date:20171016

Re: [Freesurfer] Extracting labels using mri_watershed

2017-10-16 Thread Boyd, Emma

Interesting.. would you mind sending me the command you ran and file drop the 
input and output volumes to me?: https://gate.nmr.mgh.harvard.edu/filedrop2/

Emma

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

Sent: Sunday, October 15, 2017 6:43:08 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Extracting labels using mri_watershed

Hi Emma,
I've tried this before but surprisingly not such labels in the output volume.

On Wed, Oct 11, 2017 at 9:03 PM Boyd, Emma 
> wrote:
Hi Fereshte,

mri_watershed -LABEL inputvolume.mgz outputvolume.mgz

The output volume will contain 6 labels:
0 = exterior
1 = scalp
2 = skull
3 = csf
4 = gray
5 = white
6 = fat tissue

Emma

> On Oct 11, 2017, at 3:38 AM, Fereshte 
> > wrote:
>
> Dear Experts,
> How is it possible to extract labels like scalp and skull using -LABEL flag 
> in mri_watershed ?
> Thanks for your attention.
>
>
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Re: [Freesurfer] Constrain smoothing to GM for PET data

2017-10-16 Thread Elijah Mak

Hi Doug,

I am looking for a total GM mask that includes cortical and subcortical regions.

Best Wishes,
Elijah

Dr. Elijah Mak, Research Associate
Department of Psychiatry
Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities 
Research Group
University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24


> On 16 Oct 2017, at 16:09, Douglas Greve  wrote:
> 
> that includes GM regions. not sure what you want
> 
> On 10/13/17 8:58 PM, Elijah Mak wrote:
>> Hi Doug,
>>> That subcort mask is only GM (sorry, should have indicated that when I 
>>> named it).
>>> 
>> 
>> I just looked at the subcort mask in the cvs 2mm folder and it looks like it 
>> is only subcortical? I am looking for a similar mask that also  includes the 
>> GM regions.  Any idea?
>> 
>> 
>> 
>> Best Wishes,
>> Elijah
>> 
>> 
>> 
>>> On 13 Oct 2017, at 17:06, Douglas Greve >> > wrote:
>>> 
>>> That subcort mask is only GM (sorry, should have indicated that when I 
>>> named it).
>>> 
>>> On 10/13/17 11:15 AM, Elijah Mak wrote:
 Hi Doug,
 
 Yes, but I am using the GM rather than the subcortical volume. How can we 
 get a similar GM mask on CVS 2mm space?
 
 Thanks for your help.
 
 Best Wishes,
 Elijah 
 
 Dr. Elijah Mak, Research Associate
 Department of Psychiatry,  
 Old Age Psychiatry Group | Cambridge Intellectual & Developmental 
 Disabilities Research Group
 University of Cambridge,
 Trinity College, CB21TQ, UK
 http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24 
 
 
 
 From: Douglas Greve  
 
 Reply: list Freesurfer support  
 
 Date: 13 October 2017 at 16:14:34
 To: Elijah Mak  , 
 list Freesurfer support 
 
 Subject:  Re: [Freesurfer] Constrain smoothing to GM for PET data 
 
> Are you using mri_vol2vol to go into the cvs 2mm space? If so, then use 
> $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/subcort.mask.mgz
> 
> On 10/11/17 3:15 PM, Elijah Mak wrote:
>> Hi Doug,
>> 
>> Thanks. 
>> 
>> Could I check my workflow to perform the constrained smoothing of PET 
>> MGX-GM volumes? My objective here is to normalise the PET volumes to the 
>> CVS-MNI152 space to produce group-level PET maps. As such, should I be 
>> deriving the GM + Subcortical PVFs from the cvs_avg35_inMNI152 subject 
>> for the mask in mri_fwhm?
>> 
>> 1. mri_cvs_register to bring T1s to CVS MNI152
>> 2. mri_vol2vol to bring the PET MGX-GM volumes (already in anatomical T1 
>> space) to CVS MNI152
>> 3. mri_fwhm to smooth the PET volumes, using a binarised mask of 
>> GM+Subcortical PVFs from the cvs_avg35_inMNI152 subject
>> 4. What is the best way to get the mask from the cvs_avg35_inMNI152 
>> subject? 
>> 5. Obtain group level PET maps in CVS MNI152 space using mri_concat 
>> —mean.
>> 
>> Thanks very much.
>> 
>> Best Wishes,
>> Elijah
>> 
>>> On 4 Oct 2017, at 14:51, Douglas Greve >> > wrote:
>>> 
>>> You mean for volume-based analysis? Yes, use the pvf.
>>> 
>>> On 10/4/17 9:42 AM, Elijah Mak wrote:
 Hi Doug,
 
 I have used PETSURFER to derive MGX GM volumes from PET data.  Now, I 
 would like to constrain the smoothing to the GM. Is it advisable to 
 use the PVF in the aux folder for this purpose? If not, what is the 
 best approach do this?
 
 Thanks!
 
 Best Wishes,
 Elijah
 
 
 
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>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
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Re: [Freesurfer] Constrain smoothing to GM for PET data

2017-10-16 Thread Douglas Greve


You can

mri_binarize --gm --i aparc+aseg.mgz --o gm.mask.mgz


On 10/16/17 12:41 PM, Elijah Mak wrote:

Hi Doug,

I am looking for a total GM mask that includes cortical and 
subcortical regions.


Best Wishes,
Elijah

*Dr. Elijah Mak, Research Associate
*Department of Psychiatry
Old Age Psychiatry Group | Cambridge Intellectual & Developmental 
Disabilities Research Group

University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24


On 16 Oct 2017, at 16:09, Douglas Greve > wrote:


that includes GM regions. not sure what you want


On 10/13/17 8:58 PM, Elijah Mak wrote:

Hi Doug,


That subcort mask is only GM (sorry, should have indicated that 
when I named it).


I just looked at the subcort mask in the cvs 2mm folder and it looks 
like it is only subcortical? I am looking for a similar mask that 
also  includes the GM regions.  Any idea?




Best Wishes,
Elijah



On 13 Oct 2017, at 17:06, Douglas Greve > wrote:


That subcort mask is only GM (sorry, should have indicated that 
when I named it).



On 10/13/17 11:15 AM, Elijah Mak wrote:

Hi Doug,

Yes, but I am using the GM rather than the subcortical volume. How 
can we get a similar GM mask on CVS 2mm space?


Thanks for your help.

Best Wishes,
Elijah

Dr. Elijah Mak, Research Associate
Department of Psychiatry,
Old Age Psychiatry Group | Cambridge Intellectual & Developmental 
Disabilities Research Group

University of Cambridge,
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24


From: Douglas Greve  

Reply: list Freesurfer support  


Date: 13 October 2017 at 16:14:34
To: Elijah Mak  
, list Freesurfer support 
 


Subject: Re: [Freesurfer] Constrain smoothing to GM for PET data

Are you using mri_vol2vol to go into the cvs 2mm space? If so, 
then use 
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/subcort.mask.mgz



On 10/11/17 3:15 PM, Elijah Mak wrote:

Hi Doug,

Thanks.

Could I check my workflow to perform the constrained smoothing 
of PET MGX-GM volumes? My objective here is to normalise the PET 
volumes to the CVS-MNI152 space to produce group-level PET maps. 
As such, should I be deriving the GM + Subcortical PVFs from the 
cvs_avg35_inMNI152 subject for the mask in mri_fwhm?


1. mri_cvs_register to bring T1s to CVS MNI152
2. mri_vol2vol to bring the PET MGX-GM volumes (already in 
anatomical T1 space) to CVS MNI152
3. mri_fwhm to smooth the PET volumes, using a binarised mask of 
GM+Subcortical PVFs from the cvs_avg35_inMNI152 subject
4. What is the best way to get the mask from the 
cvs_avg35_inMNI152 subject?
5. Obtain group level PET maps in CVS MNI152 space using 
mri_concat —mean.


Thanks very much.

Best Wishes,
Elijah

On 4 Oct 2017, at 14:51, Douglas Greve 
> 
wrote:


You mean for volume-based analysis? Yes, use the pvf.


On 10/4/17 9:42 AM, Elijah Mak wrote:

Hi Doug,

I have used PETSURFER to derive MGX GM volumes from PET data. 
Now, I would like to constrain the smoothing to the GM. Is it 
advisable to use the PVF in the aux folder for this purpose? 
If not, what is the best approach do this?


Thanks!

Best Wishes,
Elijah



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Re: [Freesurfer] PETSURFER: MRTM2 volumes?

2017-10-16 Thread Douglas Greve

it comes down to have you smooth it. If you do it in the volume, then 
you need to smooth it in the volume, and that is an invalid analysis 
with MG.


On 10/13/17 8:42 PM, Elijah Mak wrote:
> Hi Doug,
>
> I wonder what is the difference between this approach (mri_surf2vol) as 
> opposed to doing the MRTM2 modelling on the MGX GM output (58 frames), which 
> will give us the bp.nii.gz in volume space?
>
> Thanks.
>
> Best Wishes,
> Elijah
>
>
>
>> On 13 Oct 2017, at 16:19, Douglas Greve  wrote:
>>
>> do you mean you want to map the surface-based data into the volume? If
>> so, you can use mri_surf2vol. If you want to analyze your pet data in
>> the volume you can just do that with mri_glmfit
>>
>>
>> On 10/5/17 4:59 PM, Elijah Mak wrote:
>>> Hi Doug,
>>>
>>> Referring to the PETSURFER tutorial for dynamic PET data, I am wondering if 
>>> it is possible to obtain a volume-based equivalent of 
>>> mrtm2.lh.sm05/bp.nii.gz? As I understand, bp.nii.gz is the partial-volumed 
>>> corrected output that has been sampled onto the fsaverage surface.
>>>
>>> Thanks for your time again.
>>>
>>> Best Wishes,
>>> Elijah
>>>
>>>
>>>
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>>>
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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
>> 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] register.dof6.dat file missing with register-sess

2017-10-16 Thread Douglas Greve

which version of FS are you using? Is this a new analysis done from 
scratch or had you preprocessed before?



