_vol2surf for my MRIs after running all MRIs in
> > recon-all. So, now I 

Re: [Freesurfer] Found 0 unique series

[Raney, Talia L.]

My command line is dcmunpack -src $dcmdir -targ $homedir/$subj -fsfast -run 
$run_num restingstate nii.gz f.nii.gz  and the output is
---
  1 24 restingstate f 0 0
---
Searching for matching files
Wed Jun 15 16:34:27 EDT 2016
Wed Jun 15 16:34:27 EDT 2016
Found 65 total files.
cat: /imagelist.dat: No such file or directory
Found 0 unique series: 
Patient: Undefined variable.


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, June 15, 2016 4:08 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Found 0 unique series

what is your command line and what is the full terminal output

On 06/15/2016 04:06 PM, Raney, Talia L. wrote:
> Hi FreeSurfer users,
> I've been running dcmunpack and I get an error that said Found 0 unique 
> series, even though it has dicom files. What does this mean and what could I 
> do to fix the problem?
> 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/

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

Hi Doug - yes they do actually, I was quite pleased. I did some trials with
other subjects and the mri_vol2surf all looks good. Very similar to what I
had in our in-house software.

Would things be better if I were to isolate each sulcus as a .label and
then try the mri_label2label? Someone suggested perhaps the colours are
overlapping with the overlay

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


On Wed, Jun 15, 2016 at 4:10 PM, Douglas N Greve 
wrote:

> The problem is probably that the vol2surf command did not properly
> sample the labels onto the surface. Do the labels on subject 00350
> surfaces look ok?
>
> On 06/15/2016 04:00 PM, Trisanna Sprung-Much wrote:
> > thanks Dr. Fischl
> >
> > So the command seems to have worked! I have copied what ran in my
> > terminal. When I open the test.mgz overlay on the fsaverage pial
> > surface, things look ok but a bit funny. I am wondering if there is
> > anything I can do to the mri_surf2surf command to improve the
> > registration to fsaverage? *See my snapshots attached.*
> >
> > trisanna@kaplan:~$ mri_surf2surf --srcsubject 00350 --sval
> > /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
> > --trgsubject fsaverage --tval test.mgz --hemi lh
> > srcsubject = 00350
> > srcval = /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
> > srctype=
> > trgsubject = fsaverage
> > trgval = test.mgz
> > trgtype=
> > srcsurfreg = sphere.reg
> > trgsurfreg = sphere.reg
> > srchemi= lh
> > trghemi= lh
> > frame  = 0
> > fwhm-in= 0
> > fwhm-out   = 0
> > label-src  = (null)
> > label-trg  = (null)
> > OKToRevFaceOrder  = 1
> > Reading source surface reg
> > /data-01/trisanna/freesurfer/00350/surf/lh.sphere.reg
> > Loading source data
> > Reading target surface reg
> > /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg
> > Done
> > Mapping Source Volume onto Source Subject Surface
> > surf2surf_nnfr: building source hash (res=16).
> > Surf2Surf: Forward Loop (163842)
> >
> > surf2surf_nnfr: building target hash (res=16).
> > Surf2Surf: Reverse Loop (166912)
> > Reverse Loop had 41306 hits
> > Surf2Surf: Dividing by number of hits (163842)
> > INFO: nSrcLost = 0
> > nTrg121 = 132490, nTrgMulti = 31352, MnTrgMultiHits = 2.31749
> > nSrc121 = 137180, nSrcLost = 0, nSrcMulti = 29732, MnSrcMultiHits =
> > 2.28602
> > Saving target data
> > Saving to test.mgz
> >
> > best
> >
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Jun 15, 2016 at 12:13 PM, Bruce Fischl
> > > wrote:
> >
> > Hi Trisanna
> >
> > you would only use those options of if you were transforming a
> surface
> > Bruce
> >
> >
> > On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
> >
> > thanks Dr. Fischl
> >
> > I assume that for surface overlays one cannot specify
> > --sval-xyz and --tval-xyz or the command will treat the input
> > as a surface
> > itself?
> >
> > best
> >
> > Trisanna
> >
> >
> >
> >
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Jun 15, 2016 at 11:11 AM, Bruce Fischl
> >  > > wrote:
> >   Hi Trisanna
> >
> >   you don't need to inflate the overlays. They can just
> > use the existing surface-based (sphere.reg) registration.
> >
> >   cheers
> >   Bruce
> >   On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
> >
> > Hi there
> > So I have sulcal labels from another software
> > (.mnc format) from which I am trying to generate some
> > probability maps. I was able
> > to convert the .mnc to .mgz surface overlay using
> > mri_vol2surf for my MRIs after running all MRIs in
> > recon-all. So, now I have
> > all my painted voxels as surface overlays, as I
> > was instructed to do a few months ago.
> >
> > I was told that the next step would be to use
> > mri_surf2surf to resample the overlays to fsaverage.
> >
> > I am a bit confused as I would think that the next
> > step would be to take the surface overlays and
> > inflate them before I register
> > them to fsaverage. I see that when recon-all runs,
> > it computes the registration of the MRI surface to
> > fsaverage and saves it as
> > sphere.reg. Is there a way I can inflate my
> > surface overlays in a similar manner and then apply this
> >   

Re: [Freesurfer] registering to fsaverage

[Douglas N Greve]

The problem is probably that the vol2surf command did not properly 
sample the labels onto the surface. Do the labels on subject 00350 
surfaces look ok?

