[Freesurfer] FSFAST- Cerebellum

[Sabin Khadka]

Hi all,

I am trying to extract mean time series BOLD data using FSFAST from
Cortical ROIs + sub cortical ROIs and cerebellum.

preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6
-per-run -stc oddmri_segstats --annot fsaverage lh aparc --i
rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000
--excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
mri_segstats --annot fsaverage rh aparc --i
rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
--excludeid 2004 --avgwf CorticalTimeSeries_rh.txt

and for cortical time series

mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
/opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id
17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58
--i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
subCorticalTimeSeries.txt

But I am not sure on how exactly to extract time series from cerebellar
regions. So if I want to extract time series from regions as described in
Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in
FreeSurferCololLUT.txt? If not could you please direct me to processes that
I can use.

Cheers,
Sabin Khadka
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Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

Hi Doug

So all of my sulci for each subject have been registered to fsaverage using
mri_surf2surf. I am now wondering how I could create an average of a sulcus
using these overlays - I understand that mris_make_average_surface is an
option but I cannot seem to find whether this works for overlays and not
just surfaces (white, pial). I want to take each subject overlay on
fsaverage and average them to get a probability map for a single sulcus.

thanks

Trisanna

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


On Wed, Jun 15, 2016 at 6:25 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> 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 <
> gr...@nmr.mgh.harvard.edu> 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
>> > >

[Freesurfer] ERROR: mpr2mni305 failed

[Marita Partanen]

Hi there

I running freesurfer-Darwin-lion-stable-pub-v5.3.0 on a Mac 10.10.5. I have run 
recon-all successfully in the past, but now I am getting an error of mpr2mni305 
failed, see transforms/talairach_avi.log

This issue appears the same as a recent post 
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg47393.html but 
I couldn't see a solution. Any ideas?

Here's the full error log:

/Users/ophthalmologylab/Studies/Dyslexia_MRI/Intervention/freesurfer/DEGDY001B/mri
/Applications/freesurfer/bin/talairach_avi
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
Darwin cfri2163m.bcricwh.lan 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 
02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
Fri Jun 17 13:29:22 PDT 2016
mri_convert orig_nu.mgz talsrcimg.img
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig_nu.mgz...
TR=8.14, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 2.91038e-11, -3.72529e-09)
j_ras = (-3.72529e-09, -5.82077e-11, -1)
k_ras = (7.27596e-12, 1, -5.82077e-11)
writing to talsrcimg.img...
Analyze Output Matrix
-1.000  -0.000   0.000   126.275;
 0.000  -0.000   1.000  -112.522;
-0.000  -1.000  -0.000   132.333;
 0.000   0.000   0.000   1.000;

INFO: set hdr.hist.orient to -1
mpr2mni305 talsrcimg
Fri Jun 17 13:29:25 PDT 2016
/Applications/freesurfer/bin/mpr2mni305 talsrcimg
$Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $
target=711-2C_as_mni_average_305

-
analyzeto4dfp talsrcimg -O0 -y
-

$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $
Fri Jun 17 13:29:25 2016
Writing: talsrcimg.4dfp.hdr
$Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $
Reading: talsrcimg.hdr
header size 348 bytes
hdr.dime.datatype offset=70 value=2
hdr.dime.bitpix offset=72 value=8
hdr.hist.orient offset=252 value=-1
dimensionality 4
dimensions   256   256   256 1
Reading: talsrcimg.img
Writing: talsrcimg.4dfp.img
Writing: talsrcimg.4dfp.ifh
ifh2hdr talsrcimg -r0to255
ori=2

-
gauss_4dfp talsrcimg 1.1
-

dyld: Library not loaded: /usr/local/gfortran/lib/libgcc_s.1.dylib
  Referenced from: /Applications/freesurfer/bin/gauss_4dfp
  Reason: image not found
Trace/BPT trap
ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133
ERROR: mpr2mni305 execution aborted