On 10/15/17 4:10 PM, Yagmur Ozdemir 19 wrote:

Hello Freesurfer experts,

After I run preproc-sess with this command (
 preproc-sess -surface self lhrh -fwhm 5 -fsd Retinotopy -per-run -s 
Sess01 -s Sess02 ), I get an error saying that the register.dof6.dat 
file is missing and I should run register-sess to create it. When I 
run this with the debug option (register-sess -s Sess01 -s Sess02 -d . 
-fsd bold -per-run -debug) the system again fails to create the 
register file and gives pretty much the same error preproc-sess spit out:


MinCost:
tkregister2_cmdl --mov bold/002/template.nii.gz --reg 
bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta

regio_read_register(): No such file or directory
Could not open bold/002/register.dof6.dat
tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume bold/002/template.nii.gz
reg file   bold/002/register.dof6.dat
LoadVol    0
ZeroCRAS   0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
ERROR: reading bold/002/register.dof6.dat
Cleaning up

I thought of manually creating it with bbregister command but  I am 
not sure about which scan I should use for "volume used for motion 
correction," and I would rather prefer to fix this with preproc-sess 
command.


Also I attached a portion from file "register.dof6.dat.log" file I 
could get for my each run. I hope these excerpts help. I would deeply 
appreciate any help.


Best,
Idil


COREGpreproc() done
Testing if mov and target overlap
Numerical result out of range
mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg 
bold/002/tmp.bbregister.12926/reg.init.dat --out-reg 
bold/002/tmp.bbregister.12926/bbr.pass1.dat --subsamp-brute 100 
--subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white 
--gm-proj-frac 0.5 --gm-gt-wm 0.5

regio_read_register(): No such file or directory
Could not open bold/002/tmp.bbregister.12926/reg.init.dat
mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg 
bold/002/tmp.bbregister.12926/bbr.pass1.dat --out-reg 
bold/002/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 
1e-8 --tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost 
--dof 6 --nmax 36 --param bold/002/register.dof6.dat.param --surf 
white --brute -0.1 0.1 0.1 --cur-reg 
bold/002/tmp.bbregister.12926/reg.curopt.dat --gm-proj-frac 0.5 --nsub 
1 --gm-gt-wm 0.5

regio_read_register(): No such file or directory
Could not open bold/002/tmp.bbregister.12926/bbr.pass1.dat
MinCost:
tkregister2_cmdl --mov bold/002/template.nii.gz --reg 
bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta

tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume bold/002/template.nii.gz
reg file   bold/002/register.dof6.dat
LoadVol    0
ZeroCRAS   0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
ERROR: reading bold/002/register.dof6.dat
Cleaning up

Started at Sun Oct 15 15:32:07 EDT 2017
Ended   at Sun Oct 15 15:32:41 EDT 2017
BBR-Run-Time-Sec 34

bbregister Done
To check results, run:
tkregisterfv --mov bold/002/template.nii.gz --reg 
bold/002/register.dof6.lta --surfs



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[Freesurfer] Fw: cortical/subcortical volume based analysis

2017-10-16 Thread miracle ozzoude

  Sent from my BlackBerry 10 smartphone.From: miracle ozzoude Sent: Saturday, October 14, 2017 3:32 PMTo: Freesurfer support listSubject: Re: [Freesurfer] cortical/subcortical volume based analysisHello Bruce, Thank you for the response. I was able to look into CVS command and I wrote a command on how to register each subjects to cvs_avg35_inMNI152 template using the following: mri_cvs_register --mov subID --mni /Application/freesurfer/subjects/cvs_avg35_inMNI152/T1.mgz
--step1 --step2 --step3 --outdir  $SUBJECTS_DIR/$subID/cvs
 --asegfname aparc+aseg --openmp 8. Do i need to use the T1 in the mri folder or mri.2mm folder when performing mri_cvs_register?My next goals are to: 1) sample the volumes created using mri_cvs_register to the cvs_avg35_inMNI152 template using mri_vol2vol -reg .    -which of the outputs from mri_cvs_register should i use to achieve?final_CVSmorphed_toTEMPLATE_norm.mgz,final_CVSmorph_toTEMPLATE.m3z, or final_CVSmorphed_toTEMPLATE_aseg.mgz2)Use a cortical+subcortical mask from cvs_avg35_inMNI152 to smooth the output from mri_vol2vol.       - How can I create the cortical mask from the cvs_avg35_inMNI152/mri.2mm folder? This is because the folder already has a subcortical mask and I want to create a cortical mask, combine both (using mri_merge) and use it to smooth with 8mm. 3) Lastly, use mri_concat to combine the smoothened maps in order to perform group level analysis on them.       - when performing mri_glmfit on the combined maps, i don't need to specify the --surf fsaverage and lh/rh flags because it is a volume based analysis and it was done on MNI template not fsaverage? Thank you very muchBest, Paul


















On Sat, Oct 14, 2017 at 12:38 PM, Bruce Fischl  wrote:Hi Paul

I guess you could use CVS for this.

cheers
Bruce
On Sat, 14 Oct 2017, miracle ozzoude wrote:


Hello Bruce, 

Thank you very much. Can I still general cortical and subcortical maps with the Spherical warp of r/lh.white surface?  If yes, please what are the steps to achieve this? can I still analyze it with mri_glm?

Best, 
Paul

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: Bruce Fischl
Sent: Saturday, October 14, 2017 11:27 AM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] cortical/subcortical volume based analysis

Hi Paul

if you use a property (like gm) to drive intersubject registration it then
becomes difficult to also analyze it. If your warp was truly perfect you
could just analyze the properties of the warp, but even then it is hard to
localize effects (e.g. if you changed the smoothness of the warp field
would the effect move somewhere else?). If the warp is not perfect then
some of the effect is in your warp and some in the residual anatomical
differences. There are lots of caveats like this you have to worry about.
It's the reason we drive our spherical warp with the ?h.white surface. It
is invariant to gm atrophy and so can be used to assess it without worrying
about this kind of thing

cheers
Bruce



On Fri, 13 Oct 2017, miracle ozzoude wrote:


Hello Bruce,  

Thank you for the response. I meant the latter ( making maps etc). I want to do something similar to the subcortical volume based analysis on PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why should there be a problem with interpretation? 

Best, 
Miracle

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: Bruce Fischl
Sent: Friday, October 13, 2017 6:53 PM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] cortical/subcortical volume based analysis

Hi Paul

we typically do this type of analysis by looking at scatter plots of
structure volumes (e.g. hippocampus). Alternatively, you can make maps,
but that opens up all the problems/difficulties of interpretation of VBM.
Which did you mean?
cheers
Bruce

On Fri, 13 Oct 2017, miracle ozzoude wrote:


Hello FreeSurfer experts, 
I want to perform a whole brain volume based group analysis for cortical and subcortical regions.
That's something very similar to surface based group analysis for cortical thickness however, for
volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can
someone direct me how to go about doing it? My goal is to

Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

2017-10-16 Thread Douglas Greve

Not sure I understand. If the two transforms are only off by less than 
the 5th decimal, then why are the registrations off so much. As for why 
it would be off at the 5ht dec, it probably has to do with the way we 
store the matrix. When a volume is read in, the matrix is decomposed 
into translation, scale, and direction cosine, and then the matrix is 
thrown away. When a volume with the same geometry is written out, the 
matrix is recomputed. Some resolution is lost during the 
decomposition/recomposition, and we don't end up with the exact same matrix.


On 10/14/17 1:30 PM, Christopher Markiewicz wrote:
> Hi,
>
> I've used `bbregister` to generate a transform `bold2T1.lta` from `bold.nii` 
> to `T1.mgz` (assume we have a `T1.nii` as well for the sake of ANTs).
>
> The following produces a well-aligned output:
>
>  mri_convert --apply_transform bold2T1.lta bold.nii bold_space-T1.nii
>
> As does the following:
>
>  lta_convert --inlta bold2T1.lta --outfsl bold2T1.mat
>  c3d_affine_tool -ref T1.nii -src bold.nii bold2T1.mat -fsl2ras -oitk 
> bold2T1.txt
>  antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
> bold2T1.txt
>
> However, if one skips the FSL step, the registration is quite far off:
>
>  lta_convert --inlta bold2T1.lta --outitk bold2T1.txt
>  antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
> bold2T1.txt
>
> Comparing the ITK transform files:
>
> LTA-FSL-ITK
>
>  #Insight Transform File V1.0
>  #Transform 0
>  Transform: MatrixOffsetTransformBase_double_3_3
>  Parameters: 0.9895096215486424 0.011126830936108464 
> -0.00042204653562094823 -0.01079971161879626 0.872329255299452 
> -0.42602926756857834 -0.004755964529051335 0.42420535065804454 
> 0.8878552541301569 -1.3066136395454464 -45.60342165876236 -43.10584860730749
>  FixedParameters: 0 0 0
>
>
> LTA-ITK
>
>  #Insight Transform File V1.0
>  #Transform 0
>  Transform: AffineTransform_double_3_3
>  Parameters: 0.98950976133346558 0.011126830242574215 
> -0.00042204943019896746 -0.010799713432788849 0.87232941389083862 
> -0.42602935433387756 -0.0047559700906276703 0.42420542240142822 
> 0.88785547018051147 -2.2848172187805176 -2.9065067768096924 11.744022369384766
>  FixedParameters: 0 0 0
>
>
> To 5 significant digits, these are the same, except the last three 
> (translation) parameters. And the `AffineTransform_double_3_3` is different 
> from `MatrixOffsetTransformBase_double_3_3`, though I'm not sure whether this 
> has any effect.
>
> Here is the original LTA:
>
>  type  = 1 # LINEAR_RAS_TO_RAS
>  nxforms   = 1
>  mean  = 0. 0. 0.
>  sigma = 1.
>  1 4 4
>  1.010462999343872e+00 -1.063966564834118e-02 4.625014495104551e-03 
> -2.332115173339844e+00
>  1.228639855980873e-02 9.293417930603027e-01 -4.459420144557953e-01 
> 2.507942199707031e+00
>  4.575361963361502e-04 4.440840482711792e-01 9.132194519042969e-01 
> -1.201664733886719e+01
>  0.000e+00 0.000e+00 0.000e+00 
> 9.98807907104e-01
>  src volume info
>  valid = 1  # volume info valid
>  filename = 
> /scratch/fmriprep_wf/single_subject_02_wf/func_preproc_task_short_wf/bold_reg_wf/bbreg_wf/bbregister/uni_masked_xform.nii.gz
>  volume = 64 64 34
>  voxelsize = 3.125e+00 3.125e+00 
> 4.000e+00
>  xras   = -1.000e+00 0.000e+00 
> 0.000e+00
>  yras   = 0.000e+00 1.000e+00 
> 0.000e+00
>  zras   = 0.000e+00 0.000e+00 
> 1.000e+00
>  cras   = -1.090248107910156e+00 -1.071614074707031e+01 
> 1.619928741455078e+01
>  dst volume info
>  valid = 1  # volume info valid
>  filename = 
> /scratch/fmriprep_wf/single_subject_02_wf/anat_preproc_wf/t1_merge/sub-02_T1w_template.nii.gz
>  volume = 160 192 192
>  voxelsize = 1.000e+00 1.33015441895e+00 
> 1.33015441895e+00
>  xras   = 1.000e+00 0.000e+00 
> 0.000e+00
>  yras   = 0.000e+00 1.000e+00 
> 0.000e+00
>  zras   = 0.000e+00 0.000e+00 
> 1.000e+00
>  cras   = -3.000e+00 2.69482421875e+00 
> -8.30517578125e+00
>  subject sub-02
>  fscale 0.10
>
>
> If it would be useful, I can provide any relevant images for testing.
>
> --
> Chris Markiewicz
> Center for Reproducible Neuroscience
> Stanford University
>
>
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>