On 06/15/2016 04:00 PM, Trisanna Sprung-Much wrote:
> thanks Dr. Fischl
>
> So the command seems to have worked! I have copied what ran in my 
> terminal. When I open the test.mgz overlay on the fsaverage pial 
> surface, things look ok but a bit funny. I am wondering if there is 
> anything I can do to the mri_surf2surf command to improve the 
> registration to fsaverage? *See my snapshots attached.*
>
> trisanna@kaplan:~$ mri_surf2surf --srcsubject 00350 --sval 
> /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz 
> --trgsubject fsaverage --tval test.mgz --hemi lh
> srcsubject = 00350
> srcval = /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
> srctype=
> trgsubject = fsaverage
> trgval = test.mgz
> trgtype=
> srcsurfreg = sphere.reg
> trgsurfreg = sphere.reg
> srchemi= lh
> trghemi= lh
> frame  = 0
> fwhm-in= 0
> fwhm-out   = 0
> label-src  = (null)
> label-trg  = (null)
> OKToRevFaceOrder  = 1
> Reading source surface reg 
> /data-01/trisanna/freesurfer/00350/surf/lh.sphere.reg
> Loading source data
> Reading target surface reg 
> /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg
> Done
> Mapping Source Volume onto Source Subject Surface
> surf2surf_nnfr: building source hash (res=16).
> Surf2Surf: Forward Loop (163842)
>
> surf2surf_nnfr: building target hash (res=16).
> Surf2Surf: Reverse Loop (166912)
> Reverse Loop had 41306 hits
> Surf2Surf: Dividing by number of hits (163842)
> INFO: nSrcLost = 0
> nTrg121 = 132490, nTrgMulti = 31352, MnTrgMultiHits = 2.31749
> nSrc121 = 137180, nSrcLost = 0, nSrcMulti = 29732, MnSrcMultiHits = 
> 2.28602
> Saving target data
> Saving to test.mgz
>
> best
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Jun 15, 2016 at 12:13 PM, Bruce Fischl 
> > wrote:
>
> Hi Trisanna
>
> you would only use those options of if you were transforming a surface
> Bruce
>
>
> On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
>
> thanks Dr. Fischl
>
> I assume that for surface overlays one cannot specify
> --sval-xyz and --tval-xyz or the command will treat the input
> as a surface
> itself?
>
> best
>
> Trisanna
>
>
>
>
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Jun 15, 2016 at 11:11 AM, Bruce Fischl
>  > wrote:
>   Hi Trisanna
>
>   you don't need to inflate the overlays. They can just
> use the existing surface-based (sphere.reg) registration.
>
>   cheers
>   Bruce
>   On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
>
> Hi there
> So I have sulcal labels from another software
> (.mnc format) from which I am trying to generate some
> probability maps. I was able
> to convert the .mnc to .mgz surface overlay using
> mri_vol2surf for my MRIs after running all MRIs in
> recon-all. So, now I have
> all my painted voxels as surface overlays, as I
> was instructed to do a few months ago.
>
> I was told that the next step would be to use
> mri_surf2surf to resample the overlays to fsaverage.
>
> I am a bit confused as I would think that the next
> step would be to take the surface overlays and
> inflate them before I register
> them to fsaverage. I see that when recon-all runs,
> it computes the registration of the MRI surface to
> fsaverage and saves it as
> sphere.reg. Is there a way I can inflate my
> surface overlays in a similar manner and then apply this
> same registration to my
> surface overlays? Or am I missing something?
>
> thanks very much!
>
> Trisanna
>
>
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
>
>
>
>
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Re: [Freesurfer] Found 0 unique series

[Douglas N Greve]

what is your command line and what is the full terminal output

On 06/15/2016 04:06 PM, Raney, Talia L. wrote:
> Hi FreeSurfer users,
> I've been running dcmunpack and I get an error that said Found 0 unique 
> series, even though it has dicom files. What does this mean and what could I 
> do to fix the problem?
> Best,
> Talia
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Maps/seed on surafce

[Douglas N Greve]

what was your mkanalysis-sess command?

On 06/08/2016 02:10 PM, Martin Juneja wrote:
> Dear FreeSurfer and SPM experts,
>
> I am trying to calculate functional connectivity maps using FreeSurfer 
> pipeline: 
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough.
>
> After defining a seed region on raw anatomical image, I co-registered 
> functional data with anatomical data (as reference) and made sure that 
> the seed is at correct place on both anatomical (top left in attached 
> image) and functional (top right) data. Using SPM, I confirmed 
> co-registration was fine.
>
> But after running all the steps of FC, looks like the FC maps are not 
> correct: sig.nii.gz at -fthresh 2 3 (shown at bottom left) because I 
> am not getting significant FC at seed location. Here, bottom right 
> shows the seed location on surface after I convert the seed to 
> fsaverage space (for visualization purpose).
>
> Any thoughts, ideas or tips on what went wrong here, would be really 
> appreciated.
>
> Thanks.
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] Found 0 unique series

[Raney, Talia L.]

Hi FreeSurfer users,
I've been running dcmunpack and I get an error that said Found 0 unique series, 
even though it has dicom files. What does this mean and what could I do to fix 
the problem?
Best,
Talia
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Re: [Freesurfer] selxavg3-sess error

[Douglas N Greve]

Sorry for the delay. Do you have polar angle data? Unfortunately, FSFAST 
needs both. If you don't have polar, just copy the eccen data and call 
it polar. for what you want to do it won't make much difference.

On 06/08/2016 09:55 AM, Francesca Strappini wrote:
> I have only something similar in the temporal dynamics to the 
> eccentricity data. I attached the Xtmp.mat file.
> Thank you!
>
> Francesca
>
> 2016-06-08 15:44 GMT+02:00 Douglas Greve  >:
>
> Do you have both polar and eccen data? If so, can you send the
> Xtmp.mat file?
>
>
> On 6/8/16 6:08 AM, Francesca Strappini wrote:
>> Hi Freesurfer experts,
>>
>> I'm re-posting this message because I think it got lost.
>>
>> I'm trying to analyze some phase-encoded data with the eccentricity
>> protocol for retinotopic data and I'm having troubles with
>> selxavg3-sess.
>>
>> I run the following commands:
>>
>> mkanalysis-sess -analysis OrderDisorder.idsubj.lh -surface idsubj
>> lh -TR 2
>> -retinotopy 24 -paradigm rtopy.par -fwhm 0 -per-run -nskip 5 -fsd
>> bold
>>
>> selxavg3-sess -a OrderDisorder.idsubj.lh -s
>> idsubj_OrderDisorder_continous
>>
>> and I got this error message:
>>
>> Found 122573/130829 (93.7) voxels in mask
>> Creating Design Matrix
>>  ... creation time =  0.019 sec
>> DoMCFit = 1
>> ntptot = 875, nX = 80, DOF = 795
>> Saving X matrix to
>> 
>> /usr/local/freesurfer/fsfast/OrderDisorder_new/MK_OrderDisorder_continous/bold/OrderDisorder.MishaK.lh/Xtmp.mat
>> Error using svd
>> Input to SVD must not contain NaN or Inf.
>>
>> Error in cond (line 35)
>> s = svd(A);
>>
>> Error in fast_selxavg3 (line 279)
>>   XCond = cond(XtX);
>>
>> Thanks!
>> Best
>> Francesca
>>
>>
>>
>> --
>> Francesca Strappini, Ph.D.
>> Neurobiology Department
>> Weizmann Institute of Science
>> 234 Herzl Street, Rehovot 7610001 Israel
>> Tel.: +972 58 444 2584 
>> E-mail: francesca.strapp...@weizmann.ac.il
>> 
>>
>>
>> ___
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>> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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>
>
>
> -- 
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strapp...@weizmann.ac.il 
> 
>
>
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-- 
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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[Freesurfer] Final Call for Papers SAN2016

[Tibor Auer]

Dear colleagues,
please, accept our advanced apologies for any multiple cross-postings...

The Society of Applied Neuroscience (SAN, http://www.applied-neuroscience.org/) 
in cooperation with the Medical School of the Aristotle University of 
Thessaloniki and the Department of Neurology of the Max Planck Institute for 
Human Cognitive and Brain Sciences, have the great pleasure to invite you to 
the biennial meeting of the Society, SAN2016 
(http://applied-neuroscience.org/san2016/), which will be held in Corfu Island, 
Greece between 6-9 of October, 2016.

