[Freesurfer] Question re extracting average thickness values per subject based on cache.th13.abs.y.ocn.dat

[Gold, Andrea (NIH/NIMH) [F]]

Hi,

I’m trying to extract the average thickness per subject in significant clusters 
from a Qdec analysis, and hope to clarify 2 things re: the 
“cache.th13.abs.y.ocn.dat“  output from this command:
mri_glmfit-sim --glmdir (dir) --cache 1.3 abs --cwp 0.05 —2spaces

I’ve attached  all relevant output files.

This analysis has 2 clusters, and I understand the 2 clusters match the order 
of the clusters in the cache.th13.abs.sig.cluster.summary file (left=cluster 1, 
right=cluster 2).
1) Would you please confirm whether the rows of the cache.th13.abs.y.ocn.dat“ 
match the order of subjects listed in the qdec.fsgd file?
2) Also, I noticed the  cache.th13.abs.sig.cluster.summary file lists MNI 
coordinates – is there a way to get this to print Talairach coordinates from 
the mri_glmfit-sim command? If not, that’s fine – I can get them from qdec but 
just curious.

Thanks!
Andrea


--
Andrea Gold, Ph.D.
Section on Development and Affective Neuroscience
National Institute of Mental Health
Room 201, Bldg. 15K, MSC 2670
Bethesda, MD 20892-2670
Phone: 301-827-9804
Fax: 301-402-2010
Email: 
andrea.g...@nih.gov



cache.mri_glmfit-sim.log
Description: cache.mri_glmfit-sim.log


cache.th13.abs.y.ocn.dat
Description: cache.th13.abs.y.ocn.dat


cache.th13.abs.sig.cluster.summary
Description: cache.th13.abs.sig.cluster.summary


qdec.fsgd
Description: qdec.fsgd
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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

[Anastasia Yendiki]

Hi Elijah - This error occurs with one number of control points but not 
another? That would be very strange. I'd have to look at the full 
trac-al.log to figure it out, I can't guess what's going on just from this 
one line unfortunately.


a.y

On Fri, 19 Aug 2016, Elijah Mak wrote:


Hi Anastasia,
Thanks, it works, but only for MNI reg option. For the CVS stream, there was an 
error message during
-prior. 

ERROR: fio_pushd: 
/Users/MacPro/Documents/22995_EM/dmri/xfms/cvs/final_CVSmorph_tocvs_avg35/mri

This error message did not halt the process though. Could this be a clue?

Thanks for your patience :)

Best Wishes,

Elijah





--

Elijah Mak, Gates Scholar

PhD Candidate | Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ



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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

[Elijah Mak]

Hi Anastasia,

Thanks, it works, but only for MNI reg option. For the CVS stream, there
was an error message during -prior.

ERROR: fio_pushd:
/Users/MacPro/Documents/22995_EM/dmri/xfms/cvs/final_CVSmorph_tocvs_avg35/mri

This error message did not halt the process though. Could this be a clue?

Thanks for your patience :)

Best Wishes,

Elijah




-- 

Elijah Mak, Gates Scholar

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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Re: [Freesurfer] Freeview quits unexpectedly

[Ruopeng Wang]

BTW, what is the command you ran?

> On Aug 19, 2016, at 2:20 PM, Ruopeng Wang  wrote:
> 
> Are you running FS 5.3 or the latest 6.0 beta? If former would it be possible 
> for you to try 6.0 beta?
> 
> Best,
> Ruopeng
> 
> 
>> On Aug 19, 2016, at 1:27 PM, Corriveau-Lecavalier Nick 
>>  wrote:
>> 
>> Hello FreeSurfer developers,
>> 
>> 
>> I am trying to load a thickness file (ex: lh.long.thickness-avg.fwhm10.mgh) 
>> in freeview, but as soon as I click the file or press enter after the 
>> command line, the program quits unexpectedly. I can load T1, orig.mgz, .pial 
>> files, etc. without problem. But when it comes to files that came out of the 
>> long_mris_slopes command, freeview quits inevitably.
>> 
>> 
>> Is it a problem with freesurfer or my computer (ex: graphic card not good 
>> enough)? Do you have any idea why it keeps crashing? I am running a Macbook 
>> Air mid 2013 with OS X El Captain, 1.3 GHz Intel Core i5, 4 GB 1600 Mhz 
>> DDR3, Graphics: Intel HD Graphics 5000 1536 MB.
>> 
>> 
>> Regards,
>> 
>> 
>> Nick
>> 
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>> 
> 
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Re: [Freesurfer] Freeview quits unexpectedly