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Re: [Freesurfer] Fwd: Adding control points to aparc+aseg

2017-10-16 Thread Douglas Greve

what is the index (ie, col, row, slice) where you are seeing a problem?

On 10/16/17 11:44 AM, Nicholas Goh wrote:

Hi,

I am not sure if this email got lost in the process or is still 
awaiting approval, but I was asked to tar and gzip the images that I 
was having no luck with fixing the white matter for.

Any help would be appreciated.
Thank you,

Nicholas Goh
-- Forwarded message --
From: *Nicholas Goh* >
Date: Mon, Oct 2, 2017 at 12:33 PM
Subject: Re: [Freesurfer] Adding control points to aparc+aseg
To: Freesurfer support list >

I have still been having trouble with fixing the white matter of the 
aparc+aseg.mgz file for a subject.

I have tried using

recon-all -autorecon2-cp -autorecon3 -subjid 
recon-all -autorecon2-wm -subjid 
recon-all -autorecon2-wm -autorecon3 -subjid 

None of these have solved the issue, and I was hoping for help in 
finding a way to fix this? There are other more extreme examples, but 
this one seems to have an error at [-7, 114, 133]

Thank you for the help,

Nicholas Goh

On Thu, Sep 28, 2017 at 5:34 PM, Nicholas Goh > wrote:

Ping, is this okay to do? I Think it is but wanted to check before
sending
-- Forwarded message --
From: *Bruce Fischl* >
Date: Thu, Sep 28, 2017 at 5:23 PM
Subject: Re: [Freesurfer] Adding control points to aparc+aseg
To: Freesurfer support list >

Hi Nicholas

why don't you tar, gzip and upload your subject and we will take a
look. Make sure to tell us the coordinates of where you are trying
to fix things

cheers
Bruce

On Thu, 28 Sep 2017, Nicholas Goh wrote:

I am still having trouble with getting the aparc+aseg to
recognize sections
that should be white matter as such. Using the control points
paired
withrecon-all -autorecon2-cp -autorecon3 -subjid 

did not work, after 4 or 5 attempts with different control
points, and using
recon-all -autorecon2-wm -s 
also did not yield appreciable results. Is there anything else
that I might
be able to try to fix this?
Thank you for all the help,

Nicholas Goh

On Wed, Sep 27, 2017 at 12:49 PM, Elijah Mak
>
wrote:
      Hi Nicholas,

In such situations, I have learned that autorecon2-wm after
adding WM
voxels seems to work pretty well. Hope that helps.

Best Wishes,
Elijah

On 27 September 2017 at 16:46:43, Nicholas Goh
(ngo...@gmail.com )
wrote:

Bruce,
Thank you for the response. Attempting to use this method has
not produced results, and I am unsure how to proceed or if I had
performed it improperly. I have attached an example of the
control points being placed, if that helps any.
Thank you,

Nicholas Goh

On Wed, Sep 27, 2017 at 11:04 AM, Bruce Fischl
> wrote:
      Hi Nicholas

      yes, possibly, depending on why you are missing
      chunks. If the white matter in the regions you are
      missing has intensity values significantly < 110
      then what you are doing should help. The control.dat
      file must be place in the subject/tmp dir for us to
      find it.

      cheers
      Bruce
      On Wed, 27 Sep 2017, Nicholas Goh wrote:

            I am attempting to fix the
            aparc+aseg.mgz file for an image, and
            wanted to check to see if I am
            doing it correctly.What I was doing
            which seemed to be ineffective was
            1)create a new point set of control
            points labelled control.dat
            2)place control points along what should
            be white matter
            3)save point set
            4)run recon-all -autorecon2-cp
            -autorecon3 -subjid 

            Is this the correct way to go about
            fixing aparc+aseg files that are missing
            chunks of the brain? Is
            there a better way to go about this?
            Thanks for the help,

            Nicholas Goh

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Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance

2017-10-16 Thread Douglas Greve

they all look ok except that these should be
C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5


On 10/13/17 11:30 AM, std...@virgilio.it wrote:
> I have applied the contrasts that we discussed in the previous mails but they
> produce doubt results.
>
> In summary, I aim to look at:
> A- Difference between groups without considerer the covariate effect (I
> suppose that the maps will be in the intercept folder) --->  ANOVA between 4
> groups
> B- Clusters in which the fMRI (dependent variable) is associated to the
> structural data (covariate), taking in account the groups (I suppose that the
> maps will be in the slope folder) --->  MANOVA between 4 groups
>
> Please could you check the contrast reported below? I suspect that there are
> some errors because, looking at results:
> The slope map is the inverse in color of the intercept map and the intercept
> did not correspond to the results which I obtain by using G4V0
>
> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
> C13) gr1+gr2-vs-gr3+gr4.intercept 0.25 0.25 0.25 0.25 0 0 0 0
> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.25 0.25 0.25 0.25
> C15) group.effect.intercept
> 1 -1 0 0 0 0 0 0
> 1 0 -1 0 0 0 0 0
> 1 0 0 -1 0 0 0 0
> C16) group.effect.slope
> 0 0 0 0 1 -1 0 0
> 0 0 0 0 1 0 -1 0
> 0 0 0 0 1 0 0 -1
>
> Best regards
>
>
> Stefano
>
>
>> Messaggio originale
>> Da: "Douglas N Greve" 
>> Data: 11-ott-2017 17.28
>> A: , 
>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of
> covariance
>> the rational is to make them sum to 1.0 so that the gamma.mgh file has
>> units of mm (or whatever the input units are). It is unimportant for
>> p-values.
>>
>>
>> On 10/10/2017 01:54 PM, std...@virgilio.it wrote:
>>> Thanks
>>>
>>> In which contrast I must change "1" with "0.25"?
>>> What is the rationale to use 0.25?
>>>
>>>
>>> Sent from Virgilio Mobile
>>> 
>>>
>>> Il 10/10/2017, Douglas N Greve  ha scritto:
>>>
>>> I don't understand what you mean by "where I should use"
>>>
>>> I thought I looked through all those contrasts a few weeks ago, no?
>>>
>>>
>>> On 10/10/2017 04:22 AM, std...@virgilio.it wrote:
 You have suggested to use
 0 0 0 0 .25 .25 .25 .25
 to look the map where, considering the group differences, the covariate
 predicts the dependent variable (functional connectivity) in 4GV1.

 Below I'm reporting the contrast that I have used.
 Please could you check it and suggest correction?
 Could you explain where I should use 0 0 0 0 .25 .25 .25 .25, please?

 Thanks

 C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
 C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
 C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
 C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
 C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
 C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
 C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
 C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
 C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
 C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
 C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
 C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
 C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
 C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
 C15) group.effect.intercept
 1 -1 0 0 0 0 0 0
 1 0 -1 0 0 0 0 0
 1 0 0 -1 0 0 0 0
 C16) group.effect.slope
> 0 0 0 0 1 -1 0 0
> 0 0 0 0 1 0 -1 0
> 0 0 0 0 1 0 0 -1





 On 10/6/17 9:24 AM, std...@virgilio.it wrote:
> Thank you very much.
> Where I should put 0 0 0 0 .25 .25 .25 .25?
> Which are the contrast reported below that I should modify?
>
> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
> C15) group.effect.intercept
> 1 -1 0 0 0 0 0 0
> 1 0 -1 0 0 0 0 0
> 1 0 0 -1 0 0 0 0
> C16)

[Freesurfer] New Openings for Postdoctoral Fellows

2017-10-16 Thread Thomas Yeo

Dear Everyone,

My lab has new openings for postdoctoral fellows. Please see job
descriptions here: https://yeolab.weebly.com/jobs.html

Thanks,
Thomas
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Re: [Freesurfer] How to obtain a label for Custom ROI mask

2017-10-16 Thread Douglas Greve


run the juelich atlas through recon-all, then use mri_vol2surf



On 10/14/17 3:38 PM, Dev vasu wrote:

Dear all,

I have custom ROI mask ( MNI Space )  that i have prepared from Jülich 
atlas , I would be like to obtain corresponding surface label file, 
Could you please guide me necessary the steps that i have to follow 
inorder to obtain corresponding label for my mask.



Thanks
Vasudev


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Re: [Freesurfer] Generating Mean thickness surface file for volume ROI mask

2017-10-16 Thread Douglas Greve

May the ROI to the surface using mri_vol2surf, then use mri_segstats to 
extract the mean value



On 10/13/17 4:09 PM, Dev vasu wrote:

Dear all,

I have a   ROI mask volume file and i would like to generate Mean 
cortical thickness surface file (i.e lh.ROI.thickness.fsaverage.mgh 
and rh.ROI.thickness.fsaverage.mgh) , could some one guide me how i 
could obtain such file.