We cordially invite everyone engaged in studies of Neuroscience, to participate 
in the SAN2016 meeting. Apart from the highly promising scientific program, 
blended with numerous workshops and special sessions, there will also be a 
lively social program which will give our guests the opportunity to enjoy 
Greece and Corfu.We feel confident than you will enjoy SAN2016 both 
scientifically and socially as one of our main purposes is to give the chance 
to all colleagues to establish new fruitful international collaborations in 
areas of mutual academic and clinical interests.

SAN2016 will bring together scientists and practitioners from a wide range of 
specialist fields. These include, but are not limited to:

EEG/ MEG/ fMRI/ fNIRS
Neurofeedback
fMRI-NFB studies
Brain Computer Interfaces
Trans Cranial Magnetic Stimulation
Peripheral Biofeedback
Direct Current Stimulation
Event-Related Potentials
Brain Connectivity
Neuronal Reorganization
EEG and Cognition
QEEG Diagnosis
Emerging combined EEG and Virtual/augmented reality technology
Instrumentation
Audio-Visual Stimulation
LORETA & Methodology
Clinical, educational, sport and optimal performance applications
Rehabilitation
Integrative Therapy
Complimentary evidence-based applications
...and all fields of applied neuroscience.

All the above blended by an attractive selection of keynote and invited 
speeches, as well as, hands-on pre-conference workshops. There will be a 
practitioner track focusing on topical issues. The conference committee 
receives more proposals than space available. Careful attention to Quality of 
work, clarity and completeness of the submitted materials is likely to increase 
the chance for acceptance. All the accepted abstracts will be published in the 
Frontiers in Human Neuroscience.

SAN2016 abstract submission is supported by a Frontiers event and are directly 
submitted through the following link until the 20th of June, 2016:
http://www.frontiersin.org/events/SAN2016_Meeting/3717

Numerous special issues and research topics are also planned by Society members 
as per tradition.

We believe that SAN2016 will be a wonderful chance for you, to meet old friends 
and make new ones. We look forward to seeing you in Corfu, Greece!

Panos Bamidis
John Gruzelier
Manousos Klados
SAN2016 Conference Chairs
[photo]

Manousos Klados, PhD
Postdoctoral Researcher, Max Planck Institute for Human Cognitive & Brain 
Sciences,
+49(0)-341-9940-2507 | 
+49(0)-176-6988-1781 | 
http://www.mklados.com | Skype: 
mklados
 | Stephanstraße 1a PC D-04103 Leipzig Germany
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[Freesurfer] unit for hippocampus segmentation results

[Fengji Geng]

Hi freesurfer experts,

We used the development version of freesurfer 6.0 to segment hippocampus.
We are wondering what the unit is for the segmentation results.

Thanks,

-- 
Fengji Geng
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[Freesurfer] Convert ascii to .mgh

[Robby De Pauw]

Dear Doug

Thank you for your answer. I however encounter an error:

>> F.vol = fast_mat2vol(lfdr,F.volsize)
ERROR: szvol inconsistent with mat2d

I have attached the final output (.mgh) and the .asc file. (As the files are 
too large, I added them here: https://we.tl/MKhhmeT5Zn)

Thank you

Robby
From:  on behalf of Douglas Greve 

Reply-To: "freesurfer@nmr.mgh.harvard.edu" 
Date: Wednesday 15 June 2016 at 17:43
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Convert ascii to .mgh

I would do it in matlab, eg,

F = MRIread('F.mgh'); % This is to get the proper header information

lfdr = load('lfdr.asc');
F.vol = fast_mat2vol(lfdr,F.volsize);
MRIwrite(F,'lfdr.mgh');



On 6/15/16 4:45 AM, Robby De Pauw wrote:
Dear FreeSurfer users,

To address the problem of multiple comparison, I wanted to apply the 
localfdr-method. For this purpose, I need the F-statistic (which I can extract 
from the F.mgh scalar overlay I presume?).

I converted this to an ascii-file, which I was able to load into R, using the 
following chink of code:

mris_convert -c 
/Users/robbydepauw/Desktop/FreeSurfer/GLM/lh.Group.volume.glmdir/Groupeffect/F.mgh
 $SUBJECTS_DIR/fsaverage/surf/lh.white F.asc

After performing an local fdr analysis in R, I want to create a scalar overlay 
“lfdr.mgh”, but I fail at converting the asci file into an “.mgh”-overlay file.

Any idea how I could approach this conversion (from asci back to .mgh)?

Many thanks,

Greetings

Robby

Robby De Pauw, PT, MT, drs.
T +32 09 332 12 19 | Email robby.dep...@ugent.be

Ghent University | Rehabilitation Sciences and Physiotherapy
Campus Heymans 3B3 (022)
De Pintelaan 185 BE-9000 Ghent
Route to my office






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Re: [Freesurfer] SIENAX

[Bruce Fischl]

maybe you want to check with the FSL group? It really depends on what 
measures you want to obtain

On Wed, 15 Jun 2016, Hassan 
bakhshi wrote:

> We have some cases which we want to process , I searched about SIENAX and as 
> you are more expert in this area, I wanted to know
> Freesurfer preferences on SIENAX ???
> The other thing is process time in these two software.
> 
> Kind Regards,
> 
> 
> 
>
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Re: [Freesurfer] SIENAX

[Hassan bakhshi]

We have some cases which we want to process , I searched about SIENAX and
as you are more expert in this area, I wanted to know Freesurfer
preferences on SIENAX ???
The other thing is process time in these two software.

Kind Regards,
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[Freesurfer] Memory

[Fu, Jason (NIH/NINDS) [F]]

Is there any way to check how many autorecon processes I can run at the same 
time? I am using a linux with 16gb ram.
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Re: [Freesurfer] -hippocampal-subfields-T1T2

[Kanel, Prabesh]

Hi All,


Was this issue solved?? I am getting the similar error but couldn't find a 
solution on the mailing list.


Fitting mesh to synthetic image from ASEG took 362.0884 seconds
Transforming points
Transforming points
set final LTA type to 1
ltaReadFile(subject/mri/transforms/T1_to_T2.v10.lta): can't open file
No such file or directory
Segmentation fault (core dumped)
freesurfer/bin//mri_concatenate_lta -out_type   1 
subject/mri/transforms/T1_to_T2.v10.lta identity.nofile T1toT2.lta >/dev/null: 
Segmentation fault
Error using fgets
Invalid file identifier.  Use fopen to generate a valid file identifier.