[Ruopeng Wang]

Are you running FS 5.3 or the latest 6.0 beta? If former would it be possible 
for you to try 6.0 beta?

Best,
Ruopeng


> On Aug 19, 2016, at 1:27 PM, Corriveau-Lecavalier Nick 
>  wrote:
> 
> Hello FreeSurfer developers,
> 
> 
> I am trying to load a thickness file (ex: lh.long.thickness-avg.fwhm10.mgh) 
> in freeview, but as soon as I click the file or press enter after the command 
> line, the program quits unexpectedly. I can load T1, orig.mgz, .pial files, 
> etc. without problem. But when it comes to files that came out of the 
> long_mris_slopes command, freeview quits inevitably.
> 
> 
> Is it a problem with freesurfer or my computer (ex: graphic card not good 
> enough)? Do you have any idea why it keeps crashing? I am running a Macbook 
> Air mid 2013 with OS X El Captain, 1.3 GHz Intel Core i5, 4 GB 1600 Mhz DDR3, 
> Graphics: Intel HD Graphics 5000 1536 MB.
> 
> 
> Regards,
> 
> 
> Nick
> 
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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

[Anastasia Yendiki]

Mmm, it sounds like the shape of the tract is too convoluted for it to 
find a good fit. I'd try increasing the # of control points.


On Fri, 19 Aug 2016, Elijah Mak wrote:


Hi Anastasia,
Thank you for looking into that subject. I have tried reinitiliasation a few 
times and in all cases, it
just could not find a satisfactory control point fit during the -prior stage. 
Therefore, the -prior
stage has been running for more than 10 hours now. This occurs in other a small 
number of other subjects
as well. 

WARN: Could not find satisfactory control point fit - try 596

How can I resolve this? And what type of problem could be reflected by  this? 
Bad aparc+aseg.mgz /
registration to template? 

If all else fails, I will exclude subjects using the criteria that you set in 
the Neuroimage paper:
where a subject was excluded if there were failures of reconstruction in 2 or 
more WM tracts. 

Thank you for your help!

Best Wishes,
Elijah




--

Elijah Mak, Gates Scholar

PhD Candidate | Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ



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Re: [Freesurfer] voxel values in destrieux file

[Douglas Greve]

The error is in recon-all. If you want to fix this one outside of recon-all you 
can run
cd $SUBJECTS_DIR/subject/mri
mri_aparc2aseg --s subject --volmask --aseg aseg.presurf.hypos --a2009s


On 8/19/16 11:08 AM, pierre deman wrote:

Hello,

I am looking at the destrieux atlas generated by recon-all (I use the 
freesurfer dev version), the file aparc.a2009+aseg.mgz), and sometimes 
the value of a voxel doesn't exist in the FreesurferColorLut. I have 
quite a lot of values between 2036 and 2100 (2038, 2074, 2075 for 
example) and I don't find these values in the FreeSurferColorLut.


Is that normal ? What do they correspond at ?

Regards,
Pierre


--
DEMAN Pierre
Mobile : +33 7 82 57 80 94


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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

[Elijah Mak]

Hi Anastasia,

Thank you for looking into that subject. I have tried reinitiliasation a
few times and in all cases, it just could not find a satisfactory control
point fit during the -prior stage. Therefore, the -prior stage has been
running for more than 10 hours now. This occurs in other a small number of
other subjects as well.

WARN: Could not find satisfactory control point fit - try 596

How can I resolve this? And what type of problem could be reflected by
 this? Bad aparc+aseg.mgz / registration to template?

