[Freesurfer] Brodmann area parcellation

[sang ho shin]

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Dear Freesurfer Developers,

I am trying to get the seed mask of premotor and motor cortex. Because I
can't get it through 'recon-all -all', I tried to find brodmann area
('recon-all
-s subjid -ba-labels')

But I received ERROR message. Can you tell me how to get Brodmann area
through recon-all or freesurfer parcellation? And I appreciate if you can
help me to solve this error message as follows,

=

sinsanghoui-MBP:~ shinsangho$ export SUBJECTS_DIR=~/freesurfer_subjects

sinsanghoui-MBP:~ shinsangho$ echo $SUBJECTS_DIR

*sinsanghoui-MBP:~ shinsangho$ recon-all -s NOR82_PJI -i
~/DTI_analysis/nor82_pji_t1/coT1.nii -ba-labels*

Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

INFO: SUBJECTS_DIR is /Users/shinsangho/freesurfer_subjects

Actual FREESURFER_HOME /Applications/freesurfer

Darwin sinsanghoui-MBP 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 23
18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64

/Users/shinsangho/freesurfer_subjects/NOR82_PJI

\n mri_convert /Users/shinsangho/DTI_analysis/nor82_pji_t1/coT1.nii
/Users/shinsangho/freesurfer_subjects/NOR82_PJI/mri/orig/001.mgz \n

mri_convert.bin /Users/shinsangho/DTI_analysis/nor82_pji_t1/coT1.nii
/Users/shinsangho/freesurfer_subjects/NOR82_PJI/mri/orig/001.mgz

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from /Users/shinsangho/DTI_analysis/nor82_pji_t1/coT1.nii...

TR=1670.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (0.000121244, -1, 0)

j_ras = (-0.0235518, -2.85817e-06, 0.999723)

k_ras = (0.999723, 0.000121211, 0.0235518)

writing to
/Users/shinsangho/freesurfer_subjects/NOR82_PJI/mri/orig/001.mgz...

/Users/shinsangho/freesurfer_subjects/NOR82_PJI/label

#

#@# BA_exvivo Labels lh Fri Oct  4 17:43:23 BST 2019

\n mri_label2label --srcsubject fsaverage --srclabel
/Users/shinsangho/freesurfer_subjects/fsaverage/label/lh.BA1_exvivo.label
--trgsubject NOR82_PJI --trglabel ./lh.BA1_exvivo.label --hemi lh
--regmethod surface \n



srclabel =
/Users/shinsangho/freesurfer_subjects/fsaverage/label/lh.BA1_exvivo.label

srcsubject = fsaverage

trgsubject = NOR82_PJI

trglabel = ./lh.BA1_exvivo.label

regmethod = surface



srchemi = lh

trghemi = lh

trgsurface = white

srcsurfreg = sphere.reg

trgsurfreg = sphere.reg

usehash = 1

Use ProjAbs  = 0, 0

Use ProjFrac = 0, 0

DoPaint 0



SUBJECTS_DIR/Users/shinsangho/freesurfer_subjects

FREESURFER_HOME /Applications/freesurfer

Loading source label.

Found 4129 points in source label.

MRISread(/Users/shinsangho/freesurfer_subjects/NOR82_PJI/surf/lh.white):
could not open file

Starting surface-based mapping

Reading source registration

 /Users/shinsangho/freesurfer_subjects/fsaverage/surf/lh.sphere.reg

Rescaling ...  original radius = 100

Reading target surface

* /Users/shinsangho/freesurfer_subjects/NOR82_PJI/surf/lh.white*

*No such file or directory*

*ERROR: could not read
/Users/shinsangho/freesurfer_subjects/NOR82_PJI/surf/lh.white*

Darwin sinsanghoui-MBP 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 23
18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64



recon-all -s NOR82_PJI exited with ERRORS at Fri Oct  4 17:43:25 BST 2019



For more details, see the log file
/Users/shinsangho/freesurfer_subjects/NOR82_PJI/scripts/recon-all.log

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

==



Best wishes,

Sangho


ᐧ
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Re: [Freesurfer] question about aparcstats2table

[Kiyotaka Nemoto]

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Hi,

I use the attached script to utilize aparcstats2table.
This will generate surface, thickness, thickness_SD, and volume csv files.
Hope this helps.

Kiyotaka


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>
> Hi FreeSurfer experts,
> I want to converts a cortical stats file into a table by the
> aparcstats2table command. However, there are totally 500  subjects. And it
> is really hard to input subject numbers one by one. The Numbers are
> arranged in a regular way.
> So, can you give me some advices?
> Thanks a lot.
> Cheers,
> Chen
>
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-- 
Kiyotaka Nemoto, M.D., Ph.D.
Associate Professor
Department of Psychiatry
Division of Clinical Medicine, Faculty of Medicine
University of Tsukuba
1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan
E-mail: kiyot...@nemotos.net


fs_stats_aparc.sh
Description: application/shellscript
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[Freesurfer] Vertex by Vertex Analysis

[WON JONG CHWA]

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Hello,

I would like to perform a group difference analysis with gray-white matter
contrast between healthy controls and patients, covarying for the cortical
thickness at each vertex throughout the entire brain surface. How would we
go about doing this?

