Re: [Freesurfer] Registering Mean Diffusivity to Anatomical Space {Disarmed}

[Nillo, Ryan Michael R]

Thanks Doug!

When you say sample onto the mni152 surface, you mean to use mri_vol2surf, 
correct?

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging

> On May 27, 2020, at 11:10 AM, Douglas N. Greve  wrote:
> 
> I would probably run recon-all on the mni152, and then sample the MD map onto 
> the mni152 surface, then use mris_apply_reg to map it to an individual. 
> Also, Thomas Yeo has some possibly-better tools to do this. 
> 
> On 5/27/2020 2:02 PM, Nillo, Ryan Michael R wrote:
>> Hello FreeSurfer users,
>> 
>> I have a mean diffusivity map that exists in MNI152 space that I want to 
>> register to a subject’s anatomical space. In the end, I want to display the 
>> diffusivity on the subject’s surface. I want to ask if this is the correct 
>> way to do this:
>> 
>> 1) bbregister --s sub-01 --mov ./MD.mni152.nii --reg 
>> $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --init-fsl —dti #create 
>> registration matrix
>> 
>> 2) mri_vol2vol --mov ./MD.mni152.nii --targ 
>> $SUBJECTS_DIR/sub-01/mri/brain.mgz --reg 
>> $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --o ./MD.nii #register 
>> mean diffusivity map to subject space
>> 
>> Thanks in advance,
>> 
>> Ryan Michael Nillo
>> Staff Research Associate I
>> University of California San Francisco
>> Department of Radiology and Biomedical Imaging
>> 
>> 
>> 
>> External Email - Use Caution
>> 
>> 
>> 
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[Freesurfer] Registering Mean Diffusivity to Anatomical Space

[Nillo, Ryan Michael R]

Hello FreeSurfer users,

I have a mean diffusivity map that exists in MNI152 space that I want to 
register to a subject’s anatomical space. In the end, I want to display the 
diffusivity on the subject’s surface. I want to ask if this is the correct way 
to do this:

1) bbregister --s sub-01 --mov ./MD.mni152.nii --reg 
$SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --init-fsl —dti #create 
registration matrix

2) mri_vol2vol --mov ./MD.mni152.nii --targ $SUBJECTS_DIR/sub-01/mri/brain.mgz 
--reg $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --o ./MD.nii #register 
mean diffusivity map to subject space

Thanks in advance,

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging



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[Freesurfer] LGI help

[Nillo, Ryan Michael R]

Hello Freesurfer users/developers,

I want to run recon-all localGI on a subject who has been processed with 
Freesurfer 5.3. Whenever I run recon-all -localGI, I always get an error on 
“make_roi_paths”. There error can be found at the end of this email. I looked 
at the 5.3 release notes and found the that one issue with localGI was fixed by 
substituting a line of code. The current SearchProjectionOnPial.m that I am 
using uses this fix.

LGI: issue when using Matlab 2013. the fix is to edit the file 
$FREESURFER_HOME/matlab/SearchProjectionOnPial.m and make these changes: 
find this line:

< for t=1:step:size(perim,2)

and change to:

> si=max(size(perim));
> for t=1:step:si




make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/working/ABCD/FS/NDAR_INV021N0FLH/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_58433_.m');
 exit
=

< M A T L A B (R) >
  Copyright 1984-2015 The MathWorks, Inc.
   R2015b (8.6.0.267246) 64-bit (glnxa64)
  August 20, 2015
 
For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.
 

Academic License

>> loading datas ...
FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.04 sec)

FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial-outer-smoothed
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.02 sec)

preparing outer mesh structure ...
face 5000 / 130188
face 1 / 130188
face 15000 / 130188
face 2 / 130188
face 25000 / 130188
face 3 / 130188
face 35000 / 130188
face 4 / 130188
face 45000 / 130188
face 5 / 130188
face 55000 / 130188
face 6 / 130188
face 65000 / 130188
face 7 / 130188
face 75000 / 130188
face 8 / 130188
face 85000 / 130188
face 9 / 130188
face 95000 / 130188
face 10 / 130188
face 105000 / 130188
face 11 / 130188
face 115000 / 130188
face 12 / 130188
face 125000 / 130188
face 13 / 130188

mesh_outer = 

 vertices: [65096x3 double]
faces: [130188x3 double]
facesOfVertex: [65096x1 struct]

preparing pial mesh structure ...
...searching for mesh edges...done (134.42 sec).
... creating path file for vertex 1 / 65096
area file for outer ROIs saved at 1
In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));

Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);


Error in reorganize_verticeslist (line 28)

[nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));

Error in make_roi_paths (line 93)
reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
verticeslist, step);
 
>> 
ERROR:  make_roi_paths did not complete successfully!
Linux jamestown.radiology.ucsf.edu 3.10.0-1062.1.2.el7.x86_64 #1 SMP Mon Sep 16 
14:19:51 EDT 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s NDAR_INV021N0FLH exited with ERRORS at Tue Mar  3 11:09:41 PST 2020

For more details, see the log file 
/working/ABCD/FS/NDAR_INV021N0FLH/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Thank you for your time,

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging



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Re: [Freesurfer] mri_glmfit ill-conditioned matrix question {Disarmed}

[Nillo, Ryan Michael R]

External Email - Use Caution

Thanks, Doug. One more question: I want to see how correlated my covariate ROI 
is with LGI and compare the correlation maps between the two groups. Is my 
glmfit command the correct setup? I have tried running glmfit on a different 
fsgd and contrast matrix with only one of the two groups and have a pcc.mgh for 
that analysis. When I compare that to the pcc.mgh I get from my original 
analysis for that same group, the value at each vertex is slightly different. 

Ryan Michael Nillo
UCSF Department is Radiology and Biomedical Imaging
Lab for Precision Neuroimaging
Staff Research Associate 1