If all else fails, I will exclude subjects using the criteria that you set
in the Neuroimage paper: where a subject was excluded if there were
failures of reconstruction in 2 or more WM tracts.

Thank you for your help!

Best Wishes,
Elijah




-- 

Elijah Mak, Gates Scholar

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

[Anastasia Yendiki]

Hi Elijah - It looks to me like the forceps major had the same problem for 
both MNI and CVS in this subject, right? This subject has a relatively 
thin and somewhat convoluted forceps major, so you can try increasing the 
number of control points, say from 7 to 8. (But I'd try reinitialization 
first, before changing anything.)


Hope this helps,

a.y

On Thu, 18 Aug 2016, Elijah Mak wrote:


Dear Anastasia,
I have also uploaded the file with the problem (22995_EM.zip), and this is how
my config file looks like after modifications:

set subjlist = (22995)
set pathlist = (fmajor_PP)
set ncpts = (7)
set reinit = (1)

Thanks again!

Best Wishes,
Elijah


--

Elijah Mak

PhD Candidate | Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ



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[Freesurfer] Freeview quits unexpectedly

[Corriveau-Lecavalier Nick]

Hello FreeSurfer developers,


I am trying to load a thickness file (ex: lh.long.thickness-avg.fwhm10.mgh) in 
freeview, but as soon as I click the file or press enter after the command 
line, the program quits unexpectedly. I can load T1, orig.mgz, .pial files, 
etc. without problem. But when it comes to files that came out of the 
long_mris_slopes command, freeview quits inevitably.


Is it a problem with freesurfer or my computer (ex: graphic card not good 
enough)? Do you have any idea why it keeps crashing? I am running a Macbook Air 
mid 2013 with OS X El Captain, 1.3 GHz Intel Core i5, 4 GB 1600 Mhz DDR3, 
Graphics: Intel HD Graphics 5000 1536 MB.


Regards,


Nick

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Re: [Freesurfer] Projecting FA map onto fsaverge surface

[Taha Abdullah]

Great! looks good, thanks for the help.

Enjoy your weekend!