Thank you.
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Re: [Freesurfer] Segmentation faule recon-all

[Greve, Douglas N.,Ph.D.]

Did you check the talairach transform? See 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview

On 10/4/2019 1:37 PM, Backhausen, Lea wrote:

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Dear FreeSurfer experts,

when running the recon -all –all command (I included the -3T flag) with 
FreeSurfer Version 6.0.0  I get this error for one of my subjects:


MRInormalize: could not find any valid peaks.

Make sure the Talairach alignment is correct!

I added the recon-all log to this email.
Is there a way to fix this? Thank you for any suggestion!

Best,
Lea Backhausen



Lea Backhausen
PhD Student / Psychologist  (M.Sc.)

Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und –psychotherapie

Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden

Fetscherstraße 74, 01307 Dresden
http://www.uniklinikum-dresden.de







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Re: [Freesurfer] ERROR gtmseg

[Greve, Douglas N.,Ph.D.]

That is kind of weird. It says it has found a segmentation with number 229, but 
we don't have that code in our system. Can you find the 229 voxels in the 
aparc+aseg.mgz?

On 10/4/2019 6:28 PM, Marina Fernández wrote:

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Dear experts,

The following error occurs with one subject when I am running gtmseg command:

Computing colortable
ERROR: cannot find match for subcortical segid 229
ERROR: mri_gtmseg -s qsm_04_year3 --usf 2 --o gtmseg.mgz --apas apas+head.mgz 
--no-subseg-wm --no-keep-cc --no-keep-hypo
gtmseg existed with errors
ans=1

Do you know what happened with this subject? What can I do to solve it?

Thank you very much in advance.
Marina.



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Re: [Freesurfer] Question on Z-scoring

[Greve, Douglas N.,Ph.D.]

That looks correct to me

On 10/4/2019 5:39 PM, Nillo, Ryan Michael R wrote:
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] ERROR gtmseg

[Marina Fernández]

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Dear experts,

The following error occurs with one subject when I am running gtmseg
command:

*Computing colortable*
*ERROR: cannot find match for subcortical segid 229*
*ERROR: mri_gtmseg -s qsm_04_year3 --usf 2 --o gtmseg.mgz --apas
apas+head.mgz --no-subseg-wm --no-keep-cc --no-keep-hypo*
*gtmseg existed with errors*
*ans=1*

Do you know what happened with this subject? What can I do to solve it?

Thank you very much in advance.
Marina.
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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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Re: [Freesurfer] Tracula

[Yendiki, Anastasia]

Hi Juan - You can see usage info for dt_recon if you run it without arguments:
USAGE: dt_recon

 Required Aruments:
   --i invol
   --b bvals bvecs
   --s subjectid
   --o outputdir
...

So --b takes both bvals and bvecs one after the other, and --s is the subject 
name as found under $SUBJECTS_DIR.

Best,
a.y

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

Sent: Friday, October 4, 2019 4:13 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Tracula


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Hi, I am trying to make the recon with diffusion images for running tracula. I 
gave this command:

set cmd = dt_recon


set cmd = ($cmd --b 
$SUBJECTS_DIR/esq-15-hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing/31190669_bvals

set cmd = ($cmd --b $SUBJECTS_DIR/esq-15 
hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing/31190669_bvecs)

set cmd = ($cmd --i 
$SUBJECTS_DIR/esq-15-hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing/esq-15-hc_dwi.nii.gz)

set cmd = ($cmd --s $SUBJECTS_DIR/esq-15-hc/)

set cmd = ($cmd --o 
$SUBJECTS_DIR/esq-15-hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing)

echo $cmd

$cmd

But ir marks two kinds of error: can´t fin bvals.dat or Eddy/Motion correct and 
stops.

Could yo help me?

Thanks,

JC.
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[Freesurfer] Tracula

[Juan Rivas]

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Hi, I am trying to make the recon with diffusion images for running
tracula. I gave this command:

set cmd = dt_recon

set cmd = ($cmd --b
$SUBJECTS_DIR/esq-15-hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing/31190669_bvals


set cmd = ($cmd --b $SUBJECTS_DIR/esq-15
hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing/31190669_bvecs)

set cmd = ($cmd --i
$SUBJECTS_DIR/esq-15-hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing/esq-15-hc_dwi.nii.gz)

set cmd = ($cmd --s $SUBJECTS_DIR/esq-15-hc/)

set cmd = ($cmd --o
$SUBJECTS_DIR/esq-15-hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing)

echo $cmd

$cmd

But ir marks two kinds of error: can´t fin bvals.dat or Eddy/Motion correct
and stops.

Could yo help me?