> On Oct 28, 2019, at 11:17, Greve, Douglas N.,Ph.D.  
> wrote:
> 
> Yes
> 
>> On 10/28/19 1:04 PM, Nillo, Ryan Michael R wrote:
>> Am I correct in assuming this results in z-scoring/normalizing the 
>> covariates?
>> 
>> Ryan Michael Nillo
>> Staff Research Associate I
>> University of California San Francisco
>> Department of Radiology and Biomedical Imaging
>> 
>>> On Oct 28, 2019, at 7:33 AM, Greve, Douglas N.,Ph.D. 
>>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>> 
>>> My guess is that your covariates have almost no range to them and so 
>>> look like constant (similar to columns 1 and 2). You can try 
>>> demeaning and rescaling the covariates. You can do this by hand and 
>>> create a new FSGD file or you can add the following lines anywhere in 
>>> the fsgd:
>>> RescaleFlag 1
>>> DemeanFlag 1
>>> 
>>> 
>>> On 10/26/19 10:45 PM, Nillo, Ryan Michael R wrote:
>>>> Hello,
>>>> 
>>>> I ran mri_glmfit with the following fsgd file:
>>>> 
>>>> GroupDescriptorFile 1
>>>> Title CJD
>>>> 
>>>> Class MM1_MV1
>>>> Class MV2_VV2
>>>> 
>>>> Variablesfrontal
>>>> 
>>>> Input7693MV2_VV22.930667
>>>> Input11985MV2_VV22.410333
>>>> Input13082MV2_VV22.529333
>>>> Input13425MV2_VV22.593667
>>>> Input13667MM1_MV12.628667
>>>> Input13900MM1_MV12.675333
>>>> Input14094MM1_MV12.549333
>>>> Input15566MV2_VV22.67
>>>> Input15999MM1_MV12.641
>>>> Input16714MV2_VV22.643
>>>> Input16848MV2_VV22.63
>>>> Input16952MV2_VV22.516
>>>> Input7693aMV2_VV23.054
>>>> Input11985aMV2_VV22.42
>>>> Input13082aMV2_VV22.454
>>>> Input13425aMV2_VV22.602
>>>> Input13667aMM1_MV12.604333
>>>> Input13900aMM1_MV12.601333
>>>> Input14094aMM1_MV12.52
>>>> Input15566aMV2_VV22.71
>>>> Input15999aMM1_MV12.584333
>>>> Input16714aMV2_VV22.67
>>>> Input16848aMV2_VV22.53
>>>> Input16952aMV2_VV22.486
>>>> 
>>>> My two contrast matrices are:
>>>> one.mtx = [ 0 0 1 0 ]
>>>> two.mtx = [ 0 0 0 1 ]
>>>> 
>>>> When running the mri_glmfit command "*mri_glmfit --glmdir 
>>>> new.frontal.lgi --fsgd new.frontal.fsgd.txt --fwhm 30 --surf 
>>>> fsaverage lh --y lh.pial_lgi.fwhm0.mgh --C one.mtx --C two.mtx*”, I 
>>>> get the following output:
>>>> 
>>>> INFO: gd2mtx_method is dods
>>>> Saving design matrix to new.frontal.lgi/Xg.dat
>>>> Computing normalized matrix
>>>> Normalized matrix condition is 12820.7
>>>> Design matrix --
>>>>  0.0   1.0   0.0 2.93067;
>>>>  0.0   1.0   0.0 2.41033;
>>>>  0.0   1.0   0.0 2.52933;
>>>>  0.0   1.0   0.0 2.59367;
>>>>  1.0   0.0   2.62867 0.0;
>>>>  1.0   0.0   2.67533 0.0;
>>>>  1.0   0.0   2.54933 0.0;
>>>>  0.0   1.0   0.0 2.7;
>>>>  1.0   0.0   2.64100 0.0;
>>>>  0.0   1.0   0.0 2.64300;
>>>>  0.0   1.0   0.0 2.63000;
>>>>  0.0   1.0   0.0 2.51600;
>>>>  0.0   1.0   0.0 3.05400;
>>>>  0.0   1.0   0.0 2.42000;
>>>>  0.0   1.0   0.0 2.45400;
>>>>  0.0   1.0   0.0 2.60200;
>>>>  1.0   0.0   2.60433 0.0;
>>>>  1.0   0.0   2.60133 0.0;
>>>>  1.0   0.0   2.52333 0.0;
>>>>  0.0   1.0   0.0 2.71333;
>>>>  1.0   0.0   2.58433 0.0;
>>>>  0.0   1.0   0.

Re: [Freesurfer] mri_glmfit ill-conditioned matrix question {Disarmed}

[Nillo, Ryan Michael R]

Am I correct in assuming this results in z-scoring/normalizing the covariates?

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging

> On Oct 28, 2019, at 7:33 AM, Greve, Douglas N.,Ph.D.  
> wrote:
> 
> My guess is that your covariates have almost no range to them and so look 
> like constant (similar to columns 1 and 2). You can try demeaning and 
> rescaling the covariates. You can do this by hand and create a new FSGD file 
> or you can add the following lines anywhere in the fsgd:
> RescaleFlag 1
> DemeanFlag 1
> 
> 
> On 10/26/19 10:45 PM, Nillo, Ryan Michael R wrote:
>> Hello,
>> 
>> I ran mri_glmfit with the following fsgd file:
>> 
>> GroupDescriptorFile 1
>> Title CJD 
>> 
>> Class MM1_MV1 
>> Class MV2_VV2 
>> 
>> Variables  frontal 
>> 
>> Input 7693
>> MV2_VV2 2.930667
>> Input 11985
>> MV2_VV2 2.410333
>> Input 13082
>> MV2_VV2 2.529333
>> Input 13425
>> MV2_VV2 2.593667
>> Input 13667
>> MM1_MV1 2.628667
>> Input 13900
>> MM1_MV1 2.675333
>> Input 14094
>> MM1_MV1 2.549333
>> Input 15566
>> MV2_VV2 2.67
>> Input 15999
>> MM1_MV1 2.641
>> Input 16714
>> MV2_VV2 2.643
>> Input 16848
>> MV2_VV2 2.63
>> Input 16952
>> MV2_VV2 2.516
>> Input 7693a
>> MV2_VV2 3.054
>> Input 11985a
>> MV2_VV2 2.42
>> Input 13082a
>> MV2_VV2 2.454
>> Input 13425a
>> MV2_VV2 2.602
>> Input 13667a
>> MM1_MV1 2.604333
>> Input 13900a
>> MM1_MV1 2.601333
>> Input 14094a
>> MM1_MV1 2.52
>> Input 15566a
>> MV2_VV2 2.71
>> Input 15999a
>> MM1_MV1 2.584333
>> Input 16714a
>> MV2_VV2 2.67
>> Input 16848a
>> MV2_VV2 2.53
>> Input 16952a
>> MV2_VV2 2.486
>> 
>> My two contrast matrices are:
>> one.mtx = [ 0 0 1 0 ]
>> two.mtx = [ 0 0 0 1 ]
>> 
>> When running the mri_glmfit command "mri_glmfit --glmdir new.frontal.lgi 
>> --fsgd new.frontal.fsgd.txt --fwhm 30 --surf fsaverage lh --y 
>> lh.pial_lgi.fwhm0.mgh --C one.mtx --C two.mtx”, I get the following output:
>> 
>> INFO: gd2mtx_method is dods
>> Saving design matrix to new.frontal.lgi/Xg.dat
>> Computing normalized matrix
>> Normalized matrix condition is 12820.7
>> Design matrix --
>>  0.0   1.0   0.0   2.93067;
>>  0.0   1.0   0.0   2.41033;
>>  0.0   1.0   0.0   2.52933;
>>  0.0   1.0   0.0   2.59367;
>>  1.0   0.0   2.62867   0.0;
>>  1.0   0.0   2.67533   0.0;
>>  1.0   0.0   2.54933   0.0;
>>  0.0   1.0   0.0   2.7;
>>  1.0   0.0   2.64100   0.0;
>>  0.0   1.0   0.0   2.64300;
>>  0.0   1.0   0.0   2.63000;
>>  0.0   1.0   0.0   2.51600;
>>  0.0   1.0   0.0   3.05400;
>>  0.0   1.0   0.0   2.42000;
>>  0.0   1.0   0.0   2.45400;
>>  0.0   1.0   0.0   2.60200;
>>  1.0   0.0   2.60433   0.0;
>>  1.0   0.0   2.60133   0.0;
>>  1.0   0.0   2.52333   0.0;
>>  0.0   1.0   0.0   2.71333;
>>  1.0   0.0   2.58433   0.0;
>>  0.0   1.0   0.0   2.67333;
>>  0.0   1.0   0.0   2.5;
>>  0.0   1.0   0.0   2.48600;
>> 
>> ERROR: matrix is ill-conditioned or badly scaled, condno = 12820.7
>> 
>> Possible problem with experimental design:
>> Check for duplicate entries and/or lack of range of
>> continuous variables within a class.
>> If you seek help with this problem, make sure to send:
>>   1. Your command line:
>> mri_glmfit --glmdir new.frontal.lgi --fsgd new.frontal.fsgd.txt --fwhm 
>> 30 --surf fsaverage lh --y lh.pial_lgi.fwhm0.mgh --C one.mtx --C two.mtx 
>>   2. The FSGD file (if using one)
>>   3. And the design matrix above
>> Attempting to diagnose further 
>> SumSq: Min=2.828427 (col 1), Max=10.485683 (col 4)
>>  ... could not determine the cause of the problem
>> 
>> 
>> Can anyone give me some insight into what might be going wrong? 
>> 
>> Thanks so much,
>> 
>> Ryan Michael Nillo
>> Staff Research Associate I
>> University of California San Francisco
>> Department of Radiology and Biomedical Imaging
>> 
>> 
>> 