On Fri, Aug 19, 2016 at 11:34 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Taha - Once you've mapped from the volume onto the white surface, you
> should be able to display it on the inflated surface, and also to get
> thickness statistics (thickness is just the distance between corresponding
> points on the white and pial surface). You don't need to do anything to map
> from white to inflated within an individual.
>
> Best,
> a.y
>
>
> On Fri, 19 Aug 2016, Taha Abdullah wrote:
>
> Excellent! Thank you for the quick advice, I tried this initially but I was
>> using the wrong xfm format.
>> Since I have the FA map in subject ?h.white space, I have done the same
>> with the
>> tract endings too. I am having some difficulties conceptually, in terms of
>> projecting the end points onto either the subject specfic or
>> fsaverage inflated
>> surface. I assumed using mri_surf2surf would be sufficient to transform
>> the
>> endpts from subject surface ?h.white space to the inflated surface, but
>> it is a
>> scalar data file. Once the endpts are projected onto the inflated surface
>> it
>> seems straightforward to extract the thickness values for
>> further analysis.
>> Essentially replicating the attached image from Sølsnesa 2015.  If you
>> have any
>> suggestions that would be much appreciated. Thank you very much!
>>
>> Best,
>> Taha
>>
>>
>>
>> On Fri, Aug 19, 2016 at 9:49 AM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Taha - Trying getting a .dat registration file from bbregister
>>   and using that as the input to mri_vol2surf. There's a multimodal
>>   tutorial on the freesurfer wiki that might be of help.
>>
>>   Best,
>>   a.y
>>
>>   On Thu, 18 Aug 2016, Taha Abdullah wrote:
>>
>> Hello All,
>>
>> I am trying to project FA map (dtifit_FA.nii.gz) and the
>> endpt[1/2].pd.nii.gz from TRACULA onto fsaverage surface
>> space.
>> I was following instructions on
>> http://web.mit.edu/fsl_v5.0.8/fsl/doc/wiki/FDT(2f)UserGuide.
>> html,
>> under FreeSurfer
>> Registration, to create the various xfms files.
>>
>> Next, I registered the FA map to subject conformed space
>> using flirt
>>  *  flirt -in dtifit_FA.nii.gz -ref
>> ../../mri/orig.nii.gz -applyxfm -init
>> ./xfms_taha/fa2freesurfer.mat -out fa2FS.nii.gz
>> Then, I used mri_vol2surf to project the registered FA
>> map onto fsaverage surface with the following command.
>>  *  mri_vol2surf --mov fa2FS.nii.gz --projdist-max 6 6 1
>> --cortex --hemi rh --trgsubject fsaverage --regheader
>> taha_brain
>> --reg ./xfms_taha/fa2freesurfer.mat --o
>> FA_2fsavg_surf.mgh
>> Upon viewing in freeview the fsavg rh.white surface and
>> fa2FS.nii.gz (FA map in FreeSurfer space) did not allign
>> properly. I have tried some variations wtihout any luck.
>> I used the following command line for freeview.
>>  *  freeview -f/usr/local/freesurfer/subjec
>> ts/fsaverage/surf/rh.white:overlay=FA_2fsavg_surf.m
>> gh -v fa2FS.nii.gz
>>  *  Attached are some pics of the FA confomred map and
>> fsaverage.rh.white surface
>> Do I need a xfm file for taliarch allignment? Any advice
>> or insight would be greatly appreciated.
>>
>> Thanks in advance,
>> Taha
>>
>> Terminal output: from mri_vol2surf
>> srcvol = fa2FS.nii.gz
>> srcreg = ./xfms_taha/fa2freesurfer.mat
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = rh
>> trgsubject = fsaverage
>> surfreg = sphere.reg
>> ProjDist = 0.5
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 1
>> INFO: float2int code = 0
>> Done loading volume
>> Computing registration from header.
>>   Using
>> /usr/local/freesurfer/subjects/taha_brain/mri/orig.mgz
>> as target reference.
>> Loading label
>> /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.
>> label
>> Reading surface
>> /usr/local/freesurfer/subjects/taha_brain/surf/rh.white
>> Done reading source surface
>> Mapping Source Volume onto Source Subject Surface
>>  1 6 6 6
>> using old
>> Done mapping volume to surface
>> Number of source voxels hit = 81606
>> Reading source surface registration
>>
>> /usr/local/freesurfer/subjects/taha_brain/surf/rh.sphere.reg
>> Done loading s

Re: [Freesurfer] voxel values in destrieux file

[Douglas Greve]

Sorry, that is a bug. I introduced it  in a change a few months ago. 
I'll fix it. Thanks!



On 8/19/16 11:08 AM, pierre deman wrote:

Hello,

I am looking at the destrieux atlas generated by recon-all (I use the 
freesurfer dev version), the file aparc.a2009+aseg.mgz), and sometimes 
the value of a voxel doesn't exist in the FreesurferColorLut. I have 
quite a lot of values between 2036 and 2100 (2038, 2074, 2075 for 
example) and I don't find these values in the FreeSurferColorLut.


Is that normal ? What do they correspond at ?

Regards,
Pierre


--
DEMAN Pierre
Mobile : +33 7 82 57 80 94


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Re: [Freesurfer] Projecting FA map onto fsaverge surface

[Anastasia Yendiki]

Hi Taha - Once you've mapped from the volume onto the white surface, you 
should be able to display it on the inflated surface, and also to get 
thickness statistics (thickness is just the distance between corresponding 
points on the white and pial surface). You don't need to do anything to 
map from white to inflated within an individual.