Regards,


Prabesh


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Eugenio Iglesias 

Sent: Monday, October 19, 2015 8:59:59 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] -hippocampal-subfields-T1T2

Hi Daniel,
sorry for the late reply; I was on vacation.
It seems that the T1-T2 registration failed. Can you please send me the .log 
files for the hippocampal subfields? They should be in the following directory:
media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/scripts/
Cheers,
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


From: "Daniele Orlandi" 
To: "Freesurfer support list" 
Sent: Monday, October 12, 2015 6:58:34 PM
Subject: [Freesurfer] -hippocampal-subfields-T1T2

Dear All,
I'm trying to run the flag  -hippocampal-subfields-T1T2 with the new FS v6.0 
but I get the following error:

>Fitting mesh to synthetic image from ASEG took 217.8633 seconds
>Transforming points
>Transforming points
>ltaReadFile(/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta):
> can't open file
>No such file or directory
>ERROR: Reading transform from file 
>/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta

Do you have any suggestion?
thank you all for your collaboration
Daniele

___
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Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

Hi Trisanna

you would only use those options of if you were transforming a surface
Bruce


On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:


thanks Dr. Fischl

I assume that for surface overlays one cannot specify --sval-xyz and --tval-xyz 
or the command will treat the input as a surface
itself?

best

Trisanna




--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 15, 2016 at 11:11 AM, Bruce Fischl  
wrote:
  Hi Trisanna

  you don't need to inflate the overlays. They can just use the existing 
surface-based (sphere.reg) registration.

  cheers
  Bruce
  On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:

Hi there
So I have sulcal labels from another software (.mnc format) from 
which I am trying to generate some
probability maps. I was able
to convert the .mnc to .mgz surface overlay using mri_vol2surf for 
my MRIs after running all MRIs in
recon-all. So, now I have
all my painted voxels as surface overlays, as I was instructed to 
do a few months ago.

I was told that the next step would be to use mri_surf2surf to 
resample the overlays to fsaverage. 

I am a bit confused as I would think that the next step would be to 
take the surface overlays and
inflate them before I register
them to fsaverage. I see that when recon-all runs, it computes the 
registration of the MRI surface to
fsaverage and saves it as
sphere.reg. Is there a way I can inflate my surface overlays in a 
similar manner and then apply this
same registration to my
surface overlays? Or am I missing something?

thanks very much!

Trisanna


--
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Integrated Program in Neuroscience
Psychology




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Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

thanks Dr. Fischl

I assume that for surface overlays one cannot specify --sval-xyz and
--tval-xyz or the command will treat the input as a surface itself?

best

Trisanna




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


On Wed, Jun 15, 2016 at 11:11 AM, Bruce Fischl 
wrote:

> Hi Trisanna
>
> you don't need to inflate the overlays. They can just use the existing
> surface-based (sphere.reg) registration.
>
> cheers
> Bruce
> On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
>
> Hi there
>> So I have sulcal labels from another software (.mnc format) from which I
>> am trying to generate some probability maps. I was able
>> to convert the .mnc to .mgz surface overlay using mri_vol2surf for my
>> MRIs after running all MRIs in recon-all. So, now I have
>> all my painted voxels as surface overlays, as I was instructed to do a
>> few months ago.
>>
>> I was told that the next step would be to use mri_surf2surf to resample
>> the overlays to fsaverage.
>>
>> I am a bit confused as I would think that the next step would be to take
>> the surface overlays and inflate them before I register
>> them to fsaverage. I see that when recon-all runs, it computes the
>> registration of the MRI surface to fsaverage and saves it as
>> sphere.reg. Is there a way I can inflate my surface overlays in a similar
>> manner and then apply this same registration to my
>> surface overlays? Or am I missing something?
>>
>> thanks very much!
>>
>> Trisanna
>>
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>>
>>
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Re: [Freesurfer] convert from MNI152 to native space

[Douglas Greve]

You'll need a registration that goes from the functional to the mni152. 
This has to be done in two steps,
1. Run  mni152reg --s subject to create the anat-to-mni152 registration 
(needs FSL)

2. Run bbregister to get the anat-to-func reg (in lta format)
3. then combine them with mri_concatenate_lta, like
  mri_concatenate_lta 
$SUBJECTS/subject/mri/transforms/reg.mni152.2mm.lta bbr.lta output.lta

Then use mri_vol2vol with --reg output.lta (and not --mni152reg)


On 6/15/16 5:55 AM, Leila Reddy wrote:

Hi,

I have a binary mask from the WFU_Pickatlas. I think this mask in in 
the MNI152 space (when I load_nifti in Matlab I get dimensions of [91 
109 91]. I would like to convert this mask into the native space of 
each subject. I tried the following command but the results do not 
look right in Freeview:


 mri_vol2vol --mov mask_MNI152.nii --targ bold/005/f.nii.gz --o 
mask_in_Native.nii --mni152reg


The overlay of the mask on f.nii in Freeview is mostly outside the brain.

How can I go about this step?

Thanks for your help,
Leila


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Re: [Freesurfer] Convert ascii to .mgh

[Douglas Greve]

I would do it in matlab, eg,

F = MRIread('F.mgh'); % This is to get the proper header information

lfdr = load('lfdr.asc');
F.vol = fast_mat2vol(lfdr,F.volsize);
MRIwrite(F,'lfdr.mgh');



On 6/15/16 4:45 AM, Robby De Pauw wrote:


Dear FreeSurfer users,

To address the problem of multiple comparison, I wanted to apply the 
localfdr-method. For this purpose, I need the F-statistic (which I can 
extract from the F.mgh scalar overlay I presume?).


I converted this to an ascii-file, which I was able to load into R, 
using the following chink of code:


mris_convert -c 
/Users/robbydepauw/Desktop/FreeSurfer/GLM/lh.Group.volume.glmdir/Groupeffect/F.mgh 
$SUBJECTS_DIR/fsaverage/surf/lh.white F.asc


After performing an local fdr analysis in R, I want to create a scalar 
overlay “lfdr.mgh”, but I fail at converting the asci file into an 
“.mgh”-overlay file.


Any idea how I could approach this conversion (from asci back to .mgh)?

Many thanks,

Greetings

Robby

Robby De Pauw, PT, MT, drs.

*T *+32 09 332 12 19* | Email *robby.dep...@ugent.be 



Ghent University *| *Rehabilitation Sciences and Physiotherapy

Campus Heymans 3B3 (022)

De Pintelaan 185 BE-9000 Ghent

Route to my office 



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Re: [Freesurfer] Coregister the CT image and MRI image

[Douglas Greve]

use mri_vol2vol, like
mri_vol2vol --mov CT.nii --reg v1t2.lta --fstarg --o CT-in-anat.nii


On 6/15/16 9:58 AM, HARI GURAGAIN wrote:

Dear Douglas,

With the suggestions from Zeke, the mri_coreg is working now. I have 
one last question:
I got the new v1to2.lta. How to apply this transformation to the CT 
image? Is it by using mri_convert?