[Freesurfer] mri_glmfit ill-conditioned matrix question

[Nillo, Ryan Michael R]

Hello,

I ran mri_glmfit with the following fsgd file:

GroupDescriptorFile 1   
Title CJD   

Class MM1_MV1   
Class MV2_VV2   

Variables   frontal 

Input   7693MV2_VV2 2.930667
Input   11985   MV2_VV2 2.410333
Input   13082   MV2_VV2 2.529333
Input   13425   MV2_VV2 2.593667
Input   13667   MM1_MV1 2.628667
Input   13900   MM1_MV1 2.675333
Input   14094   MM1_MV1 2.549333
Input   15566   MV2_VV2 2.67
Input   15999   MM1_MV1 2.641
Input   16714   MV2_VV2 2.643
Input   16848   MV2_VV2 2.63
Input   16952   MV2_VV2 2.516
Input   7693a   MV2_VV2 3.054
Input   11985a  MV2_VV2 2.42
Input   13082a  MV2_VV2 2.454
Input   13425a  MV2_VV2 2.602
Input   13667a  MM1_MV1 2.604333
Input   13900a  MM1_MV1 2.601333
Input   14094a  MM1_MV1 2.52
Input   15566a  MV2_VV2 2.71
Input   15999a  MM1_MV1 2.584333
Input   16714a  MV2_VV2 2.67
Input   16848a  MV2_VV2 2.53
Input   16952a  MV2_VV2 2.486

My two contrast matrices are:
one.mtx = [ 0 0 1 0 ]
two.mtx = [ 0 0 0 1 ]

When running the mri_glmfit command "mri_glmfit --glmdir new.frontal.lgi --fsgd 
new.frontal.fsgd.txt --fwhm 30 --surf fsaverage lh --y lh.pial_lgi.fwhm0.mgh 
--C one.mtx --C two.mtx”, I get the following output:

INFO: gd2mtx_method is dods
Saving design matrix to new.frontal.lgi/Xg.dat
Computing normalized matrix
Normalized matrix condition is 12820.7
Design matrix --
 0.0   1.0   0.0   2.93067;
 0.0   1.0   0.0   2.41033;
 0.0   1.0   0.0   2.52933;
 0.0   1.0   0.0   2.59367;
 1.0   0.0   2.62867   0.0;
 1.0   0.0   2.67533   0.0;
 1.0   0.0   2.54933   0.0;
 0.0   1.0   0.0   2.7;
 1.0   0.0   2.64100   0.0;
 0.0   1.0   0.0   2.64300;
 0.0   1.0   0.0   2.63000;
 0.0   1.0   0.0   2.51600;
 0.0   1.0   0.0   3.05400;
 0.0   1.0   0.0   2.42000;
 0.0   1.0   0.0   2.45400;
 0.0   1.0   0.0   2.60200;
 1.0   0.0   2.60433   0.0;
 1.0   0.0   2.60133   0.0;
 1.0   0.0   2.52333   0.0;
 0.0   1.0   0.0   2.71333;
 1.0   0.0   2.58433   0.0;
 0.0   1.0   0.0   2.67333;
 0.0   1.0   0.0   2.5;
 0.0   1.0   0.0   2.48600;

ERROR: matrix is ill-conditioned or badly scaled, condno = 12820.7

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit --glmdir new.frontal.lgi --fsgd new.frontal.fsgd.txt --fwhm 30 
--surf fsaverage lh --y lh.pial_lgi.fwhm0.mgh --C one.mtx --C two.mtx 
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further 
SumSq: Min=2.828427 (col 1), Max=10.485683 (col 4)
 ... could not determine the cause of the problem


Can anyone give me some insight into what might be going wrong? 

Thanks so much,

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging



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[Freesurfer] Question on Z-scoring

[Nillo, Ryan Michael R]

Hello FreeSurfer users/devs,

I have a question on z-scoring. I would like to produce z-scored volume maps 
for each subject in my study. Is my process correct?

1) mri_surf2surf —srcsubject $sub —trgsubject $sub —sval $sub/surf/$h.volume 
—tval $sub/surf/$h.volume.mgh —sfmt curv (convert .volume file to .mgh file)

2) mris_preproc --hemi $h --fsgd 09172019.fsgd.txt --meas volume --mean --fwhm 
0 --o $PWD/$h.volume.pop_mean.mgh (obtain mean population volume at each vertex)

3)  mris_preproc --hemi $h --fsgd 09172019.fsgd.txt --meas volume —std --fwhm 0 
--o $PWD/$h.volume.pop_std.mgh (obtain volume standard deviation volume at each 
vertex)

4) mri_surf2surf —srcsubject fsaverage —trgsubject $sub —sval 
$PWD/$h.volume.pop_mean.mgh —tval $sub/surf/$h.volume.pop_mean.mgh —hemi $h 
(map population mean to subject space)

5) mri_surf2surf —srcsubject fsaverage —trgsubject $sub —sval 
$PWD/$h.volume.pop_std.mgh —tval $sub/surf/$h.volume.pop_std.mgh —hemi $h (map 
population std to subject space)

6) fscalc $sub/surf/$h.volume.mgh sub $sub/surf/$h.volume.pop_mean.mgh div 
$sub/surf/$h.volume.pop_std.mgh -o $sub/surf/$h.volume_z.mgh

7) mri_surf2surf —srcsubject $sub —trgsubject $sub —sval 
$sub/surf/$h.volume_z.mgh —tval $sub/surf/$h.volume_z —tfmt curv (convert .mgh 
to curv file)

After z-scoring each vertex, I want to do a group analysis between the two 
groups in my cohort. Instead of using raw volume as my measurement, I would be 
using z-scored volume.

Thanks for the help,

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging



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[Freesurfer] Converting a binary overlay file to label

[Nillo, Ryan Michael R]

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Hello FreeSurfer users/developers.

I manually created a binary overlay file on the pial surface. I am interested 
in looking at regions outside of this overlay file, so I converted 
lh.cortex.label to a binary overlay file and took the difference between the 
two. I want to take this new file and create a label so that I can run 
mris_anatomical_stats on the new region. How might I do this?

Sent from my iPhone

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Re: [Freesurfer] Surfaces with different numbers of vertices. {Disarmed} {Disarmed}

[Nillo, Ryan Michael R]

Pial-outer-smoothed was a surface created from recon-all -localGI. 