Best,
a.y

On Fri, 19 Aug 2016, Taha Abdullah wrote:


Excellent! Thank you for the quick advice, I tried this initially but I was
using the wrong xfm format.
Since I have the FA map in subject ?h.white space, I have done the same with the
tract endings too. I am having some difficulties conceptually, in terms of
projecting the end points onto either the subject specfic or fsaverage inflated
surface. I assumed using mri_surf2surf would be sufficient to transform the
endpts from subject surface ?h.white space to the inflated surface, but it is a
scalar data file. Once the endpts are projected onto the inflated surface it
seems straightforward to extract the thickness values for further analysis.
Essentially replicating the attached image from Sølsnesa 2015.  If you have any
suggestions that would be much appreciated. Thank you very much!

Best,
Taha



On Fri, Aug 19, 2016 at 9:49 AM, Anastasia Yendiki
 wrote:

  Hi Taha - Trying getting a .dat registration file from bbregister
  and using that as the input to mri_vol2surf. There's a multimodal
  tutorial on the freesurfer wiki that might be of help.

  Best,
  a.y

  On Thu, 18 Aug 2016, Taha Abdullah wrote:

Hello All,

I am trying to project FA map (dtifit_FA.nii.gz) and the
endpt[1/2].pd.nii.gz from TRACULA onto fsaverage surface
space.
I was following instructions on
http://web.mit.edu/fsl_v5.0.8/fsl/doc/wiki/FDT(2f)UserGuide.html,
under FreeSurfer
Registration, to create the various xfms files. 

Next, I registered the FA map to subject conformed space
using flirt 
 *  flirt -in dtifit_FA.nii.gz -ref
../../mri/orig.nii.gz -applyxfm -init
./xfms_taha/fa2freesurfer.mat -out fa2FS.nii.gz
Then, I used mri_vol2surf to project the registered FA
map onto fsaverage surface with the following command. 
 *  mri_vol2surf --mov fa2FS.nii.gz --projdist-max 6 6 1
--cortex --hemi rh --trgsubject fsaverage --regheader
taha_brain
    --reg ./xfms_taha/fa2freesurfer.mat --o
FA_2fsavg_surf.mgh
Upon viewing in freeview the fsavg rh.white surface and
fa2FS.nii.gz (FA map in FreeSurfer space) did not allign
properly. I have tried some variations wtihout any luck.
I used the following command line for freeview.  
 *  freeview 
-f/usr/local/freesurfer/subjects/fsaverage/surf/rh.white:overlay=FA_2fsavg_surf.m
gh -v fa2FS.nii.gz
 *  Attached are some pics of the FA confomred map and
fsaverage.rh.white surface
Do I need a xfm file for taliarch allignment? Any advice
or insight would be greatly appreciated.

Thanks in advance,
Taha 

Terminal output: from mri_vol2surf
srcvol = fa2FS.nii.gz
srcreg = ./xfms_taha/fa2freesurfer.mat
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
trgsubject = fsaverage
surfreg = sphere.reg
ProjDist = 0.5
reshape = 0
interp = nearest
float2int = round
GetProjMax = 1
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using
/usr/local/freesurfer/subjects/taha_brain/mri/orig.mgz
as target reference.
Loading label
/usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label
Reading surface
/usr/local/freesurfer/subjects/taha_brain/surf/rh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 6 6 6
using old
Done mapping volume to surface
Number of source voxels hit = 81606
Reading source surface registration 
 
/usr/local/freesurfer/subjects/taha_brain/surf/rh.sphere.reg
Done loading source registration surface
Reading target registration 
 
 /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
Done loading target registration surface
Mapping Surfaces (taha_brain -> fsaverage)
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (163842)

surf2surf_nnfr: building target hash (res=16).
Surf2Surf: Reverse Loop (

Re: [Freesurfer] Projecting FA map onto fsaverge surface

[Taha Abdullah]

Excellent! Thank you for the quick advice, I tried this initially but I was
using the wrong xfm format.

Since I have the FA map in subject ?h.white space, I have done the same
with the tract endings too. I am having some difficulties conceptually, in
terms of projecting the end points onto either the subject specfic or
fsaverage inflated surface. I assumed using mri_surf2surf would be
sufficient to transform the endpts from subject surface ?h.white space to
the inflated surface, but it is a scalar data file. Once the endpts are
projected onto the inflated surface it seems straightforward to extract the
thickness values for further analysis. Essentially replicating the attached
image from Sølsnesa 2015.  If you have any suggestions that would be much
appreciated. Thank you very much!