_

Marita Partanen, M.Sc., M.Ed.
Ph.D. Candidate in School Psychology
The University of British Columbia
2125 Main Mall
Vancouver, BC
V6T 1Z4
parta...@alumni.ubc.ca
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[Freesurfer] REPOST: 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] Postdoctoral Position in Infant MRI Analysis at UNC-Chapel Hill

[gangli]

Postdoctoral research associate positions are available in the Department
of Radiology and Biomedical Research Imaging Center (BRIC) at the
University of North Carolina at Chapel Hill (UNC-Chapel Hill). Our current
focuses are to better understand the dynamic and critical early brain
development in both health and disease, via multimodal neuroimaging
analysis. The successful candidate will support our efforts either in
advancing neuroimaging analysis technologies or in neuroscience
applications. We are seeking highly motivated individuals who have extensive
research experience in neuroimaging analysis (e.g., structural, diffusion
or functional MRI) and demonstrated academic excellence, including
publications in first-class journals and conferences. The candidate should
have a Ph.D. (or equivalent) in Neuroscience, Computer Science, Applied
Mathematics/Statistics, Electrical Engineering, Biomedical Engineering, or
related fields. Good command of programming tools including Matlab, C++,
Linux, and scripting are necessary to carry out the research work in this
group.



The successful candidate will be part of a diverse group including
neuroscientists, radiologists, psychologists, physicists, biostatistician,
and computer scientists, and will build upon the group's extensive
foundation on neuroimaging analysis. If interested, please email resume to
Dr. Gang Li (gang...@med.unc.edu

).


For more information, please visit: http://www.unc.edu/~gangl/contact.html

.
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Re: [Freesurfer] Apply mris_apply_reg for a label

[Alexandre Routier]

Hello,

I am a little but confused with the syntax: I have a drawn label
lh.manual.label
and I want it on the right hemisphere and I was thinking of this command:
mri_label2label --srcsurfreg lh.sphere.reg --targsurfreg rh.sphere.reg
--surfreg
lh.sphere.left_right --regmethod surface --hemi lh --srclabel lh.manual.label
--targlabel rh.manual.label

(I have the following sphere files for my subject : ?h.qsphere.nofix,
?h.sphere, ?h.sphere.left_right, ?h.sphere.reg)

I don't see how to include ?h.sphere.left_right to the command line.

Alexandre



2016-06-16 18:53 GMT+02:00 Bruce Fischl :

> Hi Alexandre
>
> try mri_label2label using the ?h.sphere.left_right
>
> cheers
> Bruce
>
> On Thu, 16 Jun 2016, Alexandre Routier wrote:
>
> Hello everyone,
>> I have a label for the left hemisphere for my subject but I don't
>> understand
>> the syntax to apply mris_apply_reg on this label to obtain the right
>> hemisphere version.
>>
>> mris_left_right_register was performed to get lh.sphere.left_right
>> and lh.sphere.left_right but I don't know how to use this for
>> the mris_apply_reg command.
>>
>> Thanks in advance for your answer.
>>
>> Alexandre
>>
>>
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[Freesurfer] FSFAST time series extraction

[curry_sam77]

 Hi all,
I am trying to extract mean time series BOLD data using FSFAST from Cortical 
ROIs + sub cortical ROIs and cerebellum.
preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 
-per-run -stc odd    mri_segstats --annot fsaverage lh aparc --i 
rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000 --excludeid 
1004 --avgwf CorticalTimeSeries_lh.txt     
mri_segstats --annot fsaverage rh aparc --i 
rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 --excludeid 
2004 --avgwf CorticalTimeSeries_rh.txt    
and for cortical time series
mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab 
/opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id 17 
--id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58 --i 
rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf 
subCorticalTimeSeries.txt    
But I am not sure on how exactly to extract time series from cerebellar 
regions. So if I want to extract time series from regions as described in 
Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in 
FreeSurferCololLUT.txt? If not could you please direct me to processes that I 
can use. 


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