Something like below?

mri_convert -at v1to2.lta CT.nii new_CT.nii


Any suggestion will be greatly appreciated.
Thank you again,
Hari Guragain


On Jun 9, 2016, at 5:53 PM, HARI GURAGAIN > wrote:


Dear Douglas,

I have used the same file as you pointed, but it keeps on showing the 
same error message. I copied the file to my 
/Applications/freesurfer/bin directory but it still shows the same 
error message:
‘dyld: Library not loaded: 
@executable_path/../lib/gcc/lib/libgomp.1.dylib’

Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
Reason: image not found
Trace/BPT trap:5



Does it have something to do with the library issue with mac?
Any help is appreciated.
Thank you,


On Jun 9, 2016, at 5:45 PM, Douglas N Greve 
> wrote:


try
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg.mac



On 06/09/2016 06:21 PM, HARI GURAGAIN wrote:

Dear Douglas,

The executable is not working as it says ‘Library not loaded: 
@executable_path/../lib/gcc/lib/libgomp.1.dylib’

Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
Reason: image not found
Trace/BPT trap:5

I am currently using the freeview: Version 1.0 and the operating 
system is: OS X EI Captain Version: 10.11.5
I wonder if the file you pointed works for the mac? Should I 
reinstall the freeview?

Any help would be greatly appreciated.

Thank you,

Hari


On Jun 9, 2016, at 4:28 PM, Douglas N Greve 
 wrote:


No, it is not the same command line. If you run it without args, 
it will

give you some info, but it is basically

mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta


On 06/09/2016 05:22 PM, HARI GURAGAIN wrote:

Thank you Douglas.
One more thing: Is there any syntax how to use it? I wonder if it 
is same as the mri_robust_register?



On Jun 9, 2016, at 3:43 PM, Douglas N Greve 
 wrote:


I don't think robust register will do cross-modal. You may be 
better off

using mri_coreg, which you can get from here

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


On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:

Dear Freesurfer community,

I am relatively new to this community.

I was trying to register the CT image and the MRI images (MRI 
as a the

target volume and CT as the movable volume). I used the
mri_robust_register to to do the registration as below:

/mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta
--mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /

The problem is that:  after register, the new image (v1to2.nii) 
is not

exactly aligned with the original MRI image (vol2.nii). It gives a
very different output. I wonder if I am missing anything here or I
need to do some extra steps after the above command in order to get
the correct alignment of the two images. I was hoping to get the
resultant image should be well orient with the target volume image
(vol2.nii image in my case).

I really appreciate any help here.

Hari Guragain



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Re: [Freesurfer] Define the design matrix by myself

[Douglas Greve]

The 1st and 2nd column add up to the 3rd and 4th column. To do this type 
of model, you'll have to have

1. A column of 1s (like you had before)
2. Get rid of columns 2 and 5.

This makes the 1st column of all 1s represent a CN-female.
the (new) 2nd column is the additive effect of AD. You'll basically be 
fitting this equation


thickness = offset + beta1*AD + beta2*Age + beta3*male




On 6/15/16 9:44 AM, Hao wen wrote:


Glad to know the fsgd file explanation:)

I have deleted the first colum(constant column, I made a simple 
mistake), but it didnt work even without the constant column, I got 
the same error:



ERROR: matrix is ill-conditioned or badly scaled, condno = 1.07053e+07

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.

here is the design matrix:


AD CN  age   male female

 0.000   1.000   74.300   0.000   1.000;
 0.000   1.000   73.700   0.000   1.000;
 0.000   1.000   84.500   1.000   0.000;
 0.000   1.000   78.500   1.000   0.000;
 0.000   1.000   80.800   0.000   1.000;
 0.000   1.000   65.400   0.000   1.000;
 0.000   1.000   73.100   1.000   0.000;
 0.000   1.000   72.600   1.000   0.000;
 0.000   1.000   63.200   0.000   1.000;
 0.000   1.000   71.700   0.000   1.000;
 0.000   1.000   77.700   1.000   0.000;
 0.000   1.000   76.900   0.000   1.000;
 0.000   1.000   73.200   0.000   1.000;
 0.000   1.000   76.200   0.000   1.000;
 0.000   1.000   84.700   0.000   1.000;
 0.000   1.000   69.600   1.000   0.000;
 0.000   1.000   70.100   0.000   1.000;
 0.000   1.000   70.900   1.000   0.000;
 0.000   1.000   77.000   1.000   0.000;
 0.000   1.000   74.500   0.000   1.000;
 0.000   1.000   74.400   1.000   0.000;
 0.000   1.000   72.900   0.000   1.000;
 0.000   1.000   74.000   0.000   1.000;
 0.000   1.000   70.600   0.000   1.000;
 0.000   1.000   78.200   0.000   1.000;
 0.000   1.000   70.600   0.000   1.000;
 0.000   1.000   80.300   1.000   0.000;
 0.000   1.000   65.100   0.000   1.000;
 0.000   1.000   69.800   0.000   1.000;
 0.000   1.000   71.100   0.000   1.000;
 1.000   0.000   81.300   0.000   1.000;
 1.000   0.000   75.400   0.000   1.000;
 1.000   0.000   73.900   1.000   0.000;
 1.000   0.000   64.100   0.000   1.000;
 1.000   0.000   80.100   0.000   1.000;
 1.000   0.000   78.300   0.000   1.000;
 1.000   0.000   73.200   0.000   1.000;
 1.000   0.000   75.300   1.000   0.000;
 1.000   0.000   65.600   0.000   1.000;
 1.000   0.000   62.400   0.000   1.000;
 1.000   0.000   77.200   1.000   0.000;
 1.000   0.000   70.700   1.000   0.000;
 1.000   0.000   70.100   1.000   0.000;
 1.000   0.000   82.600   1.000   0.000;
 1.000   0.000   80.200   1.000   0.000;
 1.000   0.000   65.900   1.000   0.000;
 1.000   0.000   59.700   1.000   0.000;
 1.000   0.000   71.800   0.000   1.000;
 1.000   0.000   72.400   1.000   0.000;
 1.000   0.000   80.500   1.000   0.000;
 1.000   0.000   62.900   0.000   1.000;
 1.000   0.000   67.400   0.000   1.000;
 1.000   0.000   80.200   1.000   0.000;
 1.000   0.000   85.500   0.000   1.000;
 1.000   0.000   65.900   0.000   1.000;
 1.000   0.000   89.100   1.000   0.000;
 1.000   0.000   56.400   0.000   1.000;
 1.000   0.000   82.700   0.000   1.000;
 1.000   0.000   68.300   0.000   1.000;
 1.000   0.000   74.000   0.000   1.000;

here is my contraix matrix:


-1 1 0 0 0


I dont know why? It is because of the column male and female that we 
can not treat them like this?



Hope to hear from you soon


Merci!


*De :* freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Douglas Greve 


*Envoyé :* mardi 14 juin 2016 17:23:08
*À :* Freesurfer support list
*Objet :* Re: [Freesurfer] Define the design matrix by myself
When passed to mris_preproc, the fsgd file is only to specify the 
subjects. Using the fsgd file for both mris_preproc and mri_glmfit 
assure that the order of the subjects is the same


On 6/14/16 6:10 AM, Hao wen wrote:


Hello:

To make it more clear!


I thought from FSGD file in mris_preproc, it will regard the group 
and gender as class, so in the X.dat will be gender*group; will not 
be possible to have the seperate columns for gender and group? do I 
understand it correctly?