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging

> On Jul 1, 2019, at 11:41 AM, Greve, Douglas N.,Ph.D.  
> wrote:
> 
> how was pial-outer-smoothed create?
> 
> On 7/1/2019 2:33 PM, Nillo, Ryan Michael R wrote:
>> Hi Doug,
>> 
>> lh.test.nii was created with:
>> 
>> mri_vol2surf --mov ./misc/lh.probability.nii --trgsubject fsaverage_1 
>> --regheader fsaverage_1 --hemi lh --fwhm 30 --surf pial-outer-smoothed --o 
>> ./lh.test.nii
>> 
>> Where lh.probability.nii is a probability mask created from about 63 
>> subjects.
>> 
>> Thanks in advance for the help,
>> 
>> Ryan Michael Nillo
>> Staff Research Associate I
>> University of California San Francisco
>> Department of Radiology and Biomedical Imaging
>> 
>>> On Jul 1, 2019, at 11:13 AM, Greve, Douglas N.,Ph.D. 
>>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>> 
>>> Who did you create lh.test.nii? 
>>> 
>>> On 7/1/2019 1:47 PM, Nillo, Ryan Michael R wrote:
>>>> Hi Bruce,
>>>> 
>>>> We wanted to map values from a previous analysis to a representation of 
>>>> the brain with the sulci filled — something that resembles the output 
>>>> lh.pial-outer-smoothed from the recon-all -localGI. I tried using 
>>>> mri_surf2surf, but I get the error: 
>>>> 
>>>> ERROR: dimension inconsistency in source data
>>>>Number of surface vertices = 163842
>>>>Number of value vertices = 73466
>>>> 
>>>> My command: mri_surf2surf --srcsubject fsaverage_1 --trgsubject fsaverage 
>>>> --sval ./lh.test.nii --tval lh.pial-outer-smoothed2white.nii --hemi lh 
>>>> 
>>>> fsaverage_1 is a copy of fsaverage that I ran recon-all -localGI on to get 
>>>> the pial-outer-smoothed surface. 
>>>> Ryan Michael Nillo
>>>> Staff Research Associate I
>>>> University of California San Francisco
>>>> Department of Radiology and Biomedical Imaging
>>>> 
>>>>> On Jul 1, 2019, at 10:27 AM, Bruce Fischl >>>> <mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>>>>> 
>>>>> Hi Ryan
>>>>> 
>>>>> I'm not sure why you would have a surface with 73K vertices on fsaverage. 
>>>>> Why not use one of the ico representations (40K or 160K vertices)? In any 
>>>>> case, mri_surf2surf should do the trick, although you will probably need 
>>>>> to create a new subject with a set of 73K vertex surfaces
>>>>> 
>>>>> cheers
>>>>> Bruce
>>>>> On Mon, 1 Jul 2019, Nillo, Ryan Michael R wrote:
>>>>> 
>>>>>> Hello Freesurfer users/developers,
>>>>>> I have surface with ~73,400 vertices generated from the Freesurfer 
>>>>>> version 6
>>>>>> fsaverage brain, left hemisphere. I have a surface map that was created 
>>>>>> by
>>>>>> mapping a volume to the fsaverage white surface. Is there a way to map 
>>>>>> the
>>>>>> surface map to the new surface with less vertices? Is there a way to map
>>>>>> values from the 73,000 vertices-map to the standard fsaverage pal 
>>>>>> surface?
>>>>>> Thanks in advance,
>>>>>> Ryan Michael Nillo
>>>>>> Staff Research Associate I
>>>>>> University of California San Francisco
>>>>>> Department of Radiology and Biomedical Imaging
>>>>> ___
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>>>>>  
>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwICAg=iORugZls2LlYyCAZRB3XLg=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U=aI3KHyWjwZdI30RWj_f9dSUns7AMWcCrba9ZabJNI7w=Dl9keiwCh5CkYL34O0rnLQUOtm3qH01lSoG5FGod7Ow=>
>>>> 
>>>> 
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Re: [Freesurfer] Surfaces with different numbers of vertices. {Disarmed}

[Nillo, Ryan Michael R]

Hi Doug,

lh.test.nii was created with:

mri_vol2surf --mov ./misc/lh.probability.nii --trgsubject fsaverage_1 
--regheader fsaverage_1 --hemi lh --fwhm 30 --surf pial-outer-smoothed --o 
./lh.test.nii

Where lh.probability.nii is a probability mask created from about 63 subjects.

Thanks in advance for the help,

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging

> On Jul 1, 2019, at 11:13 AM, Greve, Douglas N.,Ph.D.  
> wrote:
> 
> Who did you create lh.test.nii? 
> 
> On 7/1/2019 1:47 PM, Nillo, Ryan Michael R wrote:
>> Hi Bruce,
>> 
>> We wanted to map values from a previous analysis to a representation of the 
>> brain with the sulci filled — something that resembles the output 
>> lh.pial-outer-smoothed from the recon-all -localGI. I tried using 
>> mri_surf2surf, but I get the error: 
>> 
>> ERROR: dimension inconsistency in source data
>>Number of surface vertices = 163842
>>Number of value vertices = 73466
>> 
>> My command: mri_surf2surf --srcsubject fsaverage_1 --trgsubject fsaverage 
>> --sval ./lh.test.nii --tval lh.pial-outer-smoothed2white.nii --hemi lh 
>> 
>> fsaverage_1 is a copy of fsaverage that I ran recon-all -localGI on to get 
>> the pial-outer-smoothed surface. 
>> Ryan Michael Nillo
>> Staff Research Associate I
>> University of California San Francisco
>> Department of Radiology and Biomedical Imaging
>> 
>>> On Jul 1, 2019, at 10:27 AM, Bruce Fischl >> <mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>>> 
>>> Hi Ryan
>>> 
>>> I'm not sure why you would have a surface with 73K vertices on fsaverage. 
>>> Why not use one of the ico representations (40K or 160K vertices)? In any 
>>> case, mri_surf2surf should do the trick, although you will probably need to 
>>> create a new subject with a set of 73K vertex surfaces
>>> 
>>> cheers
>>> Bruce
>>> On Mon, 1 Jul 2019, Nillo, Ryan Michael R wrote:
>>> 
>>>> Hello Freesurfer users/developers,
>>>> I have surface with ~73,400 vertices generated from the Freesurfer version 
>>>> 6
>>>> fsaverage brain, left hemisphere. I have a surface map that was created by
>>>> mapping a volume to the fsaverage white surface. Is there a way to map the
>>>> surface map to the new surface with less vertices? Is there a way to map
>>>> values from the 73,000 vertices-map to the standard fsaverage pal surface?
>>>> Thanks in advance,
>>>> Ryan Michael Nillo
>>>> Staff Research Associate I
>>>> University of California San Francisco
>>>> Department of Radiology and Biomedical Imaging
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>> 
>> 
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>> 
>> 
>> 
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Re: [Freesurfer] Surfaces with different numbers of vertices.

[Nillo, Ryan Michael R]

Hi Bruce,

We wanted to map values from a previous analysis to a representation of the 
brain with the sulci filled — something that resembles the output 
lh.pial-outer-smoothed from the recon-all -localGI. I tried using 
mri_surf2surf, but I get the error: 

ERROR: dimension inconsistency in source data
   Number of surface vertices = 163842
   Number of value vertices = 73466

My command: mri_surf2surf --srcsubject fsaverage_1 --trgsubject fsaverage 
--sval ./lh.test.nii --tval lh.pial-outer-smoothed2white.nii --hemi lh 

fsaverage_1 is a copy of fsaverage that I ran recon-all -localGI on to get the 
pial-outer-smoothed surface. 
Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging

> On Jul 1, 2019, at 10:27 AM, Bruce Fischl  wrote:
> 
> Hi Ryan
> 
> I'm not sure why you would have a surface with 73K vertices on fsaverage. Why 
> not use one of the ico representations (40K or 160K vertices)? In any case, 
> mri_surf2surf should do the trick, although you will probably need to create 
> a new subject with a set of 73K vertex surfaces
> 
> cheers
> Bruce
> On Mon, 1 Jul 2019, Nillo, Ryan Michael R wrote:
> 
>> Hello Freesurfer users/developers,
>> I have surface with ~73,400 vertices generated from the Freesurfer version 6
>> fsaverage brain, left hemisphere. I have a surface map that was created by
>> mapping a volume to the fsaverage white surface. Is there a way to map the
>> surface map to the new surface with less vertices? Is there a way to map
>> values from the 73,000 vertices-map to the standard fsaverage pal surface?
>> Thanks in advance,
>> Ryan Michael Nillo
>> Staff Research Associate I
>> University of California San Francisco
>> Department of Radiology and Biomedical Imaging
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[Freesurfer] Surfaces with different numbers of vertices.

[Nillo, Ryan Michael R]

Hello Freesurfer users/developers,

I have surface with ~73,400 vertices generated from the Freesurfer version 6 
fsaverage brain, left hemisphere. I have a surface map that was created by 
mapping a volume to the fsaverage white surface. Is there a way to map the 
surface map to the new surface with less vertices? Is there a way to map values 
from the 73,000 vertices-map to the standard fsaverage pal surface?