I have 120 subjects and I have done recon-all for all subjects.


Thanks
Vasudev


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Re: [Freesurfer] Problem flipping a label into other hemisphere

2017-10-16 Thread Douglas Greve

Sorry, try this

mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label 
--streg ../surf/lh.sphere.left_right ../surf/rh.sphere.left_right

On 10/13/17 2:58 PM, Neuro Lists wrote:

Hi all,
I was just wondering if there was any further insight into what I 
might be doing wrong on this.

Thanks again!

On Thu, Oct 12, 2017 at 10:30 AM, Neuro Lists 
> 
wrote:

Hi Doug and Bruce,
I forgot to mention that I had tried that as well but without
success. As a sanity check, tried flipping a label from the 'bert'
subject and it still comes out wrong. I've uploaded a screen shot
of the result:

https://imgur.com/a/J6Phx

Thank you for any input you might have!

These were the exact steps the following (I also tried playing
around with the options to --streg but without luck):

cd ${SUBJECTS_DIR}/bert
cd surf
mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right
rh.sphere.left_right
cd ../label

mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label
--streg ../surf/lh.sphere.left_right ../surf/rh.sphere

$Id: mris_apply_reg.c,v 1.9 2016/12/06 19:40:48 greve Exp $

cwd /home/joe/subjects/bert/label

cmdline ../../scripts/mris_apply_reg --src-label lh.BA45.label
--trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right
../surf/rh.sphere

sysname Linux

hostname computer

machine x86_64

user     joe

srcvalfile (null)

trgvalfile lh_flip.BA45.label

nsurfs 2

jac 0

revmap 0

1 Loading ../surf/lh.sphere.left_right

2 Loading ../surf/rh.sphere

Loading label lh.BA45.label

4060 points in input label

MRISapplyReg: nsurfs = 2, revmap=0, jac=0,  hash=1

MRISapplyReg: building hash tables (res=16).

MRISapplyReg: Forward Loop (133299)

MRISapplyReg: Dividing by number of hits (133299)

MRISapplyReg: nSrcLost = 38462

4505 points in output label

mris_apply_reg done

On Thu, Oct 12, 2017 at 5:06 AM, Douglas Greve
> wrote:

Try

mris_apply_reg --src-label your.lh.label --trg your.rh.label 
-streg lh.sphere.left_right rh.sphere

On 10/11/17 5:43 PM, Neuro Lists wrote:

Hi all,
I've searched the lists extensively and have not been able to
resolve my problem. I'd greatly appreciated any help.

I have run the recon-all pipeline on a number of subjects,
made the appropriate fixes and am happy with the surfaces.
For each subject, I have a number of ROIs that are created
programmatically and they are exactly as they should be.
These ROIs are on the "regular" surfaces, not the inflated
ones. In other words, opening the brainmask.mgz in freeview
and just loading the label file results in the ROI being
where I expect it to be.

 I'm now trying to flip the ROI onto the contralateral
hemisphere and this is going terribly wrong. No matter what I
try, the ROI ends up being generated far outside of the brain.

I was originally trying to use the xhemi pipeline, but then I
realized from the forums that I could just
use mris_left_right_register.

I've done:

cd subject/surf
mris_left_right_register lh.sphere rh.sphere
lh.sphere.left_right rh.sphere.left_right

I've then tried using a number of varieties of mri_apply_reg
that have been listed on the forum:
1) mris_apply_reg --src-label your.lh.label --trg
your.rh.label -streg lh.sphere lh.sphere.left_right
2) mris_apply_reg --src-label lh.source.label --streg
lh.sphere.left_right
rh.sphere.left_right --trg rh.lh.source.label

No matter what I try though, the flipped ROI ends up being
way outside of the brain when I overlay it on the brainmask.
Is this because the flipped ROI should instead be visualized
on the inflated hemisphere? If so, how can I get it to
overlay properly onto the brainmask so that I can be sure
it's correct? My ultimate goal is to get anatomical stats
from the original and flipped ROIs.

Thanks for your help!

Joe

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Re: [Freesurfer] Fwd: Adding control points to aparc+aseg

2017-10-16 Thread Douglas Greve

I don't know what coordinates those are. Can you give indices? indices 
are non-neg

On 10/16/17 12:59 PM, Nicholas Goh wrote:
An example of the aparc+aseg not covering all that it needs to can be 
found around [-7, 114, 133]

On Mon, Oct 16, 2017 at 12:47 PM, Douglas Greve 
> wrote:

what is the index (ie, col, row, slice) where you are seeing a
problem?

On 10/16/17 11:44 AM, Nicholas Goh wrote:

Hi,

I am not sure if this email got lost in the process or is still
awaiting approval, but I was asked to tar and gzip the images
that I was having no luck with fixing the white matter for.
Any help would be appreciated.
Thank you,

Nicholas Goh
-- Forwarded message --
From: *Nicholas Goh* >
Date: Mon, Oct 2, 2017 at 12:33 PM
Subject: Re: [Freesurfer] Adding control points to aparc+aseg
To: Freesurfer support list >

I have still been having trouble with fixing the white matter of
the aparc+aseg.mgz file for a subject.
I have tried using

recon-all -autorecon2-cp -autorecon3 -subjid 
recon-all -autorecon2-wm -subjid 
recon-all -autorecon2-wm -autorecon3 -subjid 

None of these have solved the issue, and I was hoping for help in
finding a way to fix this? There are other more extreme examples,
but this one seems to have an error at [-7, 114, 133]
Thank you for the help,

Nicholas Goh

On Thu, Sep 28, 2017 at 5:34 PM, Nicholas Goh > wrote:

Ping, is this okay to do? I Think it is but wanted to check
before sending
-- Forwarded message --
From: *Bruce Fischl* >
Date: Thu, Sep 28, 2017 at 5:23 PM
Subject: Re: [Freesurfer] Adding control points to aparc+aseg
To: Freesurfer support list >

Hi Nicholas

why don't you tar, gzip and upload your subject and we will
take a look. Make sure to tell us the coordinates of where
you are trying to fix things

cheers
Bruce

On Thu, 28 Sep 2017, Nicholas Goh wrote:

I am still having trouble with getting the aparc+aseg to
recognize sections
that should be white matter as such. Using the control
points paired
withrecon-all -autorecon2-cp -autorecon3 -subjid 

did not work, after 4 or 5 attempts with different
control points, and using
recon-all -autorecon2-wm -s 
also did not yield appreciable results. Is there anything
else that I might
be able to try to fix this?
Thank you for all the help,

Nicholas Goh

On Wed, Sep 27, 2017 at 12:49 PM, Elijah Mak
>
wrote:
      Hi Nicholas,

In such situations, I have learned that autorecon2-wm
after adding WM
voxels seems to work pretty well. Hope that helps.

Best Wishes,
Elijah

On 27 September 2017 at 16:46:43, Nicholas Goh
(ngo...@gmail.com )
wrote:

Bruce,
Thank you for the response. Attempting to use this method has
not produced results, and I am unsure how to proceed or
if I had
performed it improperly. I have attached an example of the
control points being placed, if that helps any.
Thank you,

Nicholas Goh

On Wed, Sep 27, 2017 at 11:04 AM, Bruce Fischl
> wrote:
      Hi Nicholas

      yes, possibly, depending on why you are missing
      chunks. If the white matter in the regions you are
      missing has intensity values significantly < 110
      then what you are doing should help. The control.dat
      file must be place in the subject/tmp dir for us to
      find it.

      cheers
      Bruce
      On Wed, 27 Sep 2017, Nicholas Goh wrote:

            I am attempting to fix the
aparc+aseg.mgz file for an image, and
            wanted to check to see if I am
            doing it correctly.What I was doing
            which seemed to be ineffective was
            1)create a new point set of control
            points

Re: [Freesurfer] register.dof6.dat file missing with register-sess

2017-10-16 Thread Yagmur Ozdemir 19

I am using version 6.0.0 and this is made from scratch. Just a couple of days 
ago I processed a different subject but used the special retinotopy procedure 
and didn't come across this problem. I first noticed this error in selxavg-sess 
and went back and used mkbrainmask, register-sess and preprocessed a couple of 
times again with -force and either per-run or -session to try troubleshooting.

Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, October 16, 2017 6:18 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] register.dof6.dat file missing with register-sess


which version of FS are you using? Is this a new analysis done from scratch or 
had you preprocessed before?

On 10/15/17 4:10 PM, Yagmur Ozdemir 19 wrote:
Hello Freesurfer experts,

After I run preproc-sess with this command (
 preproc-sess -surface self lhrh -fwhm 5 -fsd Retinotopy -per-run -s Sess01 -s 
Sess02 ), I get an error saying that the register.dof6.dat file is missing and 
I should run register-sess to create it. When I run this with the debug option 
(register-sess -s Sess01 -s Sess02 -d . -fsd bold -per-run -debug) the system 
again fails to create the register file and gives pretty much the same error 
preproc-sess spit out:

MinCost:
tkregister2_cmdl --mov bold/002/template.nii.gz --reg 
bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta
regio_read_register(): No such file or directory
Could not open bold/002/register.dof6.dat
tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume bold/002/template.nii.gz
reg file   bold/002/register.dof6.dat
LoadVol0
ZeroCRAS   0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
ERROR: reading bold/002/register.dof6.dat
Cleaning up

I thought of manually creating it with bbregister command but  I am not sure 
about which scan I should use for "volume used for motion correction," and I 
would rather prefer to fix this with preproc-sess command.

Also I attached a portion from file "register.dof6.dat.log" file I could get 
for my each run. I hope these excerpts help. I would deeply appreciate any help.