Or the FSGD file used in mris-preproc has nothing to do with the 
design matrix?  It is used just to gather the thickness info from all 
the subjects?



Thank you


*De :* freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Hao wen 


*Envoyé :* mardi 14 juin 2016 09:25:06
*À :* Freesurfer support list
*Objet :* Re: [Freesurfer] Define the design matrix by myself
Yes, actually, I just want to know what does that mean when we use *, 

Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

Hi Trisanna

you don't need to inflate the overlays. They can just use the existing 
surface-based (sphere.reg) registration.


cheers
Bruce
On Wed, 15 Jun 2016, 
Trisanna Sprung-Much wrote:



Hi there
So I have sulcal labels from another software (.mnc format) from which I am 
trying to generate some probability maps. I was able
to convert the .mnc to .mgz surface overlay using mri_vol2surf for my MRIs 
after running all MRIs in recon-all. So, now I have
all my painted voxels as surface overlays, as I was instructed to do a few 
months ago.

I was told that the next step would be to use mri_surf2surf to resample the 
overlays to fsaverage. 

I am a bit confused as I would think that the next step would be to take the 
surface overlays and inflate them before I register
them to fsaverage. I see that when recon-all runs, it computes the registration 
of the MRI surface to fsaverage and saves it as
sphere.reg. Is there a way I can inflate my surface overlays in a similar 
manner and then apply this same registration to my
surface overlays? Or am I missing something?

thanks very much!

Trisanna


--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology



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[Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

Hi there

So I have sulcal labels from another software (.mnc format) from which I am
trying to generate some probability maps. I was able to convert the .mnc to
.mgz surface overlay using mri_vol2surf for my MRIs after running all MRIs
in recon-all. So, now I have all my painted voxels as surface overlays, as
I was instructed to do a few months ago.

I was told that the next step would be to use mri_surf2surf to resample the
overlays to fsaverage.

I am a bit confused as I would think that the next step would be to take
the surface overlays and inflate them before I register them to fsaverage.
I see that when recon-all runs, it computes the registration of the MRI
surface to fsaverage and saves it as sphere.reg. *Is there a way I can
inflate my surface overlays in a similar manner and then apply this same
registration to my surface overlays?* Or am I missing something?

thanks very much!

Trisanna


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] Fwd: concerting surface format

[Matt Glasser]

Look at mris_convert.  If that doesn¹t help would also see if BrainVisa
allows conversion to a third format that mris_convert works with.  Finally,
does BrainVisa not support GIFTI (the standard, cross-neuroimaging software
surface format)?

Peace,

Matt.

From:   on behalf of Trisanna
Sprung-Much 
Reply-To:  Freesurfer support list 
Date:  Wednesday, June 15, 2016 at 9:33 AM
To:  Freesurfer support list 
Subject:  [Freesurfer] Fwd: concerting surface format



Hi there

is there a way to convert .mesh (BrainVisa) to the Freesurfer surface
format? mri_convert doesn't seem to do it.

best wishes

Trisanna

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



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Re: [Freesurfer] Fwd: concerting surface format

[Olivier Coulon]

Hello Trisanna,
as pointed out by Matt as I started to write this email, the solution is 
in the Gifti format. If you install brainvisa, it provides tools to 
convert from .mesh to .gii. You can then read these in FreeSurfer or 
convert them using mri_convert. You can write to me privately if you 
want to have more details about how to perform the conversion using 
Brainvisa.

Best,

Olivier


Bruce Fischl 
15 juin 2016 16:39
Hi Trisanna,

perhaps check with the BrainVisa people? We don't know the specs of that
format. Maybe you could read it into matlab, then write it out in our
format with write_surf.m?

cheers
Bruce

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Trisanna Sprung-Much 
15 juin 2016 16:33

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Trisanna Sprung-Much 
14 juin 2016 22:12
Hi there

is there a way to convert .mesh (BrainVisa) to the Freesurfer surface 
format? mri_convert doesn't seem to do it.


best wishes

Trisanna

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


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--

Olivier Coulon,
Aix-Marseille University,
LSIS Laboratory
CNRS Director of Research,

olivier.cou...@univ-amu.fr 
http://olivier.meca-brain.org
MeCA Research Group
http://www.meca-brain.org
Institut des Neurosciences de La Timone
Faculté de Médecine,
27 Bd Jean Moulin,
13005 - Marseille, France
Tél: +33 (0)4 91 32 40 59


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Re: [Freesurfer] Fwd: concerting surface format

[Bruce Fischl]

Hi Trisanna,

perhaps check with the BrainVisa people? We don't know the specs of that 
format. Maybe you could read it into matlab, then write it out in our 
format with write_surf.m?

cheers
Bruce

On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:

> 
> 
> Hi there
> 
> is there a way to convert .mesh (BrainVisa) to the Freesurfer surface
> format? mri_convert doesn't seem to do it.
> 
> best wishes
> 
> Trisanna
> 
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
> 
> 
>
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[Freesurfer] Fwd: concerting surface format

[Trisanna Sprung-Much]

Hi there

is there a way to convert .mesh (BrainVisa) to the Freesurfer surface
format? mri_convert doesn't seem to do it.

best wishes

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] Compile and Install on El Capitan

[Z K]

Ill be attempting a build on an El Capitan machine today and will update 
the page accordingly.

-Zeke

On 06/15/2016 04:48 AM, Aziz Nanthaamornphong wrote:
> Hi,
>
> Can we compile & install Freesurfer on El Capitan? Unfortunately, I
> found the document for Lion
> (https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page).
>
> Thank you,
> Aziz
>
>
>
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Re: [Freesurfer] Coregister the CT image and MRI image

[HARI GURAGAIN]

Dear Douglas,

With the suggestions from Zeke, the mri_coreg is working now. I have one last 
question:
I got the new v1to2.lta. How to apply this transformation to the CT image? Is 
it by using mri_convert?
Something like below?
mri_convert -at v1to2.lta CT.nii new_CT.nii

Any suggestion will be greatly appreciated.
Thank you again,
Hari Guragain


> On Jun 9, 2016, at 5:53 PM, HARI GURAGAIN  wrote:
> 
> Dear Douglas,
> 
> I have used the same file as you pointed, but it keeps on showing the same 
> error message. I copied the file to my /Applications/freesurfer/bin directory 
> but it still shows the same error message:
>>> ‘dyld: Library not loaded: @executable_path/../lib/gcc/lib/libgomp.1.dylib’
>>> Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
>>> Reason: image not found
>>> Trace/BPT trap:5
> 
> 
> Does it have something to do with the library issue with mac?
> Any help is appreciated.
> Thank you,
> 
> 
>> On Jun 9, 2016, at 5:45 PM, Douglas N Greve  
>> wrote:
>> 
>> try
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg.mac
>> 
>> 
>> 
>> On 06/09/2016 06:21 PM, HARI GURAGAIN wrote:
>>> Dear Douglas,
>>> 
>>> The executable is not working as it says ‘Library not loaded: 
>>> @executable_path/../lib/gcc/lib/libgomp.1.dylib’
>>> Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
>>> Reason: image not found
>>> Trace/BPT trap:5
>>> 
>>> I am currently using the freeview: Version 1.0 and the operating system is: 
>>> OS X EI Captain Version: 10.11.5
>>> I wonder if the file you pointed works for the mac? Should I reinstall the 
>>> freeview?
>>> Any help would be greatly appreciated.
>>> 
>>> Thank you,
>>> 
>>> Hari
>>> 
>>> 
 On Jun 9, 2016, at 4:28 PM, Douglas N Greve  
 wrote:
 