Thanks in advance,

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging



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[Freesurfer] Help for smoothing the pial surface

[Nillo, Ryan Michael R]

Hello FreeSurfer users/developers,

I want to generate a smooth pial surface similar to the one displayed on the 
LGI page (https://surfer.nmr.mgh.harvard.edu/fswiki/LGI 
) without having to run the 
entire recon-all process. Additionally, I want to map this surface to the white 
surface. Is there an easy way to do this? 

Thanks in advance,
Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging

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[Freesurfer] Smoothing the pill surface

[Nillo, Ryan Michael R]

Hello FreeSurfer users/developers,

I want to generate a smooth pial surface similar to the one displayed on the 
LGI page (https://surfer.nmr.mgh.harvard.edu/fswiki/LGI) without having to run 
the entire recon-all process. Additionally, I want to map this surface to the 
white surface. Is there an easy way to do this? 

Thanks in advance,
Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging



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Re: [Freesurfer] Projecting subcortical ROI to the cortical surface

[Nillo, Ryan Michael R]

External Email - Use Caution

Hi Bruce,

We want to study whether or not presence of periventricular heterotopias affect 
the thickness, volume, or surface area of the nearest cortical ROI. Since the 
condition we are studying is caused by failure of neurons to migrate to the 
cortex, we hypothesized that the nearest cortical ROI would be thinner/smaller 
compared to those without the heterotopia.

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging

On May 15, 2019, at 3:10 PM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:

Hi Ryan

I don't think projection of that kind of ROI is well-posed. Different parts of 
it are probably closest to wildly different parts of cortex. What are you 
trying to acheive?

cheers
Bruce


On Wed, 15 May 2019, Nillo, Ryan Michael R wrote:

External Email - Use Caution
Hello FreeSurfer users/developers,
I have a subcortical ROI that I want to project to the nearest cortical vertex 
(see screenshot). So
far, I have used the command mri_vol2surf --mov subject/mri/lh.het.nii --reg
subject/mri/transforms/talairach.lta --hemi lh —o subject/surf/lh.het.mgh to 
project these voxels to
the nearest vertex on the cortex. I am not sure if this is the correct way to 
do this because using
mris_anatomical_stats on the result does not produce any thickness file. Any 
help would be greatly
appreciated.
 [IMAGE]
Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging
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Re: [Freesurfer] Color scale error

[Nillo, Ryan Michael R]

External Email - Use Caution

Toggling the colorbar on and off in the GUI updates the values and appearance. 
Changing the threshold also seems to work once I press the “apply” button on 
the configuration window.

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging

On May 1, 2019, at 12:52 PM, Ruopeng Wang  wrote:

Can you try turning off/on the scale bar or change the threshold a little bit 
and see if it updates?

Ruopeng

On May 1, 2019, at 2:48 PM, Nillo, Ryan Michael R 
mailto:ryanmichael.ni...@ucsf.edu>> wrote:

External Email - Use Caution

Hello FreeSurfer Developers.

I am using FSv6 and I am having problems loading a colorbar. I am trying to run 
this code: freeview -f 
/data/sugrue2/ABCD/fsaverage/surf/rh.pial:overlay=/data/sugrue2/ABCD/temp/testing.mgh:overlay_threshold=0,1:overlay_method=linear
 -viewport 3d -hide-3d-slices -nocursor —colorscale. The resulting color scale 
makes no sense in that it does not properly display the min and max values 
specified. As you can see in the screenshot, the color scale runs from 1e-10 to 
-1e-10. Configuring the colors from the GUI seems to fix the issue, but Ideally 
I would like to automate the screenshot process.

Any help is greatly appreciated.



Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging

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Re: [Freesurfer] Obtaining stats for a custom label

[Nillo, Ryan Michael R]

External Email - Use Caution

Correction to the previous email: I can view the label in the rh.white, not 
lh.white.

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging

On Apr 24, 2019, at 10:50 AM, Nillo, Ryan Michael R 
mailto:ryanmichael.ni...@ucsf.edu>> wrote:

 lh.white surface

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Re: [Freesurfer] Obtaining stats for a custom label

[Nillo, Ryan Michael R]

External Email - Use Caution

Hi Doug,

I used the command below to convert a volume to a label file. The volume is a 
binary mask highlighting a subcortical ROI that I am projecting to the closest 
vertex. I can visualize the label on the fsaverage lh.white surface.
mri_vol2label --i 
/working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/mri/rh.custom.nii
 --id 1 --l 
/working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging

On Apr 24, 2019, at 9:48 AM, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:

How did you create the label? Is it a surface-based label? Ie, does it have 
valid vertex indices as the first item in each label point in the label file?

On 4/24/2019 2:44 AM, Nillo, Ryan Michael R wrote:

External Email - Use Caution

Hello Freesurfer developers,

I am using the code below to generate the stats table for the ROI.
mris_anatomical_stats -l 
/working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label
 -b subject rh white

However, when I run this command, I get this output:

limiting computations to label 
/working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label.
reading volume 
/working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/mri/wm.mgz...
reading input surface 
/working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.white...
reading input pial surface 
/working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.pial...
reading input white surface 
/working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.white...

table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name

I am getting no values for any of the metrics listed above. Is this a bug?

Thanks in advance,

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging




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[Freesurfer] Obtaining stats for a custom label

[Nillo, Ryan Michael R]

External Email - Use Caution

Hello Freesurfer developers,

I am using the code below to generate the stats table for the ROI.
mris_anatomical_stats -l 
/working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label
 -b subject rh white

However, when I run this command, I get this output:

limiting computations to label 
/working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label.
reading volume 
/working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/mri/wm.mgz...
reading input surface 
/working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.white...
reading input pial surface 
/working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.pial...
reading input white surface 
/working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.white...

table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name

I am getting no values for any of the metrics listed above. Is this a bug?

Thanks in advance,

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging

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[Freesurfer] Projecting a subcortical label to the surface

[Nillo, Ryan Michael R]

External Email - Use Caution

Hello FreeSurfer users,

I have a subcortical segmentation that I want to project to the nearest 
cortical vertex. Would I use the mri_vol2surf command to accomplish this, or do 
I need to convert the segmentation into a label, then project the label to the 
fsaverage cortical surface?

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging

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[Freesurfer] mri_vol2surf error

[Nillo, Ryan Michael R]

External Email - Use Caution

Hello FS users,

I am having a problem with mri_vol2surf. I want to project subcortical voxels 
onto the cortical surface. I found out that I can do this with the mri_vol2surf 
command. I am following the example given on the documentation, but I am 
getting this error: mri_vol2surf: could not read surface 
/working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc//surf/lh.white. I am 
trying to project to the surface of the fsaverage. Does this error mean that FS 
is unable to find the fsaverage surface?

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging

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[Freesurfer] Color scale is off

[Nillo, Ryan Michael R]

External Email - Use Caution

Hello FreeSurfer users,

I am using FreeSurfer version 6 with the latest dev version of freeview on a 
Linux machine. When I load a surface into freeview with a color scale, I notice 
the scale does not correlate with the values in the surface. The min and max 
values are always some small number (e.g. 3.0 x 10^-6). This happens even if I 
set the threshold in the command line. To fix it, I would need to configure the 
surface and click “apply”. In the past, the color scale would format itself 
correctly without me having to go through that configure step.