Best,
Idil


COREGpreproc() done
Testing if mov and target overlap
Numerical result out of range
mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg 
bold/002/tmp.bbregister.12926/reg.init.dat --out-reg 
bold/002/tmp.bbregister.12926/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 
--tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 
--gm-gt-wm 0.5
regio_read_register(): No such file or directory
Could not open bold/002/tmp.bbregister.12926/reg.init.dat
mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg 
bold/002/tmp.bbregister.12926/bbr.pass1.dat --out-reg 
bold/002/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 
--tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost --dof 6 --nmax 
36 --param bold/002/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 
--cur-reg bold/002/tmp.bbregister.12926/reg.curopt.dat --gm-proj-frac 0.5 
--nsub 1 --gm-gt-wm 0.5
regio_read_register(): No such file or directory
Could not open bold/002/tmp.bbregister.12926/bbr.pass1.dat
MinCost:
tkregister2_cmdl --mov bold/002/template.nii.gz --reg 
bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta
tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume bold/002/template.nii.gz
reg file   bold/002/register.dof6.dat
LoadVol0
ZeroCRAS   0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
ERROR: reading bold/002/register.dof6.dat
Cleaning up

Started at Sun Oct 15 15:32:07 EDT 2017
Ended   at Sun Oct 15 15:32:41 EDT 2017
BBR-Run-Time-Sec 34

bbregister Done
To check results, run:
tkregisterfv --mov bold/002/template.nii.gz --reg bold/002/register.dof6.lta 
--surfs



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Re: [Freesurfer] PETSURFER: MRTM2 volumes?

2017-10-16 Thread Elijah Mak

Got it, thanks! I have already performed smoothing on the MGX surfaces so I’d 
like to proceed with mri_surf2vol.

According to the “hidden secrets of success” for mri_surf2vol, there are 2 
methods.  Is the command below correct?

mri_surf2vol --so lh.bp.nii.gz (the PET surface BPNDs) --so rh.bp.nii.gz 
--subject fsaverage --o smoothed.bpnd.in.volume.nii.gz 

The next step is to bring the volumes into CVS-MNI152 space. Mri_cvs_register 
has been done on the T1.

Thanks Doug.

Best Wishes,
Elijah

Dr. Elijah Mak, Research Associate
Department of Psychiatry
Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities 
Research Group
University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24

> On 16 Oct 2017, at 16:08, Douglas Greve  wrote:
> 
> it comes down to have you smooth it. If you do it in the volume, then 
> you need to smooth it in the volume, and that is an invalid analysis 
> with MG.
> 
> 
> On 10/13/17 8:42 PM, Elijah Mak wrote:
>> Hi Doug,
>> 
>> I wonder what is the difference between this approach (mri_surf2vol) as 
>> opposed to doing the MRTM2 modelling on the MGX GM output (58 frames), which 
>> will give us the bp.nii.gz in volume space?
>> 
>> Thanks.
>> 
>> Best Wishes,
>> Elijah
>> 
>> 
>> 
>>> On 13 Oct 2017, at 16:19, Douglas Greve  wrote:
>>> 
>>> do you mean you want to map the surface-based data into the volume? If
>>> so, you can use mri_surf2vol. If you want to analyze your pet data in
>>> the volume you can just do that with mri_glmfit
>>> 
>>> 
>>> On 10/5/17 4:59 PM, Elijah Mak wrote:
 Hi Doug,

 Referring to the PETSURFER tutorial for dynamic PET data, I am wondering 
 if it is possible to obtain a volume-based equivalent of 
 mrtm2.lh.sm05/bp.nii.gz? As I understand, bp.nii.gz is the partial-volumed 
 corrected output that has been sampled onto the fsaverage surface.

 Thanks for your time again.

 Best Wishes,
 Elijah

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Re: [Freesurfer] mri_aparc2aseg output file values

2017-10-16 Thread Douglas Greve

I don't think you can use the mris_label2annot ctab. What happens if you 
run freeview using the default ctab?



On 10/10/17 3:19 PM, Sims, Sara A wrote:


Freesurfer people,

*I have a label file that I want to make into a volume file only in 
the white matter to use in diffusion tractography.*


*I was told to use mri_aparc2aseg to put the labels onto the WM 
surface and make them into a volume. I made the label files into 
annotation files using the following commands:*


mris_label2annot --ctab clut.2lhV1.ctab --s 100206 --h lh --l 
/data/user/snolin/subjects_reconall/100206/label/2_LH_V1.label --a 2V1


mris_label2annot --ctab clut.2rhV1.ctab --s 100206 --h rh --l 
/data/user/snolin/subjects_reconall/100206/label/2_RH_V1.label --a 2V1


*These ran with no errors and made annotation files. Then I ran 
mri_aparc2aseg using the following command:*


mri_aparc2aseg --s 100206 --annot 2V1 --new-ribbon

*This is my log file:*

SUBJECTS_DIR /data/user/snolin/subjects_reconall

subject 100206

outvol /data/user/snolin/subjects_reconall/100206/mri/2V1+aseg.mgz

useribbon 0

baseoffset 0

RipUnknown 0

Reading lh white surface

 /data/user/snolin/subjects_reconall/100206/surf/lh.white

Reading lh pial surface

 /data/user/snolin/subjects_reconall/100206/surf/lh.pial

Loading lh annotations from 
/data/user/snolin/subjects_reconall/100206/label/lh.2V1.annot


reading colortable from annotation file...

colortable with 2 entries read (originally clut.2lhV1.ctab)

Reading rh white surface

 /data/user/snolin/subjects_reconall/100206/surf/rh.white

Reading rh pial surface

 /data/user/snolin/subjects_reconall/100206/surf/rh.pial

Loading rh annotations from 
/data/user/snolin/subjects_reconall/100206/label/rh.2V1.annot


reading colortable from annotation file...

colortable with 2 entries read (originally clut.2rhV1.ctab)

Have color table for lh white annotation

Have color table for rh white annotation

Loading ribbon segmentation from 
/data/user/snolin/subjects_reconall/100206/mri/ribbon.mgz


Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /data/user/snolin/subjects_reconall/100206/mri/aseg.mgz

ASeg Vox2RAS: ---

-1.0 0.0   0.0   128.0;

0.0 0.0   1.0  -128.0;

0.0 -1.0   0.0   128.0;

0.0 0.0   0.0   1.0;

-

Labeling Slice

  0   1 2   3   4   5   6   7   8   9  10  11  12  13  14  15  16 17  
18  19


 20  21  22 23  24  25  26  27  28  29  30  31  32  33  34  35  36  37 
38  39


 40  41  42 43  44  45  46  47  48  49  50  51  52  53  54  55  56  57 
58  59


 60  61  62 63  64  65  66  67  68  69  70  71  72  73  74  75  76  77 
78  79


 80  81  82 83  84  85  86  87  88  89  90  91  92  93  94  95  96  97 
98  99


100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 
117 118 119


120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 
137 138 139


140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 
157 158 159


160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 
177 178 179


180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 
197 198 199


200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 
217 218 219


220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 
237 238 239


240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 
1764


Used brute-force search on 0 voxels

Writing output aseg to 
/data/user/snolin/subjects_reconall/100206/mri/2V1+aseg.mgz


*It creates the 2V1+aseg.mgz file and I tried opening it in freeview 
with the color lookup table that I used when I made it into an 
annotation file and its all black. Without the color lookup table it 
is all white.*


*Clicking around the values are 41, 0, or 2000 etc., but I can’t 
visually see anything. What have I done wrong here?*


**

*As I mentioned before, I just want to use these label file for 
diffusion tractography, so if I am heading down the wrong path, I 
would appreciate advice.*


Freesurfer version: 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c


Platform: linux based cluster

Thank you!

Sara Sims



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Re: [Freesurfer] register.dof6.dat file missing with register-sess

2017-10-16 Thread Douglas Greve

I don't know what might be going wrong here. Have you tried to re-run it 
from scratch? Are you out of disk space?



On 10/16/17 12:59 PM, Yagmur Ozdemir 19 wrote:
I am using version 6.0.0 and this is made from scratch. Just a couple 
of days ago I processed a different subject but used the special 
retinotopy procedure and didn't come across this problem. I first 
noticed this error in selxavg-sess and went back and used mkbrainmask, 
register-sess and preprocessed a couple of times again with -force and 
either per-run or -session to try troubleshooting.


Idil

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]

*Sent:* Monday, October 16, 2017 6:18 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] register.dof6.dat file missing with 
register-sess


which version of FS are you using? Is this a new analysis done from 
scratch or had you preprocessed before?



On 10/15/17 4:10 PM, Yagmur Ozdemir 19 wrote:

Hello Freesurfer experts,

After I run preproc-sess with this command (
 preproc-sess -surface self lhrh -fwhm 5 -fsd Retinotopy -per-run -s 
Sess01 -s Sess02 ), I get an error saying that the register.dof6.dat 
file is missing and I should run register-sess to create it. When I 
run this with the debug option (register-sess -s Sess01 -s Sess02 -d 
. -fsd bold -per-run -debug) the system again fails to create the 
register file and gives pretty much the same error preproc-sess spit out:


MinCost:
tkregister2_cmdl --mov bold/002/template.nii.gz --reg 
bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta

regio_read_register(): No such file or directory
Could not open bold/002/register.dof6.dat
tkregister_tcl 
/home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl

INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume bold/002/template.nii.gz
reg file   bold/002/register.dof6.dat
LoadVol    0
ZeroCRAS   0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
ERROR: reading bold/002/register.dof6.dat
Cleaning up

I thought of manually creating it with bbregister command but  I am 
not sure about which scan I should use for "volume used for motion 
correction," and I would rather prefer to fix this with preproc-sess 
command.


Also I attached a portion from file "register.dof6.dat.log" file I 
could get for my each run. I hope these excerpts help. I would deeply 
appreciate any help.