Best,
Taha



On Fri, Aug 19, 2016 at 9:49 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Taha - Trying getting a .dat registration file from bbregister and
> using that as the input to mri_vol2surf. There's a multimodal tutorial on
> the freesurfer wiki that might be of help.
>
> Best,
> a.y
>
> On Thu, 18 Aug 2016, Taha Abdullah wrote:
>
> Hello All,
>>
>> I am trying to project FA map (dtifit_FA.nii.gz) and the
>> endpt[1/2].pd.nii.gz from TRACULA onto fsaverage surface space.
>> I was following instructions on http://web.mit.edu/fsl_v5.0.8/
>> fsl/doc/wiki/FDT(2f)UserGuide.html, under FreeSurfer
>> Registration, to create the various xfms files.
>>
>> Next, I registered the FA map to subject conformed space using flirt
>>  *  flirt -in dtifit_FA.nii.gz -ref ../../mri/orig.nii.gz -applyxfm -init
>> ./xfms_taha/fa2freesurfer.mat -out fa2FS.nii.gz
>> Then, I used mri_vol2surf to project the registered FA map onto fsaverage
>> surface with the following command.
>>  *  mri_vol2surf --mov fa2FS.nii.gz --projdist-max 6 6 1 --cortex --hemi
>> rh --trgsubject fsaverage --regheader taha_brain
>> --reg ./xfms_taha/fa2freesurfer.mat --o FA_2fsavg_surf.mgh
>> Upon viewing in freeview the fsavg rh.white surface and fa2FS.nii.gz (FA
>> map in FreeSurfer space) did not allign
>> properly. I have tried some variations wtihout any luck. I used the
>> following command line for freeview.
>>  *  freeview -f 
>> /usr/local/freesurfer/subjects/fsaverage/surf/rh.white:overlay=FA_2fsavg_surf.mgh
>> -v fa2FS.nii.gz
>>  *  Attached are some pics of the FA confomred map and fsaverage.rh.white
>> surface
>>
>> Do I need a xfm file for taliarch allignment? Any advice or insight would
>> be greatly appreciated.
>>
>> Thanks in advance,
>> Taha
>>
>> Terminal output: from mri_vol2surf
>> srcvol = fa2FS.nii.gz
>> srcreg = ./xfms_taha/fa2freesurfer.mat
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = rh
>> trgsubject = fsaverage
>> surfreg = sphere.reg
>> ProjDist = 0.5
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 1
>> INFO: float2int code = 0
>> Done loading volume
>> Computing registration from header.
>>   Using /usr/local/freesurfer/subjects/taha_brain/mri/orig.mgz as target
>> reference.
>> Loading label /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.
>> label
>> Reading surface /usr/local/freesurfer/subjects/taha_brain/surf/rh.white
>> Done reading source surface
>> Mapping Source Volume onto Source Subject Surface
>>  1 6 6 6
>> using old
>> Done mapping volume to surface
>> Number of source voxels hit = 81606
>> Reading source surface registration
>>   /usr/local/freesurfer/subjects/taha_brain/surf/rh.sphere.reg
>> Done loading source registration surface
>> Reading target registration
>>/usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
>> Done loading target registration surface
>> Mapping Surfaces (taha_brain -> fsaverage)
>> surf2surf_nnfr: building source hash (res=16).
>> Surf2Surf: Forward Loop (163842)
>>
>> surf2surf_nnfr: building target hash (res=16).
>> Surf2Surf: Reverse Loop (143161)
>> Reverse Loop had 26084 hits
>> Surf2Surf: Dividing by number of hits (163842)
>> INFO: nSrcLost = 0
>> Done mapping surfaces
>> nSrc121 = 107182, nSrcLost = 0, nSrcMulti = 35979, MnSrcMultiHits =
>> 2.29979
>> nTrg121 = 142955, nTrgMulti = 20887, MnTrgMultiHits = 2.24882
>> Masking with /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.
>> label
>> Writing to FA_2fsavg_surf.mgh
>> Dim: 163842 1 1
>>
>>
>> --
>> Taha Abdullah
>> Department of Physiology
>> Northwestern University Feinberg School of Medicine
>> Masters of Science Physiology and Biophysics, Georgetown University 2015
>> Work: (312)-503-0413
>>
>>
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Re: [Freesurfer] error in manual edit by freeview