Example command line: freeview -f 
fsaverage/surf/ph.pial:overlay=lh.thickness.betas:overlay_threshold=0,0.05:overlay_method=linear
 -colorscale -ss lh.lateral.thickness.beta.tiff

Thanks in advance,

Ryan Nillo


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Re: [Freesurfer] Setting the origin in native space

[Nillo, Ryan Michael R]

External Email - Use Caution

Thanks for your help, Bruce. This worked like a charm! How would I register the 
output segmentation back to the subject's T1.mgz? When I use mri_convert, the 
ROIs have a weird border around them.


thanks again,

Ryan


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

Sent: Wednesday, December 19, 2018 11:43:03 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Setting the origin in native space

Hi Ryan

I think mri_convert -at   

should do the trick.

cheers
Bruce


On Wed, 19 Dec
2018, Nillo, Ryan Michael R wrote:

>External Email - Use Caution
>
> Hello FreeSurfer users,
>
> I want to use the suit software to segment the cerebellum, however the 
> software requires the origin be set at the anterior composure. I know the 
> Talairach image’s origin is set at the anterior commisure and that there is a 
> Talairach transformation in mri/transforms. Is there a way to use this 
> information to set the origin to the anterior commisure in the native space 
> image?
>
> Thanks in advance,
> Ryan Nillo
> Staff Research Associate
> UCSF Department of Radiology and Biomedical Imaging
>
>
> ___
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Freesurfer Info Page - Harvard 
University<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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To see the collection of prior postings to the list, visit the Freesurfer 
Archives.. A searchable archive which of messages PRIOR to March 2004 is at 
this site A searchable archive which includes messages AFTER March 2004 is at 
this site. Using Freesurfer



>
>
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[Freesurfer] Setting the origin in native space

[Nillo, Ryan Michael R]

External Email - Use Caution

Hello FreeSurfer users,

I want to use the suit software to segment the cerebellum, however the software 
requires the origin be set at the anterior composure. I know the Talairach 
image’s origin is set at the anterior commisure and that there is a Talairach 
transformation in mri/transforms. Is there a way to use this information to set 
the origin to the anterior commisure in the native space image?

Thanks in advance,
Ryan Nillo
Staff Research Associate
UCSF Department of Radiology and Biomedical Imaging


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[Freesurfer] Using the SUIT atlas

[Nillo, Ryan Michael R]

External Email - Use Caution

Hi FreeSurfer users,

I am using the SUIT atlas (http://www.diedrichsenlab.org/imaging/suit.htm) to 
parcellate the cerebellum.To ensure there are no problems with registration, 
the SUIT pipeline requires that the origin of the input images are centered at 
the anterior commissure. Does FreeSurfer have any tools to set this origin from 
the command line?

Thank you for your help,
Ryan Nillo 
Research Associate I
UCSF Department of Radiology and Biomedical Imaging

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[Freesurfer] Extracting values from a single vertex

[Nillo, Ryan Michael R]

External Email - Use Caution

Hi FreeSurfer users,


I want to extract thickness values at a single vertex. I searched on the 
support list and found an mris_convert command to use. However, the file I want 
to extract values from is a volume with multiple frames. When I try to use 
mris_convert on it, I only got the value at a vertex on the first frame. The 
goal is to set that vertex as a seed point and use the values as a regressor 
for glm. Is there a way to do this with FreeSurfer's commandline tools, or 
should I do this in Matlab?


Mahalo,


Ryan M Nillo

Staff Research Associate I

UCSF Department of Radiology and Biomedical Imaging
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Re: [Freesurfer] automating custom color map

[Nillo, Ryan Michael R]

External Email - Use Caution

Thank you so much, Ruopeng. Do you have an estimated timeline for when this 
option might be done?


Ryan


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

Sent: Thursday, November 1, 2018 7:18:34 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] automating custom color map

I think there is no option to set custom color code for overlay from 
command-line. I’ll add that option and let you know when it’s ready.

Best,
Ruopeng

On Nov 1, 2018, at 4:51 PM, Nillo, Ryan Michael R 
mailto:ryanmichael.ni...@ucsf.edu>> wrote:

External Email - Use Caution

Hi Freesurfer Users,

I used linear regression to map regional beta values on the fsaverage surface. 
I want to use a colormap that goes from blue to gray or gray to red (no cyan 
and yellow). I've been using a custom colormap shown in example.tiff. I've been 
making this by going into freeview and adjusting the parameters from the GUI. 
Is there a way to load this and create a snapshot from the command line? I know 
you can adjust certain parameters like overlay threshold and change the 
colormap, but I don't see an option for "custom". The end goal is to make 
multiple regression models and automate the screenshot process.

Best,

Ryan M Nillo
Staff Research Associate I
UCSF Department of Radiology and Biomedical Imaging
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[Freesurfer] Research Opportunity

[Nillo, Ryan Michael R]

External Email - Use Caution

UCSF, Dept. of Radiology & Biomedical Imaging is seeking a Postdoctoral Scholar 
for The Laboratory for Precision Neuroimaging


We are seeking a postdoctoral candidate with a strong background in genetics 
human imaging and a desire to use a multi-disciplinary approach to pursue 
neurodegenerative and neurodevelopment research. The candidate should have a 
strong statistical/computational background with experience with data analytic 
tools such as Matlab, R, and PLINK and potentially, MRI image analysis tools 
such as Freesurfer, FSL, and SPM. Applicants should have a Ph.D. or M.D. degree 
with less than five years of postdoctoral experience. Highly motivated 
individuals with a record of productive research are encouraged to apply. The 
position is available starting immediately.

Salary is commensurate with qualifications and experience.


Job Requirements:

1.CV/NIH biosketch (must contain previous research experience)

2.Cover Letter - Short statement on why you are interested in this position and 
how this position will help you achieve your career goals

3.Three references


If interested please contact Dr. Leo Sugrue at 
leo.sug...@ucsf.edu



Ryan M Nillo

Staff Research Associate I

UCSF Department of Radiology and Biomedical Imaging
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Re: [Freesurfer] hippocampal subfield segmentation

[Nillo, Ryan Michael R]

ad_aux (line 92)



Error in myMRIread (line 63)



Error in segmentSubjectT1_autoEstimateAlveusML (line 158)



MATLAB:badSwitchExpression

Started at Tue Aug 21 16:43:10 PDT 2018
Ended   at Tue Aug 21 16:43:39 PDT 2018
#@#%# recon-all-run-time-hours 0.008
recon-all -s sub_0006_T1_20160920_1723 finished without error at Tue Aug 21 
16:43:39 PDT 2018
done



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, 
Eugenio 
Sent: Tuesday, August 21, 2018 3:17:15 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfield segmentation


External Email - Use Caution

Hi Ryan,

Is it possible that you're mixing versions of FreeSurfer in your PATH and/or 
LD_LIBRARY_PATH? Maybe you could try unsetting them before you source 
FreeSurfer?

Cheers,

/Eugenio


Juan Eugenio Iglesias

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Nillo, Ryan Michael R 

Sent: Tuesday, August 21, 2018 9:58:25 PM
To: Freesurfer support list
Subject: [Freesurfer] hippocampal subfield segmentation


External Email - Use Caution

Hello FreeSurfer users,

I want to segment hippocampal subfields, but did not have much luck running it. 
I downloaded the matlab compiler runtime according to this: 
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime. Now, there is a 
directory called MCRv80 in my FREESURFER_HOME. The first error says 
kvlAutoCrop: command not found. However, $FREESURFER_HOME.bin is on my path. 
Does anything seem incorrect?