Best,
Idil


COREGpreproc() done
Testing if mov and target overlap
Numerical result out of range
mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii 
--init-reg bold/002/tmp.bbregister.12926/reg.init.dat --out-reg 
bold/002/tmp.bbregister.12926/bbr.pass1.dat --subsamp-brute 100 
--subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white 
--gm-proj-frac 0.5 --gm-gt-wm 0.5

regio_read_register(): No such file or directory
Could not open bold/002/tmp.bbregister.12926/reg.init.dat
mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii 
--init-reg bold/002/tmp.bbregister.12926/bbr.pass1.dat --out-reg 
bold/002/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 
1e-8 --tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost 
--dof 6 --nmax 36 --param bold/002/register.dof6.dat.param --surf 
white --brute -0.1 0.1 0.1 --cur-reg 
bold/002/tmp.bbregister.12926/reg.curopt.dat --gm-proj-frac 0.5 
--nsub 1 --gm-gt-wm 0.5

regio_read_register(): No such file or directory
Could not open bold/002/tmp.bbregister.12926/bbr.pass1.dat
MinCost:
tkregister2_cmdl --mov bold/002/template.nii.gz --reg 
bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta
tkregister_tcl 
/home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl

INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume bold/002/template.nii.gz
reg file   bold/002/register.dof6.dat
LoadVol    0
ZeroCRAS   0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
ERROR: reading bold/002/register.dof6.dat
Cleaning up

Started at Sun Oct 15 15:32:07 EDT 2017
Ended   at Sun Oct 15 15:32:41 EDT 2017
BBR-Run-Time-Sec 34

bbregister Done
To check results, run:
tkregisterfv --mov bold/002/template.nii.gz --reg 
bold/002/register.dof6.lta --surfs



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The information in

Re: [Freesurfer] Fwd: Adding control points to aparc+aseg

2017-10-16 Thread Nicholas Goh

An example of the aparc+aseg not covering all that it needs to can be found
around [-7, 114, 133]

On Mon, Oct 16, 2017 at 12:47 PM, Douglas Greve 
wrote:

> what is the index (ie, col, row, slice) where you are seeing a problem?
>
> On 10/16/17 11:44 AM, Nicholas Goh wrote:
>
> Hi,
>
> I am not sure if this email got lost in the process or is still awaiting
> approval, but I was asked to tar and gzip the images that I was having no
> luck with fixing the white matter for.
> Any help would be appreciated.
> Thank you,
>
> Nicholas Goh
> -- Forwarded message --
> From: Nicholas Goh 
> Date: Mon, Oct 2, 2017 at 12:33 PM
> Subject: Re: [Freesurfer] Adding control points to aparc+aseg
> To: Freesurfer support list 
>
>
> I have still been having trouble with fixing the white matter of the
> aparc+aseg.mgz file for a subject.
> I have tried using
>
> recon-all -autorecon2-cp -autorecon3 -subjid 
> recon-all -autorecon2-wm -subjid 
> recon-all -autorecon2-wm -autorecon3 -subjid 
>
> None of these have solved the issue, and I was hoping for help in finding
> a way to fix this? There are other more extreme examples, but this one
> seems to have an error at [-7, 114, 133]
> Thank you for the help,
>
> Nicholas Goh
>
> On Thu, Sep 28, 2017 at 5:34 PM, Nicholas Goh  wrote:
>
>> Ping, is this okay to do? I Think it is but wanted to check before sending
>> -- Forwarded message --
>> From: Bruce Fischl 
>> Date: Thu, Sep 28, 2017 at 5:23 PM
>> Subject: Re: [Freesurfer] Adding control points to aparc+aseg
>> To: Freesurfer support list 
>>
>>
>> Hi Nicholas
>>
>> why don't you tar, gzip and upload your subject and we will take a look.
>> Make sure to tell us the coordinates of where you are trying to fix things
>>
>> cheers
>> Bruce
>>
>>
>> On Thu, 28 Sep 2017, Nicholas Goh wrote:
>>
>> I am still having trouble with getting the aparc+aseg to recognize
>>> sections
>>> that should be white matter as such. Using the control points paired
>>> withrecon-all -autorecon2-cp -autorecon3 -subjid 
>>>
>>> did not work, after 4 or 5 attempts with different control points, and
>>> using
>>> recon-all -autorecon2-wm -s 
>>> also did not yield appreciable results. Is there anything else that I
>>> might
>>> be able to try to fix this?
>>> Thank you for all the help,
>>>
>>> Nicholas Goh
>>>
>>> On Wed, Sep 27, 2017 at 12:49 PM, Elijah Mak 
>>> wrote:
>>>   Hi Nicholas,
>>>
>>> In such situations, I have learned that autorecon2-wm after adding WM
>>> voxels seems to work pretty well. Hope that helps.
>>>
>>> Best Wishes,
>>> Elijah
>>>
>>> On 27 September 2017 at 16:46:43, Nicholas Goh (ngo...@gmail.com)
>>> wrote:
>>>
>>> Bruce,
>>> Thank you for the response. Attempting to use this method has
>>> not produced results, and I am unsure how to proceed or if I had
>>> performed it improperly. I have attached an example of the
>>> control points being placed, if that helps any.
>>> Thank you,
>>>
>>> Nicholas Goh
>>>
>>> On Wed, Sep 27, 2017 at 11:04 AM, Bruce Fischl
>>>  wrote:
>>>   Hi Nicholas
>>>
>>>   yes, possibly, depending on why you are missing
>>>   chunks. If the white matter in the regions you are
>>>   missing has intensity values significantly < 110
>>>   then what you are doing should help. The control.dat
>>>   file must be place in the subject/tmp dir for us to
>>>   find it.
>>>
>>>   cheers
>>>   Bruce
>>>   On Wed, 27 Sep 2017, Nicholas Goh wrote:
>>>
>>> I am attempting to fix the
>>> aparc+aseg.mgz file for an image, and
>>> wanted to check to see if I am
>>> doing it correctly.What I was doing
>>> which seemed to be ineffective was
>>> 1)create a new point set of control
>>> points labelled control.dat
>>> 2)place control points along what should
>>> be white matter
>>> 3)save point set
>>> 4)run recon-all -autorecon2-cp
>>> -autorecon3 -subjid 
>>>
>>> Is this the correct way to go about
>>> fixing aparc+aseg files that are missing
>>> chunks of the brain? Is
>>> there a better way to go about this?
>>> Thanks for the help,
>>>
>>> Nicholas Goh
>>>
>>>
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Re: [Freesurfer] PETSURFER: MRTM2 volumes?

2017-10-16 Thread Douglas Greve


You have to do it one hemi at a time, eg,

mri_surf2vol --hemi lh --so lh.bp.nii.gz --subject fsaverage --o 
smoothed.bpnd.in.volume.nii.gz


mri_surf2vol --hemi rh --so rh.bp.nii.gz --subject fsaverage --merge 
smoothed.bpnd.in.volume.nii.gz  --o smoothed.bpnd.in.volume.nii.gz



On 10/16/17 12:57 PM, Elijah Mak wrote:
Got it, thanks! I have already performed smoothing on the MGX surfaces 
so I’d like to proceed with mri_surf2vol.


According to the “hidden secrets of success” for mri_surf2vol, there 
are 2 methods.  Is the command below correct?


mri_surf2vol --so lh.bp.nii.gz (the PET surface BPNDs) --so 
rh.bp.nii.gz --subject fsaverage --o smoothed.bpnd.in.volume.nii.gz


The next step is to bring the volumes into CVS-MNI152 space. 
Mri_cvs_register has been done on the T1.


Thanks Doug.

Best Wishes,
Elijah

*
*
*Dr. Elijah Mak, Research Associate
*Department of Psychiatry
Old Age Psychiatry Group | Cambridge Intellectual & Developmental 
Disabilities Research Group

University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24


On 16 Oct 2017, at 16:08, Douglas Greve > wrote:


it comes down to have you smooth it. If you do it in the volume, then
you need to smooth it in the volume, and that is an invalid analysis
with MG.


On 10/13/17 8:42 PM, Elijah Mak wrote:

Hi Doug,

I wonder what is the difference between this approach (mri_surf2vol) 
as opposed to doing the MRTM2 modelling on the MGX GM output (58 
frames), which will give us the bp.nii.gz in volume space?


Thanks.

Best Wishes,
Elijah



On 13 Oct 2017, at 16:19, Douglas Greve > wrote:


do you mean you want to map the surface-based data into the volume? If
so, you can use mri_surf2vol. If you want to analyze your pet data in
the volume you can just do that with mri_glmfit


On 10/5/17 4:59 PM, Elijah Mak wrote:

Hi Doug,

Referring to the PETSURFER tutorial for dynamic PET data, I am 
wondering if it is possible to obtain a volume-based equivalent of 
mrtm2.lh.sm05/bp.nii.gz? As I understand, bp.nii.gz is the 
partial-volumed corrected output that has been sampled onto the 
fsaverage surface.


Thanks for your time again.

Best Wishes,
Elijah



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Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

2017-10-16 Thread Christopher Markiewicz

Doug,

Sorry if I muddied things by going into the significant digits - accurate to 5 
seems reasonable. I was simply meaning to say that the rotation and scaling 
parameters are not the issue, to save the reader time inspecting them.

The translations (final three parameters) are off by anywhere 3 to 54mm, though.

LTA-FSL-ITK: 1.3066136395454464 -45.60342165876236 -43.10584860730749
LTA-ITK: -2.2848172187805176 -2.9065067768096924 11.744022369384766

I'm guessing lta_convert has the wrong model of the origin in ITK style 
affines, at least as applied by antsApplyTransforms.

Chris

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

Sent: Monday, October 16, 2017 12:39:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] lta_convert does not produce ITK transforms that are 
correctly applied by antsApplyTransforms

Not sure I understand. If the two transforms are only off by less than
the 5th decimal, then why are the registrations off so much. As for why
it would be off at the 5ht dec, it probably has to do with the way we
store the matrix. When a volume is read in, the matrix is decomposed
into translation, scale, and direction cosine, and then the matrix is
thrown away. When a volume with the same geometry is written out, the
matrix is recomputed. Some resolution is lost during the
decomposition/recomposition, and we don't end up with the exact same matrix.