[Ruopeng Wang]

Hi Cong,

It appears the brainmask you attached has an artifact slice for some reason. 
However I have no idea how it got there. Doug?

Best,
Ruopeng

> On Aug 18, 2016, at 10:19 PM, 3110103...@zju.edu.cn wrote:
> 
> Hi Doug and Ruopeng
>Can you receive pictures and brainmask.mgz file in attachment?  I don't 
> know why this slice mismatch with other slices,  other files such as T1 and 
> wm.mgz and other subjects works well. Thank you very much.
> 
> Regards
> Cong
> 
>> Date: Wed, 17 Aug 2016 10:49:35 -0400
>> From: Douglas Greve 
>> Subject: Re: [Freesurfer] error in manual edit by freeview
>> 
>> I'm not sure what you are describing. Can you send a picture?
>> 
>> 
>> On 8/17/16 8:42 AM, ?? wrote:
>>> Hi dear all
>>> I am using freeview to edit segmentation, I found one slice in coronal 
>>> view in brainmask.mgz mismatch with other slice, this slice obviously move 
>>> down.  WM and T1.mgz are normal, I don?t know how to move this wrong slice 
>>> back.  Any advice will be appreciated.
>>> 
>>> thanks very much.
>>> CONG
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[Freesurfer] voxel values in destrieux file

[pierre deman]

Hello,

I am looking at the destrieux atlas generated by recon-all (I use the
freesurfer dev version), the file aparc.a2009+aseg.mgz), and sometimes the
value of a voxel doesn't exist in the FreesurferColorLut. I have quite a
lot of values between 2036 and 2100 (2038, 2074, 2075 for example) and I
don't find these values in the FreeSurferColorLut.

Is that normal ? What do they correspond at ?

Regards,
Pierre


-- 
DEMAN Pierre
Mobile : +33 7 82 57 80 94
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Re: [Freesurfer] red and blue gradient color map for freeview

[Anastasia Yendiki]

Hi Eun Young - Not sure if anyone has a more elegant solution but it 
sounds like you could split your positive and negative activations into 2 
volumes and use the 2 different colormaps for them.

Best,
a.y

On Thu, 18 Aug 2016, Eun Young Choi wrote:

> Hi all,
> 
> I'd like to have a freeview color map that has both a red-yellow gradient and 
> a blue-light blue gradient (the typical
> colors for positive and negative fcMRI correlations) and ideally no color for 
> 0... None of the standard color maps in
> freeview work well and I can't seem to find one online. Has anyone created 
> one? Or know where I can view the text file
> for the standard color maps that come with freeview, so I can create one 
> myself?
> 
> Thank you!
> Eun Young
> 
>
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Re: [Freesurfer] Projecting FA map onto fsaverge surface

[Anastasia Yendiki]

Hi Taha - Trying getting a .dat registration file from bbregister and 
using that as the input to mri_vol2surf. There's a multimodal tutorial on 
the freesurfer wiki that might be of help.


Best,
a.y

On Thu, 18 Aug 2016, Taha Abdullah wrote:


Hello All,

I am trying to project FA map (dtifit_FA.nii.gz) and the endpt[1/2].pd.nii.gz 
from TRACULA onto fsaverage surface space.
I was following instructions on 
http://web.mit.edu/fsl_v5.0.8/fsl/doc/wiki/FDT(2f)UserGuide.html, under 
FreeSurfer
Registration, to create the various xfms files. 