My path looks like this:
/data/sugrue2/rnillo/tools:/data/sugrue2/rnillo:/netopt/afni:/working/sdl_analysis/software/dcm2niix/build/bin:/netopt/rhel7/versions/cmtk/lib/cmtk/bin:/working/sdl_analysis/software/vtk-dicom/build/bin:/netopt/dicom/bin:/working/sdl_analysis/software/ANTs/antsbin/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/mni/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin:/netopt/share/bin/local/sdl/fix:/netopt/rhel7/fsl/bin:/working/sdl_analysis/software/git_pipeline/CommandLineProg:/netopt/share/local/bin/sdl/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/bin:/usr/local/sbin:/working/sdl_analysis/software/git_unwarp:/working/sdl_analysis/software/parallel:/working/sdl_analysis/software/git_tools:/working/sdl_analysis/software/anaconda3/bin:/bin:/sbin:/usr/bin::/netopt/rhel7/bin:/netopt/rhel7/bin/local:/netopt/share/bin:/netopt/share/bin/local:/netopt/bin:/netopt/bin/local:/netopt/dicom/bin:/netopt/rhel7/matlab/bin:/netopt/ctf/bin:/netopt/share/hosts::/netopt/caret/bin:/netopt/afni:/netopt/freesurfer/bin/Linux:/netopt/freesurfer/bin/noarch:/netopt/sybase/12.5.3/OCS-12_5/bin:/netopt/rhel7/fsl/bin:/netopt/sge_n1ge6/bin/lx24-amd64:/netopt/rhel7/tivoli/tsm/client/ba/bin::/netopt/share/bin/local/sdl:/netopt/bin/local/brain:/netopt/share/bin/local/brain:/netopt/bin/local/ncl:/netopt/share/bin/local/ncl:.
MatlabRuntime - Free Surfer 
Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime>
surfer.nmr.mgh.harvard.edu
Matlab Runtime. The brainstem and hippocampal subfield modules in FreeSurfer 
6.0 and the development version require the Matlab R2012b (v8.0) runtime (note 
that development versions from January 2018 onwards require the Matlab R2014b - 
v8.4 - runtime instead).




ERROR MESSAGE:

#
#@# Hippocampal Subfields processing (T1 only) left Tue Aug 21 13:45:25 PDT 2018
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/runtime/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/bin/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/os/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/working/sdl_analysis/software/freesurfer6/freesurfer/bin:
Warning: Unable to open display '10.48.0.125:0'.  You will not be able to 
display graphics on the screen.
Registering imageDump.mgz to hippocampal mask from ASEG
/working/sdl_analysis/software/freesurfer6/freesurfer/bin/kvlAutoCrop: line 3: 
kvlAutoCrop.bin: command not found
gzip: 
/data/sugrue2/MTS/sub_0006_T1_20160920_1723/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz.gz:
 No such file or directory
ERROR: problem reading fname
SWITCH expression must be a scalar or string constant.

Error in myMRIread>load_mgh (line 550)



Error in

[Freesurfer] hippocampal subfield segmentation

[Nillo, Ryan Michael R]

External Email - Use Caution

Hello FreeSurfer users,

I want to segment hippocampal subfields, but did not have much luck running it. 
I downloaded the matlab compiler runtime according to this: 
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime. Now, there is a 
directory called MCRv80 in my FREESURFER_HOME. The first error says 
kvlAutoCrop: command not found. However, $FREESURFER_HOME.bin is on my path. 
Does anything seem incorrect?

My path looks like this:
/data/sugrue2/rnillo/tools:/data/sugrue2/rnillo:/netopt/afni:/working/sdl_analysis/software/dcm2niix/build/bin:/netopt/rhel7/versions/cmtk/lib/cmtk/bin:/working/sdl_analysis/software/vtk-dicom/build/bin:/netopt/dicom/bin:/working/sdl_analysis/software/ANTs/antsbin/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/mni/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin:/netopt/share/bin/local/sdl/fix:/netopt/rhel7/fsl/bin:/working/sdl_analysis/software/git_pipeline/CommandLineProg:/netopt/share/local/bin/sdl/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/bin:/usr/local/sbin:/working/sdl_analysis/software/git_unwarp:/working/sdl_analysis/software/parallel:/working/sdl_analysis/software/git_tools:/working/sdl_analysis/software/anaconda3/bin:/bin:/sbin:/usr/bin::/netopt/rhel7/bin:/netopt/rhel7/bin/local:/netopt/share/bin:/netopt/share/bin/local:/netopt/bin:/netopt/bin/local:/netopt/dicom/bin:/netopt/rhel7/matlab/bin:/netopt/ctf/bin:/netopt/share/hosts::/netopt/caret/bin:/netopt/afni:/netopt/freesurfer/bin/Linux:/netopt/freesurfer/bin/noarch:/netopt/sybase/12.5.3/OCS-12_5/bin:/netopt/rhel7/fsl/bin:/netopt/sge_n1ge6/bin/lx24-amd64:/netopt/rhel7/tivoli/tsm/client/ba/bin::/netopt/share/bin/local/sdl:/netopt/bin/local/brain:/netopt/share/bin/local/brain:/netopt/bin/local/ncl:/netopt/share/bin/local/ncl:.
MatlabRuntime - Free Surfer 
Wiki
surfer.nmr.mgh.harvard.edu
Matlab Runtime. The brainstem and hippocampal subfield modules in FreeSurfer 
6.0 and the development version require the Matlab R2012b (v8.0) runtime (note 
that development versions from January 2018 onwards require the Matlab R2014b - 
v8.4 - runtime instead).




ERROR MESSAGE:

#
#@# Hippocampal Subfields processing (T1 only) left Tue Aug 21 13:45:25 PDT 2018
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/runtime/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/bin/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/os/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/working/sdl_analysis/software/freesurfer6/freesurfer/bin:
Warning: Unable to open display '10.48.0.125:0'.  You will not be able to 
display graphics on the screen.
Registering imageDump.mgz to hippocampal mask from ASEG
/working/sdl_analysis/software/freesurfer6/freesurfer/bin/kvlAutoCrop: line 3: 
kvlAutoCrop.bin: command not found
gzip: 
/data/sugrue2/MTS/sub_0006_T1_20160920_1723/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz.gz:
 No such file or directory
ERROR: problem reading fname
SWITCH expression must be a scalar or string constant.

Error in myMRIread>load_mgh (line 550)



Error in myMRIread>myMRIread_aux (line 92)



Error in myMRIread (line 63)



Error in segmentSubjectT1_autoEstimateAlveusML (line 158)



MATLAB:badSwitchExpression
#
#@# Hippocampal Subfields processing (T1 only) right Tue Aug 21 13:45:43 PDT 
2018
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/runtime/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/bin/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/os/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/working/sdl_analysis/software/freesurfer6/freesurfer/bin:
Warning: Unable to open display '10.48.0.125:0'.  You will not be able to 
display graphics on the screen.
Registering imageDump.mgz to hippocampal mask 

[Freesurfer] Thickness measurements.

[Nillo, Ryan Michael R]

External Email - Use Caution

Hello FreeSurfer experts,


I want to use FreeSurfer to generate thickness files using my own surfaces. Is 
there a way to use white and pial surfaces not generated from the 
mris_make_surfaces to create thickness files?


Mahalo,


Ryan M Nillo

Staff Research Associate I

UCSF Department of Radiology and Biomedical Imaging
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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.

[Freesurfer] Longitudinal Processing question

[Nillo, Ryan Michael R]

External Email - Use Caution

Hello FreeSurfer experts,

I have a few questions on the longitudinal processing stream. I am interested 
in studying longitudinal morphometry changes in a pediatric population. The age 
range of this population is between 4-20 years with age deltas between a few 
months to < 2 years. I want to know what are appropriate/acceptable age deltas 
used for longitudinal processing. I looked through the archives and one 
researcher asked about age deltas. One of the answers was that “if the time 
delta is relatively small, this has good chances to work”. What does 
“relatively small” mean? If the time points exit the longitudinal pipeline 
without errors and the surfaces look correct, does this mean the data is 
relevant?? When I correct for head size, should I use the eTIV values from the 
cross-sectional directories or the longitudinal directories?

Thanks in advance,

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging


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

[Freesurfer] mri_glmfit question

[Nillo, Ryan Michael R]

External Email - Use Caution

Hello FreeSurfer Users,


I want to run an ROI-based analysis on mri_glmfit as opposed to vertex-based. I 
know that if I run mri_glmfit with the --table flag and give it the output of 
asegstats2table or aparcstats2table, it will run the analysis on the ROIs and 
output tables showing significance. In each contrast directory that was created 
from mri_glmfit, I see there is a pcc.mgh. Is there any way to display this on 
the surface or put it into a table format?