On 10/14/17 1:30 PM, Christopher Markiewicz wrote:
> Hi,
>
> I've used `bbregister` to generate a transform `bold2T1.lta` from `bold.nii` 
> to `T1.mgz` (assume we have a `T1.nii` as well for the sake of ANTs).
>
> The following produces a well-aligned output:
>
>  mri_convert --apply_transform bold2T1.lta bold.nii bold_space-T1.nii
>
> As does the following:
>
>  lta_convert --inlta bold2T1.lta --outfsl bold2T1.mat
>  c3d_affine_tool -ref T1.nii -src bold.nii bold2T1.mat -fsl2ras -oitk 
> bold2T1.txt
>  antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
> bold2T1.txt
>
> However, if one skips the FSL step, the registration is quite far off:
>
>  lta_convert --inlta bold2T1.lta --outitk bold2T1.txt
>  antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
> bold2T1.txt
>
> Comparing the ITK transform files:
>
> LTA-FSL-ITK
>
>  #Insight Transform File V1.0
>  #Transform 0
>  Transform: MatrixOffsetTransformBase_double_3_3
>  Parameters: 0.9895096215486424 0.011126830936108464 
> -0.00042204653562094823 -0.01079971161879626 0.872329255299452 
> -0.42602926756857834 -0.004755964529051335 0.42420535065804454 
> 0.8878552541301569 -1.3066136395454464 -45.60342165876236 -43.10584860730749
>  FixedParameters: 0 0 0
>
>
> LTA-ITK
>
>  #Insight Transform File V1.0
>  #Transform 0
>  Transform: AffineTransform_double_3_3
>  Parameters: 0.98950976133346558 0.011126830242574215 
> -0.00042204943019896746 -0.010799713432788849 0.87232941389083862 
> -0.42602935433387756 -0.0047559700906276703 0.42420542240142822 
> 0.88785547018051147 -2.2848172187805176 -2.9065067768096924 11.744022369384766
>  FixedParameters: 0 0 0
>
>
> To 5 significant digits, these are the same, except the last three 
> (translation) parameters. And the `AffineTransform_double_3_3` is different 
> from `MatrixOffsetTransformBase_double_3_3`, though I'm not sure whether this 
> has any effect.
>
> Here is the original LTA:
>
>  type  = 1 # LINEAR_RAS_TO_RAS
>  nxforms   = 1
>  mean  = 0. 0. 0.
>  sigma = 1.
>  1 4 4
>  1.010462999343872e+00 -1.063966564834118e-02 4.625014495104551e-03 
> -2.332115173339844e+00
>  1.228639855980873e-02 9.293417930603027e-01 -4.459420144557953e-01 
> 2.507942199707031e+00
>  4.575361963361502e-04 4.440840482711792e-01 9.132194519042969e-01 
> -1.201664733886719e+01
>  0.000e+00 0.000e+00 0.000e+00 
> 9.98807907104e-01
>  src volume info
>  valid = 1  # volume info valid
>  filename = 
> /scratch/fmriprep_wf/single_subject_02_wf/func_preproc_task_short_wf/bold_reg_wf/bbreg_wf/bbregister/uni_masked_xform.nii.gz
>  volume = 64 64 34
>  voxelsize = 3.125e+00 3.125e+00 
> 4.000e+00
>  xras   = -1.000e+00 0.000e+00 
> 0.000e+00
>  yras   = 0.000e+00 1.000e+00 
> 0.000e+00
>  zras   = 0.000e+00 0.000e+00 
> 1.000e+00
>  cras   = -1.090248107910156e+00 -1.071614074707031e+01 
> 1.619928741455078e+01
>  dst volume info
>  valid = 1  # volume info valid
>  filename = 
> /scratch/fmriprep_wf/single_subject_02_wf/anat_preproc_wf/t1_merge/sub-02_T1w_template.nii.gz
>  volume = 160 192 192
>  voxelsize = 1.000e+00

[Freesurfer] LGI calculation

2017-10-16 Thread Serian doma

Dear All,

I designed an adaptive filter according to local gyrification index values
and then want to see the lgi histogram of new smoothed brain volume.
However freesurfer gave an error as:

ERROR: mritotal failed, see transforms/talairach.log

It seems that the input volume orientation has changed. But the input
volume is the smoothed version of norm.mgz which is also an output of
freesurfer.

Could anyone come up with a solution for this issue?


-- 

Serian DOMA
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Re: [Freesurfer] Constrain smoothing to GM for PET data

2017-10-16 Thread Douglas Greve


that includes GM regions. not sure what you want


On 10/13/17 8:58 PM, Elijah Mak wrote:

Hi Doug,


That subcort mask is only GM (sorry, should have indicated that when 
I named it).


I just looked at the subcort mask in the cvs 2mm folder and it looks 
like it is only subcortical? I am looking for a similar mask that also 
 includes the GM regions.  Any idea?



Best Wishes,
Elijah



On 13 Oct 2017, at 17:06, Douglas Greve > wrote:


That subcort mask is only GM (sorry, should have indicated that when 
I named it).



On 10/13/17 11:15 AM, Elijah Mak wrote:

Hi Doug,

Yes, but I am using the GM rather than the subcortical volume. How 
can we get a similar GM mask on CVS 2mm space?


Thanks for your help.

Best Wishes,
Elijah

Dr. Elijah Mak, Research Associate
Department of Psychiatry,
Old Age Psychiatry Group | Cambridge Intellectual & Developmental 
Disabilities Research Group

University of Cambridge,
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24


From: Douglas Greve  

Reply: list Freesurfer support  


Date: 13 October 2017 at 16:14:34
To: Elijah Mak  
, list Freesurfer support 
 

Subject: Re: [Freesurfer] Constrain smoothing to GM for PET data

Are you using mri_vol2vol to go into the cvs 2mm space? If so, then 
use 
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/subcort.mask.mgz



On 10/11/17 3:15 PM, Elijah Mak wrote:

Hi Doug,

Thanks.

Could I check my workflow to perform the constrained smoothing of 
PET MGX-GM volumes? My objective here is to normalise the PET 
volumes to the CVS-MNI152 space to produce group-level PET maps. 
As such, should I be deriving the GM + Subcortical PVFs from the 
cvs_avg35_inMNI152 subject for the mask in mri_fwhm?


1. mri_cvs_register to bring T1s to CVS MNI152
2. mri_vol2vol to bring the PET MGX-GM volumes (already in 
anatomical T1 space) to CVS MNI152
3. mri_fwhm to smooth the PET volumes, using a binarised mask of 
GM+Subcortical PVFs from the cvs_avg35_inMNI152 subject
4. What is the best way to get the mask from the 
cvs_avg35_inMNI152 subject?
5. Obtain group level PET maps in CVS MNI152 space using 
mri_concat —mean.


Thanks very much.

Best Wishes,
Elijah

On 4 Oct 2017, at 14:51, Douglas Greve > wrote:


You mean for volume-based analysis? Yes, use the pvf.


On 10/4/17 9:42 AM, Elijah Mak wrote:

Hi Doug,

I have used PETSURFER to derive MGX GM volumes from PET data.  
Now, I would like to constrain the smoothing to the GM. Is it 
advisable to use the PVF in the aux folder for this purpose? If 
not, what is the best approach do this?


Thanks!

Best Wishes,
Elijah



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Re: [Freesurfer] Normalize to mni

2017-10-16 Thread Douglas Greve

I'm not sure what you mean/want. If you run preproc-sess with the 
-mni305 flag, it will resample to mni305 space and mask out 
non-subcortical structures



On 10/12/17 11:14 AM, Jan Willem Koten wrote:


Normalize to mni

Dear Doug,

We have a very simple question. In a first step we segmented brains 
using the recon all command. Our functional pipeline created a 
„fstcmc.nii.gz“ file. We would like to do some subcortical analysis 
and need to perfrorm this in MNI 305 space. We also need the 
subcortical labels for the actual analysis itself. Does someone know 
the trick? In short how do we get from fstcmc.nii.gz“ to subcortical 
functional ROI's?


Greetings Jan

Jan Willem Koten (van Grevenbicht)

Zollernstrasse 57, 52070 Aachen, Germany
Telephone: (0049) (0)241 212 44


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Re: [Freesurfer] Longitudinal analysis using data with only two timepoints and LME

2017-10-16 Thread Martin Reuter

Hi Christoph,

1) I would use only intercept as random effect. I like to keep the model simple 
and - as you say - there is only a max of 2 time points. If you like you can do 
a model comparison (see wiki page) to compare the two models. 

2) I would use the exact time in years (as float with decimal places). I don’t 
see a good reason or mapping all follow-ups to 6 years when the exact date is 
known.

3) No idea. Does it even matter? The single time points are mainly used to 
estimate cross subject variance for that I don’t even know how much the time is 
used. You could try out to put 6 (or better if you know the exact date, put the 
exact time distance to the subject clinical baseline visit). 

Best, Martin


> On 13. Oct 2017, at 16:16, Christoph Abé  wrote:
> 
> Dear FreeSurfer community,
> 
>  
> 
> I have a few questions regarding the usage of the LME matlab tools for 
> longitudinal data analyses, and how to set up the model. We have patients and 
> control data that we want to compare with respect to cortical changes over 
> time (two time points: baseline and follow-up). We are also dealing with 
> several cases (100 out of 300) with only one time point. The model is set up 
> with “time” between scans, group, group*time, sex, and age as regressors. 
> But, dealing with only two time points raised some questions:
> 
> 
> 
> 1) I have read mixed opinions about fitting random slopes when dealing with 
> two time points. Even though it seems to make sense to model individual 
> random slopes, a fit through two time points may actually cause a problem. It 
> also seems redundant to include 2 random factors (intercept and slope) in 
> that case, as fitting random intercepts seems to be sufficient for the 
> covariance estimation. So my question: Is it recommended to model only one 
> random factor (intercept), or even wrong to model two (intercept and slope), 
> when dealing with 2 TPs (especially when dealing with drop outs)?
> 
> 
> 
> 2) This question is regarding how to set up the time variable. We have a 
> large variance in that measure, meaning the follow-up scans were done between 
> 5-7 years after baseline. As this contributes to the variance of the 
> dependent variable, I would like to include the exact time interval as 
> continuous number in the model (thus a slightly different number for each 
> participant), rather than using time as a two-level factor (e.g. “0” for 
> baseline and “6” for all follow-up cases). I am wondering which approach is 
> recommended and whether there are any significant benefits of using one 
> method (time as two-level factor) over the other (time as continuous) in a 
> LME model with two time points.
> 
> 
> 
> 3) We have several cases with data at one single time point (ca 100 out of 
> 300). In the design matrix, I include single rows for drop out cases, with 
> time=0. I assume that their number of repeated measures (1) will be handled 
> by the ni-vector generated by the sorting procedure (sortData in matlab). 
> However, we also have cases who were scanned only during clinical follow-up 
> intervention (6 years after the baseline data was collected). Ideally, I 
> would like to avoid assigning those to the baseline time point, for several 
> reasons (e.g. treatment effects, potential scanner drifts over 6 years, etc). 
> Instead, I want to assign them to the follow-up time point. If the better 
> choice in point 2) is to use the actual (continuous) numbers for “time”, I am 
> thinking about assigning the population median of the time difference between 
> scans to those cases. Is this a reasonable approach? Does not seem to be the 
> cleanest way of doing it, as we introduce some error, but may be a reasonable 
> trade off to avoid dropping data of ca. 50 individuals. What is your opinion 
> on that matter? 
> 
>  
> 
> Thanks for any help and opinions.
> 
> Best,
> 
> Christoph
> 
> 
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[Freesurfer] TRACULA bedpostx step with gpu

2017-10-16 Thread Mehta, Chintan

Dear FreeSurfer users,

I am using Freesurfer 6.0 and Tracula 6.0 for processing MRI and DTI scans. The 
second step of the trac-all pipeline performs the ball-and-stick fit with the 
bedpost function from FSL. Documentation for FSL suggests that the use of GPUs 
can considerably speed this process (from ~15 hours on a single-threaded 
machine to 30 minutes on GPU; see bulletpoint 7 under processing pipeline at 
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Processing_pipeline).