 No, it is not the same command line. If you run it without args, it will
 give you some info, but it is basically
 
 mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta
 
 
 On 06/09/2016 05:22 PM, HARI GURAGAIN wrote:
> Thank you Douglas.
> One more thing: Is there any syntax how to use it? I wonder if it is same 
> as the mri_robust_register?
> 
> 
>> On Jun 9, 2016, at 3:43 PM, Douglas N Greve  
>> wrote:
>> 
>> I don't think robust register will do cross-modal. You may be better off
>> using mri_coreg, which you can get from here
>> 
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
>> 
>> 
>> On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:
>>> Dear Freesurfer community,
>>> 
>>> I am relatively new to this community.
>>> 
>>> I was trying to register the CT image and the MRI images (MRI as a the
>>> target volume and CT as the movable volume). I used the
>>> mri_robust_register to to do the registration as below:
>>> 
>>> /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta
>>> --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /
>>> 
>>> The problem is that:  after register, the new image (v1to2.nii) is not
>>> exactly aligned with the original MRI image (vol2.nii). It gives a
>>> very different output. I wonder if I am missing anything here or I
>>> need to do some extra steps after the above command in order to get
>>> the correct alignment of the two images. I was hoping to get the
>>> resultant image should be well orient with the target volume image
>>> (vol2.nii image in my case).
>>> 
>>> I really appreciate any help here.
>>> 
>>> Hari Guragain
>>> 
>>> 
>>> 
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>> -- 
>> 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/
>> 
>> ___
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>> 
>> 
>> The information in this e-mail is intended only for the person to whom 
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the 
>> e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
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>> in error
>> but does not contain patient information, please 

Re: [Freesurfer] Define the design matrix by myself

[Hao wen]

Glad to know the fsgd file explanation:)

I have deleted the first colum(constant column, I made a simple mistake), but 
it didnt work even without the constant column, I got the same error:


ERROR: matrix is ill-conditioned or badly scaled, condno = 1.07053e+07

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.


here is the design matrix:


AD CN  age   male female

 0.000   1.000   74.300   0.000   1.000;
 0.000   1.000   73.700   0.000   1.000;
 0.000   1.000   84.500   1.000   0.000;
 0.000   1.000   78.500   1.000   0.000;
 0.000   1.000   80.800   0.000   1.000;
 0.000   1.000   65.400   0.000   1.000;
 0.000   1.000   73.100   1.000   0.000;
 0.000   1.000   72.600   1.000   0.000;
 0.000   1.000   63.200   0.000   1.000;
 0.000   1.000   71.700   0.000   1.000;
 0.000   1.000   77.700   1.000   0.000;
 0.000   1.000   76.900   0.000   1.000;
 0.000   1.000   73.200   0.000   1.000;
 0.000   1.000   76.200   0.000   1.000;
 0.000   1.000   84.700   0.000   1.000;
 0.000   1.000   69.600   1.000   0.000;
 0.000   1.000   70.100   0.000   1.000;
 0.000   1.000   70.900   1.000   0.000;
 0.000   1.000   77.000   1.000   0.000;
 0.000   1.000   74.500   0.000   1.000;
 0.000   1.000   74.400   1.000   0.000;
 0.000   1.000   72.900   0.000   1.000;
 0.000   1.000   74.000   0.000   1.000;
 0.000   1.000   70.600   0.000   1.000;
 0.000   1.000   78.200   0.000   1.000;
 0.000   1.000   70.600   0.000   1.000;
 0.000   1.000   80.300   1.000   0.000;
 0.000   1.000   65.100   0.000   1.000;
 0.000   1.000   69.800   0.000   1.000;
 0.000   1.000   71.100   0.000   1.000;
 1.000   0.000   81.300   0.000   1.000;
 1.000   0.000   75.400   0.000   1.000;
 1.000   0.000   73.900   1.000   0.000;
 1.000   0.000   64.100   0.000   1.000;
 1.000   0.000   80.100   0.000   1.000;
 1.000   0.000   78.300   0.000   1.000;
 1.000   0.000   73.200   0.000   1.000;
 1.000   0.000   75.300   1.000   0.000;
 1.000   0.000   65.600   0.000   1.000;
 1.000   0.000   62.400   0.000   1.000;
 1.000   0.000   77.200   1.000   0.000;
 1.000   0.000   70.700   1.000   0.000;
 1.000   0.000   70.100   1.000   0.000;
 1.000   0.000   82.600   1.000   0.000;
 1.000   0.000   80.200   1.000   0.000;
 1.000   0.000   65.900   1.000   0.000;
 1.000   0.000   59.700   1.000   0.000;
 1.000   0.000   71.800   0.000   1.000;
 1.000   0.000   72.400   1.000   0.000;
 1.000   0.000   80.500   1.000   0.000;
 1.000   0.000   62.900   0.000   1.000;
 1.000   0.000   67.400   0.000   1.000;
 1.000   0.000   80.200   1.000   0.000;
 1.000   0.000   85.500   0.000   1.000;
 1.000   0.000   65.900   0.000   1.000;
 1.000   0.000   89.100   1.000   0.000;
 1.000   0.000   56.400   0.000   1.000;
 1.000   0.000   82.700   0.000   1.000;
 1.000   0.000   68.300   0.000   1.000;
 1.000   0.000   74.000   0.000   1.000;


here is my contraix matrix:


-1 1 0 0 0


I dont know why? It is because of the column male and female that we can not 
treat them like this?


Hope to hear from you soon


Merci!


De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Douglas Greve 

Envoyé : mardi 14 juin 2016 17:23:08
À : Freesurfer support list
Objet : Re: [Freesurfer] Define the design matrix by myself

When passed to mris_preproc, the fsgd file is only to specify the subjects. 
Using the fsgd file for both mris_preproc and mri_glmfit assure that the order 
of the subjects is the same

On 6/14/16 6:10 AM, Hao wen wrote:

Hello:

To make it more clear!


I thought from FSGD file in mris_preproc, it will regard the group and gender 
as class, so in the X.dat will be gender*group; will not be possible to have 
the seperate columns for gender and group? do I understand it correctly?

Or the FSGD file used in mris-preproc has nothing to do with the design matrix? 
 It is used just to gather the thickness info from all the subjects?