Mahalo,


Ryan M Nillo

Staff Research Associate I

UCSF Department of Radiology and Biomedical Imaging
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found

[Nillo, Ryan Michael R]

External Email - Use Caution

Hello FreeSurfer users,

I am trying to run hippocampal subfield segmentation on our subjects on 
FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an 
error relatively early:

/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin//kvlAutoCrop: line 3: 
kvlAutoCrop.bin: command not found

When I looked into /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin, 
kvlAutoCrop.bin was located there, as expected. When I tried to run the step 
manually, it produced the correct output, but the next step gave me the similar 
error: command not found. I looked into 
/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin and saw all the other 
binaries were there, as well. The binaries are correctly exported on my PATH. I 
also made sure to download the Matlab compiler runtime and made sure they were 
on my PATH.

I am running freesurfer on a Linux machine with the RedHat 7.5 OS.Any help is 
greatly appreciated.

Thanks,
Ryan

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[Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found

[Nillo, Ryan Michael R]

External Email - Use Caution

Hello FreeSurfer users,

I am trying to run hippocampal subfield segmentation on our subjects on 
FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an 
error relatively early:

/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin//kvlAutoCrop: line 3: 
kvlAutoCrop.bin: command not found

When I looked into /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin, 
kvlAutoCrop.bin was located there, as expected. When I tried to run the step 
manually, it produced the correct output, but the next step gave me the similar 
error: command not found. I looked into 
/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin and saw all the other 
binaries were there, as well. The binaries are correctly exported on my PATH. I 
also made sure to download the Matlab compiler runtime and made sure they were 
on my PATH.

Any help is greatly appreciated.

Thanks,
Ryan



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[Freesurfer] localGI issues

[Nillo, Ryan Michael R]

Hello experts,


I am using FreeSurfer version 6 and am trying to run recon-all -localGI. Each 
time I run it, it fails on make_roi_paths. Below is an excerpt of the 
recon-all.log file. Any help is much appreciated.


#@# Local Gyrification Index lh Thu Nov  9 14:06:42 PST 2017

 mris_compute_lgi --i lh.pial

=
rm -Rf /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial
=
=
mkdir -p /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial
=
=
mris_fill -c -r 1 lh.pial 
/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=
reading surface from lh.pial...
writing filled volume to 
/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.
=
make_outer_surface('/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
 exit
=

< M A T L A B (R) >
  Copyright 1984-2015 The MathWorks, Inc.
   R2015b (8.6.0.267246) 64-bit (glnxa64)
  August 20, 2015


For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.


Academic License

>> reading filled volume...
closing volume...
morphological closing done.
writing outer surface...

=
mris_extract_main_component 
/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer 
/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main
=

counting number of connected components...
   76848 voxel in cpt #1: X=2 [v=76848,e=230538,f=153692] located at 
(-26.925182, 5.953999, 4.185574)
For the whole surface: X=2 [v=76848,e=230538,f=153692]
One single component has been found
nothing to do
done

=
mris_smooth -nw -n 30 
/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main
 ./lh.pial-outer-smoothed
=
smoothing for 30 iterations
smoothing surface tessellation for 30 iterations...
smoothing complete - recomputing first and second fundamental forms...
=
mris_euler_number ./lh.pial-outer-smoothed
=
euler # = v-e+f = 2g-2: 76848 - 230538 + 153692 = 2 --> 0 holes
  F =2V-4:  153692 = 153696-4 (0)
  2E=3F:461076 = 461076 (0)

total defect index = 0
=
mris_convert -n lh.pial-outer-smoothed 
/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc
=
=
find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_8510_.m');
 exit
=

< M A T L A B (R) >
  Copyright 1984-2015 The MathWorks, Inc.
   R2015b (8.6.0.267246) 64-bit (glnxa64)
  August 20, 2015


For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.


Academic License

>> FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.07 sec)

FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial-outer-smoothed
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.01 sec)


deltaT =

   10.1400


=
make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_8510_.m');
 exit
=

< M A T L A B (R) >
  Copyright 1984-2015 The MathWorks, Inc.
   R2015b (8.6.0.267246) 64-bit (glnxa64)
  August 20, 2015


For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.


Academic License

>> loading datas ...
FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.07 sec)

FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial-outer-smoothed
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.02 sec)

preparing outer mesh structure ...
face 5000 / 153692
face 1 / 153692
face 15000 / 153692
face 2 / 153692
face 25000 / 153692
face 3 / 153692
face 35000 / 153692
face 4 / 153692
face 45000 / 153692
face 5 / 153692
face 55000 / 153692
face 6 / 153692
face 65000 / 153692
face 7 / 153692
face 75000 / 

[Freesurfer] LGI error

[Nillo, Ryan Michael R]

Hello FS users,

I am using FreeSurfer version 5.3 to calculate local verification index and 
processing stopped at make_roi_paths. Here, I was given the error below. I 
searched in the archives and found a solution to the problem was to edit a few 
lines on SearchProjectionOnPial.m. The new script is included below the error. 
Any advice on how to fix this would be greatly appreciated.


Make_roi_paths error

=
make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/data/sugrue2/NF1_qdec/P0007/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_20907_.m');
 exit
=

< M A T L A B (R) >
  Copyright 1984-2015 The MathWorks, Inc.
   R2015b (8.6.0.267246) 64-bit (glnxa64)
  August 20, 2015


For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.


modified_matlab =

/working/sdl_analysis/software/freesufer_5.3_matlab


Academic License

>> loading datas ...
FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.07 sec)

FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial-outer-smoothed
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.02 sec)

preparing outer mesh structure ...
face 5000 / 132292
face 1 / 132292
face 15000 / 132292
face 2 / 132292
face 25000 / 132292
face 3 / 132292
face 35000 / 132292
face 4 / 132292
face 45000 / 132292
face 5 / 132292
face 55000 / 132292
face 6 / 132292
face 65000 / 132292
face 7 / 132292
face 75000 / 132292
face 8 / 132292
face 85000 / 132292
face 9 / 132292
face 95000 / 132292
face 10 / 132292
face 105000 / 132292
face 11 / 132292
face 115000 / 132292
face 12 / 132292
face 125000 / 132292
face 13 / 132292

mesh_outer =

 vertices: [66148x3 double]
faces: [132292x3 double]
facesOfVertex: [66148x1 struct]

preparing pial mesh structure ...
...searching for mesh edges...done (140.10 sec).
... creating path file for vertex 1 / 66148
area file for outer ROIs saved at 1
In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));

Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);


Error in reorganize_verticeslist (line 28)

[nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));

Error in make_roi_paths (line 93)
reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
verticeslist, step);

SearchProjectionOnPial.m Script
function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim, 
step)

% step is typically set between 5 and 10. Default is 7, increasing it will
% limit redundancies in the resulting path file.

verticeslist=[];
si=max(size(perim));
for t=1:step:si

[nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:));
verticeslist= [verticeslist nearestIndexMT];
end
verticeslist=unique(verticeslist);


Sincerely,
Ryan Nillo
UCSF Center for Radiology and Biomedical Imaging
Staff Research Associate




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[Freesurfer] -hemi flag

[Nillo, Ryan Michael R]

Hi FreeSurfer users,

I am using FreeSurfer v5.3 and have noticed that when -hemi is used as a flag 
in recon-all, the half I did not specify is not present in wm.mgz. The full 
command is recon-all -autorecon2 -autorecon3 -hemi (l or r)h -subjid 
subject_name -sd SUBJECTS_DIR. After running, white matter is missing in the 
half of wm.mgz not specified under the -hemi flag, but the surfaces and 
segmentation in aparc+aseg are unaffected. Is this a bug?

Ryan Michael Nillo
UCSF Center for Radiology and Biomedical Imaging
Staff Research Associate


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