Using GPU requires calling "bedpostx_gpu" (instead of "bedpostx") on a machine 
with a NVIDIA GPU and CUDA toolkit, both of which I have access to.  The 
"bedpostx_gpu" function has, otherwise, the same flags as "bedpostx".


While there is another post on the FreeSurfer forum on this topic 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg54498.html), 
the answer there does not refer to how "bedpostx_gpu" can be used.


Is there a way to call on "bedpostx_gpu" instead of "bedpostx" in the second 
step of the trac-all pipeline? More precisely, is there a way to adjust the  
command:

> trac-all -bedp -c dmrirc

to take advantage of GPU capabilities?


Alternatively, is the source code for the "trac-all" binary available? For 
example, if is there a bash script that performs the same steps as the 
"trac-all -bedp -c dmrirc" available, then GPU capabilities can be exploited by 
running that script except replacing "bedpostx" with "bedpostx_gpu".


Thank you.


Best,

Chintan




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Re: [Freesurfer] TRACULA bedpostx step with gpu

2017-10-16 Thread Yendiki, Anastasia

Hi Chintan - Freesurfer is open source, so all of our source code is available, 
but trac-all is actually a shell script, so you can find it under 
$FREESURFER_HOME/bin/.

TRACULA just expects the output files of bedpostX, and does not care if they 
were generated on GPUs or CPUs. Just provide the $subjectID/dmri directory 
(created by the first step of trac-all) as the argument to either version of 
bedpostX. After it's done, you can skip to the 3rd step of trac-all.

Hope this helps,

a.y

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Mehta, Chintan 
[chintan.me...@yale.edu]
Sent: Monday, October 16, 2017 5:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA bedpostx step with gpu


Dear FreeSurfer users,

I am using Freesurfer 6.0 and Tracula 6.0 for processing MRI and DTI scans. The 
second step of the trac-all pipeline performs the ball-and-stick fit with the 
bedpost function from FSL. Documentation for FSL suggests that the use of GPUs 
can considerably speed this process (from ~15 hours on a single-threaded 
machine to 30 minutes on GPU; see bulletpoint 7 under processing pipeline at 
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Processing_pipeline).


Using GPU requires calling "bedpostx_gpu" (instead of "bedpostx") on a machine 
with a NVIDIA GPU and CUDA toolkit, both of which I have access to.  The 
"bedpostx_gpu" function has, otherwise, the same flags as "bedpostx".


While there is another post on the FreeSurfer forum on this topic 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg54498.html), 
the answer there does not refer to how "bedpostx_gpu" can be used.


Is there a way to call on "bedpostx_gpu" instead of "bedpostx" in the second 
step of the trac-all pipeline? More precisely, is there a way to adjust the  
command:

> trac-all -bedp -c dmrirc

to take advantage of GPU capabilities?


Alternatively, is the source code for the "trac-all" binary available? For 
example, if is there a bash script that performs the same steps as the 
"trac-all -bedp -c dmrirc" available, then GPU capabilities can be exploited by 
running that script except replacing "bedpostx" with "bedpostx_gpu".


Thank you.


Best,

Chintan




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[Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance

2017-10-16 Thread stdp82

Thanks.
The maps produced in slope and intercept folders are very similar and opposite 
in colors.
I have already applied this contrast but I think that they did not fit with my 
goals.
Why the intercept did not produce the same results of G4VO?
The slope effect is very similar to the inverse of intercept...


>Messaggio originale
>Da: "Douglas Greve" 
>Data: 16-ott-2017 17.41
>A: 
>Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of 
covariance
>
>they all look ok except that these should be
>C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
>C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
>
>
>On 10/13/17 11:30 AM, std...@virgilio.it wrote:
>> I have applied the contrasts that we discussed in the previous mails but 
they
>> produce doubt results.
>>
>> In summary, I aim to look at:
>> A- Difference between groups without considerer the covariate effect (I
>> suppose that the maps will be in the intercept folder) --->  ANOVA between 
4
>> groups
>> B- Clusters in which the fMRI (dependent variable) is associated to the
>> structural data (covariate), taking in account the groups (I suppose that 
the
>> maps will be in the slope folder) --->  MANOVA between 4 groups
>>
>> Please could you check the contrast reported below? I suspect that there 
are
>> some errors because, looking at results:
>> The slope map is the inverse in color of the intercept map and the 
intercept
>> did not correspond to the results which I obtain by using G4V0
>>
>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
>> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.25 0.25 0.25 0.25 0 0 0 0
>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.25 0.25 0.25 0.25
>> C15) group.effect.intercept
>> 1 -1 0 0 0 0 0 0
>> 1 0 -1 0 0 0 0 0
>> 1 0 0 -1 0 0 0 0
>> C16) group.effect.slope
>> 0 0 0 0 1 -1 0 0
>> 0 0 0 0 1 0 -1 0
>> 0 0 0 0 1 0 0 -1
>>
>> Best regards
>>
>>
>> Stefano
>>
>>
>>> Messaggio originale
>>> Da: "Douglas N Greve" 
>>> Data: 11-ott-2017 17.28
>>> A: , 
>>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of
>> covariance
>>> the rational is to make them sum to 1.0 so that the gamma.mgh file has
>>> units of mm (or whatever the input units are). It is unimportant for
>>> p-values.
>>>
>>>
>>> On 10/10/2017 01:54 PM, std...@virgilio.it wrote:
 Thanks

 In which contrast I must change "1" with "0.25"?
 What is the rationale to use 0.25?


 Sent from Virgilio Mobile
 

 Il 10/10/2017, Douglas N Greve  ha scritto:

 I don't understand what you mean by "where I should use"

 I thought I looked through all those contrasts a few weeks ago, no?


 On 10/10/2017 04:22 AM, std...@virgilio.it wrote:
> You have suggested to use
> 0 0 0 0 .25 .25 .25 .25
> to look the map where, considering the group differences, the covariate
> predicts the dependent variable (functional connectivity) in 4GV1.
>
> Below I'm reporting the contrast that I have used.
> Please could you check it and suggest correction?
> Could you explain where I should use 0 0 0 0 .25 .25 .25 .25, please?
>
> Thanks
>
> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
> C15) group.effect.intercept
> 1 -1 0 0 0 0 0 0
> 1 0 -1 0 0 0 0 0
> 1 0 0 -1 0 0 0 0
> C16) group.effect.slope
>> 0 0 0 0 1 -1 0 0
>> 0 0 0 0 1 0 -1 0
>> 0 0 0 0 1 0 0 -1
>
>
>
>
>
> On 10/6/17 9:24 AM, std...@virgilio.it wrote:
>> Thank you very much.
>> Where I should put 0 0 0 0 .25 .25 .25 .25?
>> Which are the contrast reported below that I should modify?
>>
>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
>> C3)

Re: [Freesurfer] Questions about the transformation of DKatlas from surface to volume

2017-10-16 Thread Bruce Fischl

do you really want the atlas in MNI space or do you want an individual
subject parcellation mapped to MNI? If the atlas, I think it already is, or
at least it lives on the fsaverage surface which has associated MNI coords.

Doug can confirm.

cheers
Bruce

On Mon, 16 Oct 2017, cain
wrote:

Thanks for your quick reply. For the third question, if I use talairach.xfm to
transform the atlas in volume, it will go to the MNI305 space. However, how to
transform the atlas from the Talariach to MNI152 space? And I will the atlas in
volume format in other software related to the functional MRI. Thank you for
the great help !
At 2017-10-15 23:35:58, "Bruce Fischl" wrote:

Hi Zhiqiang

(1) No, the manual parcellations were done in individual subject space,
then compiled into an atlas in fsaverage/spherical warp coords.

(2) We inflate the white surface, but I don't think inflating the pial
would be much different. YOu can do it yourself if you want with
mris_inflate

(3) No, this converts it to individual subject space. You could transform
it to MNI with mri_vol2vol using the talairach.xfm that is in the subjects
mri/transforms dir.

cheers
Bruce

On Sun, 15 Oct 2017, Zhiqiang Sha wrote:

Hi,
I have three questions about the transformation.
(1) Is Desikan-Killiany Atlas in Talairach space? The volume was transposed onto the
"inflated"
cortical surface based on the image in freesurfer/average/mni305.cor.mgz ?
(2) DK_atlas seems to be obtained from the inflation of interface of gray and
white matter. Did you
release the inflated surfaces based on the inner and outer surfaces ?
(3) I have transformed this atlas from surface to volume using mri_aparc2aseg
with default
parameters (e.g. mri_aparc2aseg --s bert). Is this transformed volume in
Talariach space ? Do I need
transform it to MNI space again ?

I am looking forward to your reply. Thank you very much !

Best Wishes,
Zhiqiang Sha

【网易自营】好吃到爆！鲜香弹滑加热即食，经典13香/麻辣小龙虾仅75元3斤>>

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[Freesurfer] TRACULA bedpostx step with gpu

Re: [Freesurfer] TRACULA bedpostx step with gpu

[Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance

Re: [Freesurfer] Questions about the transformation of DKatlas from surface to volume

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