Thank you


De : 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 de la part de Hao wen 

Envoyé : mardi 14 juin 2016 09:25:06
À : Freesurfer support list
Objet : Re: [Freesurfer] Define the design matrix by myself

Yes, actually, I just want to know what does that mean when we use *, for 
example Gender*Group, does this mean group and gender has a interaction? So 
what i want to know, if we can create design matrix like this:
   X = 1 + age + gender + group,
I dont want the interact between group and gender

Hope to hear from you soon!
Merci
Hao

De : 
freesurfer-boun...@nmr.mgh.harvard.edu
 

Re: [Freesurfer] SIENAX

[Bruce Fischl]

Hmmm, I'm not sure I understand your question. SIENAX is indeed from the 
FSL group and different than what we do. What are you trying to accomplish?


On Wed, 15 Jun 2016, Hassan bakhshi 
wrote:



Hi,

I lately heard about SIENAX and when I looked into it it seems like
Freesurfer, 
using the same brain extraction process and etc.

I wanted to ask if it is more complete than Freesurfer or not? and why
researcher are going after it?

It is for Oxford University I think.

Kind Regards,
 

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[Freesurfer] controlling for ICV in LME

[Clara Kühn]

Dear FreeSurfer experts,

I conducted a study with 3 groups of children (2 trainings, 1 control) and I 
want to analyze them longitudinally with LMEs. While preparing my data 2 topics 
came up that I would like to know more about.

A. controlling for ICV/mean thickness/surface area

1) I want to look at changes in cortical thickness and surface area at the 
whole brain level. Would I then have to control for mean thickness/ area, 
respectively, per parcellation? Or rather ICV?
2) Is it the same for looking at changes in thickness and area in different 
ROIs?
3) Since I have (up to) 3 scans per kid, do I include mean thickness/area/ICV 
for each scan or should I use it from baseline or a mean of all scans?

B. demeaning covariates

1) Is it necessary to demean the covariates? I have not seen any hints on the 
FS wiki pages about that yet.
2) Would I also have to demean the dependent variable (in my case whole brain 
cortical thickness/surface area)?

Thank you!
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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[Freesurfer] convert from MNI152 to native space

[Leila Reddy]

Hi,
I have a binary mask from the WFU_Pickatlas. I think this mask in in the MNI152 
space (when I load_nifti in Matlab I get dimensions of [91 109 91]. I would 
like to convert this mask into the native space of each subject. I tried the 
following command but the results do not look right in Freeview:
 mri_vol2vol --mov mask_MNI152.nii --targ bold/005/f.nii.gz --o 
mask_in_Native.nii --mni152reg
The overlay of the mask on f.nii in Freeview is mostly outside the brain.

How can I go about this step?

Thanks for your help,Leila
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[Freesurfer] SIENAX

[Hassan bakhshi]

Hi,

I lately heard about SIENAX and when I looked into it it seems like
Freesurfer,
using the same brain extraction process and etc.

I wanted to ask if it is more complete than Freesurfer or not? and why
researcher are going after it?

It is for Oxford University I think.

Kind Regards,
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[Freesurfer] Compile and Install on El Capitan

[Aziz Nanthaamornphong]

Hi,

Can we compile & install Freesurfer on El Capitan? Unfortunately, I found
the document for Lion (
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page).

Thank you,
Aziz
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[Freesurfer] Convert ascii to .mgh

[Robby De Pauw]

Dear FreeSurfer users,

To address the problem of multiple comparison, I wanted to apply the 
localfdr-method. For this purpose, I need the F-statistic (which I can extract 
from the F.mgh scalar overlay I presume?).

I converted this to an ascii-file, which I was able to load into R, using the 
following chink of code:

mris_convert -c 
/Users/robbydepauw/Desktop/FreeSurfer/GLM/lh.Group.volume.glmdir/Groupeffect/F.mgh
 $SUBJECTS_DIR/fsaverage/surf/lh.white F.asc

After performing an local fdr analysis in R, I want to create a scalar overlay 
“lfdr.mgh”, but I fail at converting the asci file into an “.mgh”-overlay file.

Any idea how I could approach this conversion (from asci back to .mgh)?

Many thanks,

Greetings

Robby

Robby De Pauw, PT, MT, drs.
T +32 09 332 12 19 | Email robby.dep...@ugent.be

Ghent University | Rehabilitation Sciences and Physiotherapy
Campus Heymans 3B3 (022)
De Pintelaan 185 BE-9000 Ghent
Route to my office

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Re: [Freesurfer] tkmedit

[kojima_masaki_mail]

Thanks! I will use it.

Best, 
Kojima 


- Original Message -
>From: Bruce Fischl 
>To: kojima_masaki_m...@yahoo.co.jp; Freesurfer support list 
> 
>Date: 2016/6/15, Wed 10:32
>Subject: Re: [Freesurfer] tkmedit
> 
>yes!
>On Wed, 15 Jun 2016, kojima_masaki_m...@yahoo.co.jp wrote:
>
>> Hi Bruce
>> 
>> Thank you for useful advice.
>> I referred to FreesurfuerWiki and tried to use tkmedit to check whether
>> recon is accurate or not.
>> Now I am trying to use freeview.
>> Is it possible to do these procedure with freeview instead of tkmedit?
>> 
>> Regards,
>> 
>> Kojima
>> 
>>
>>       - Original Message -
>>       From: Bruce Fischl 
>>       To: kojima_masaki_m...@yahoo.co.jp; Freesurfer support list
>>       
>>       Date: 2016/6/14, Tue 21:50
>>       Subject: Re: [Freesurfer] tkmedit
>> 
>> Hi Kojima
>> 
>> tkmedit has been deprecated. Can you try using freeview instead?
>> 
>> cheers
>> Bruce
>> On Tue, 14
>> Jun 2016, kojima_masaki_m...@yahoo.co.jp wrote:
>> 
>> > Hi. 
>> >
>> > I have this error, when I was doing 
>> > tkmeditPSY1001fs/Users/MRI/Desktop/fsurfer_test_kojima/Surf_data_main/PSY1001fs/mr
>> i/brainma
>> > sk.mgz -aux
>> >
>> /Users/MRI/Desktop/fsurfer_test_kojima/Surf_data_main/PSY1001fs/mri/wm.mgz
>> > -surfs
>> >
>> > ERROR:
>> > Assertion failed: (!c->out.queue_len), function write_vec, file
>> xcb_conn.c,
>> > line 195.
>> > Abort
>> >
>> > what is the problem?
>> >
>> > Kojima
>> >
>> >
>> > [IMAGE]
>> >
>> >
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>> addressed. If you believe this e-mail was sent to you in error and the
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>> and properly
>> dispose of the e-mail.
>> 
>> 
>> 
>>
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>addressed. If you believe this e-mail was sent to you in error and the e-mail
>contains patient information, please contact the Partners Compliance HelpLine 
>at
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>properly
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>
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