Next, I registered the FA map to subject conformed space using flirt 
 *  flirt -in dtifit_FA.nii.gz -ref ../../mri/orig.nii.gz -applyxfm -init 
./xfms_taha/fa2freesurfer.mat -out fa2FS.nii.gz
Then, I used mri_vol2surf to project the registered FA map onto fsaverage 
surface with the following command. 
 *  mri_vol2surf --mov fa2FS.nii.gz --projdist-max 6 6 1 --cortex --hemi rh 
--trgsubject fsaverage --regheader taha_brain
--reg ./xfms_taha/fa2freesurfer.mat --o FA_2fsavg_surf.mgh
Upon viewing in freeview the fsavg rh.white surface and fa2FS.nii.gz (FA map in 
FreeSurfer space) did not allign
properly. I have tried some variations wtihout any luck. I used the following 
command line for freeview.  
 *  freeview -f 
/usr/local/freesurfer/subjects/fsaverage/surf/rh.white:overlay=FA_2fsavg_surf.mgh
 -v fa2FS.nii.gz
 *  Attached are some pics of the FA confomred map and fsaverage.rh.white 
surface
Do I need a xfm file for taliarch allignment? Any advice or insight would be 
greatly appreciated.

Thanks in advance,
Taha 

Terminal output: from mri_vol2surf
srcvol = fa2FS.nii.gz
srcreg = ./xfms_taha/fa2freesurfer.mat
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
trgsubject = fsaverage
surfreg = sphere.reg
ProjDist = 0.5
reshape = 0
interp = nearest
float2int = round
GetProjMax = 1
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /usr/local/freesurfer/subjects/taha_brain/mri/orig.mgz as target 
reference.
Loading label /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label
Reading surface /usr/local/freesurfer/subjects/taha_brain/surf/rh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 6 6 6
using old
Done mapping volume to surface
Number of source voxels hit = 81606
Reading source surface registration 
  /usr/local/freesurfer/subjects/taha_brain/surf/rh.sphere.reg
Done loading source registration surface
Reading target registration 
   /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
Done loading target registration surface
Mapping Surfaces (taha_brain -> fsaverage)
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (163842)

surf2surf_nnfr: building target hash (res=16).
Surf2Surf: Reverse Loop (143161)
Reverse Loop had 26084 hits
Surf2Surf: Dividing by number of hits (163842)
INFO: nSrcLost = 0
Done mapping surfaces
nSrc121 = 107182, nSrcLost =     0, nSrcMulti = 35979, MnSrcMultiHits = 2.29979
nTrg121 = 142955, nTrgMulti = 20887, MnTrgMultiHits = 2.24882
Masking with /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label
Writing to FA_2fsavg_surf.mgh
Dim: 163842 1 1


--
Taha Abdullah 
Department of Physiology
Northwestern University Feinberg School of Medicine 
Masters of Science Physiology and Biophysics, Georgetown University 2015
Work: (312)-503-0413

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[Freesurfer] LME contrast 3 groups

[Sarah Hirsiger]

Dear FreeSurfer experts,

 I would appreciate a confirmation regarding correctness of my approach.


I am trying to run an LME model for three groups (group1=controls, group2 and 
group3) and two time points.

I followed the tutorial on 
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels 

and adapted the four group example. However, I am not 100% sure if my adaption 
is correct and would appreciate your input.

 

The design matrix for the model contains the following columns:

 

1)   Intercept

2)   time (tij)

3)   one for Group2 and zero otherwise

4)   column 3) .* time

5)   one for Group3 and zero otherwise 

6)   column 5) .* time

 

To test the null hypothesis of no group differences in the rate of change over 
time among the three groups I applied the following contrast:

 0 0 0 1 0 0

 0 0 0-1 0 1  

Is this contrast correct?

In a second step, I would use the additional three contrasts to identify which 
groups were different:

0 0 0 1 0 0   and 0 0 0 0 0 1 and 0 0 0 -1 0 0 1

 

I really appreciate your help!

Best wishes



Sarah


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