Thanks,

JC.
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Re: [Freesurfer] Curvature estimation from Hessian

[LOSKE, PHILIPP (PGR)]

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Hi Bruce,

thank you for your explanation. I think I might have an idea, why the Hessian 
matrix works in this case, maybe you can confirm or correct me if I'm wrong. 
Usually, if you're having a 2d surface in space, the principle curvatures are 
the eigenvalues of the shape operator (which needs calculation of first and 
second fundamental form), not the Hessian. Only in the particular case of a 
vanishing gradient, the eigenvalues are the same as those of the Hessian. F.e. 
for a quadratic function, the gradient vanishes at the minimum (in 1d first 
derivative is zero). Since you're modelling a quadratic function in a local 
neighborhood around each vertex, its minimum lies at the vertex, is that 
correct? if this is so, then the gradient should vanish and Hessian matrix 
should be fine and my confusion is resolved :). In the literature I found just 
vague explanations, sometimes mentioning the shape operator, sometimes the 
Hessian. I just want to make sure I understand this process correctly.

Cheers
Philipp


Date: Thu, 3 Oct 2019 10:03:52 -0400 (EDT)


Hi Philipp

the Hessian is estimated at each vertex by doing a quadratic fit to the
local surface as the height function over the tangent plane of all the
vertices in a 2-neighborhood of that vertex. I'm not sure what the gradient
vanishing is about, but the curvatures are just the eigenvalues of the
Hessian, so I don't think the gradient has anything to do with it. Not that
we also have some discrete tools for computing curvature

make sense?
cheers
Bruce
On Thu, 3 Oct 2019, LOSKE, PHILIPP
(PGR) wrote:

>
> External Email - Use Caution
>
> Hi,
>
> I am trying to understand how exactly FreeSurfer estimates the curvature
> values from the white surface. From the mailing lists I understood that the
> white surface is modeled by fitting a second-order polynomial function and
> curvatures are estimated from the Hessian matrix at each vertex (thank you
> Bruce). However, I still have trouble to understand how this works in
> detail. First, as I understand it, curvature can only be derived from the
> Hessian if the gradient vanishes (why is this the case?), and from
> differential geometry, shouldn't instead the shape operator be calculated at
> each vertex on the surface? Second, are the Gaussian and mean curvatures
> then directly calculated from?Hessian/Shape operator or first principle
> curvatures (and are they saved somewhere?). I tried to find a detailed
> explanation in some of the FreeSurfer papers, but couldn't find anything
> really.
>
> Thank you very much in advance!
>
> Cheers
> Philipp



The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. 
SC013683.
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Re: [Freesurfer] Exporting ROI segmentation in T1 DICOM header

[Correia de Aguiar, V.M.]

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Dear both,

many thanks for your replies. I will try both options and see what happens.

Best,
Vânia de Aguiar, PhD
Assistant Professor in Neurolinguistics
University of Groningen
Faculty of Arts

Oude Kijk in 't Jatstraat 26
Room 1315.0408
9712 EK, Groningen
The Netherlands


On Thu, Oct 3, 2019 at 5:49 PM Paul Wighton  wrote:

> External Email - Use Caution
>
> Hi Vânia,
>
> You can use this repository to convert some FreeSurfer outputs to dicom.
> https://github.com/corticometrics/fs2dicom
>
> Unfortunately, the aparc+aseg is not supported at this time, only the
> aseg.mgz.
>
> -Paul
>
> On Thu, Oct 3, 2019 at 9:57 AM Bruce Fischl 
> wrote:
>
>> Hi Vânia
>>
>> you can convert the aparc+aseg.mgz to nifti and find something that goes
>> from there to dicom, but we don't at the moment support writing dicom,
>> although I think Paul (ccd) has worked on it and might have something to
>> add
>>
>> cheers
>> Bruce
>>
>>
>> On Thu, 3 Oct 2019, Correia
>> de Aguiar, V.M. wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > Dear Freesurfer developers,
>> >
>> > Is it possible to export the ROI segmentations that are stored
>> > in ?h.aparc.a2009s.annot or ?h.aparc.annot files into the header of the
>> > DICOM file? I would like to open those files with corresponding
>> > segmentations in RayStation.
>> >
>> > Many thanks for your time.
>> > Regards,
>> >
>> > Vânia de Aguiar, PhD
>> > Assistant Professor in Neurolinguistics
>> > University of Groningen
>> > Faculty of Arts
>> >
>> > Oude Kijk in 't Jatstraat 26
>> > Room 1315.0408
>> > 9712 EK, Groningen
>> > The Netherlands
>> >
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[Freesurfer] Label created in the symmetric space

[Jose Graterol]

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Dear Freesurfer Experts,

I would appreciate your help. I will explain first what I have done and
where my problem is.

I want to measure the cortical thickness in stroke patients. Therefore I
followed Douglas' instructions provided in this link
to
join both affected hemispheres (left or right, depending on the patient)
and to analyze them with xhemi.

After mri_glmfit and mri_glmfit-sim (--cwpvalthresh 0,05 --cache 4 abs/neg)
have run I obtained 2 significant clusters. One in the precentral area,
which I am interested in. When I check the *abs/neg.y.ocn.dat file the
values are all -0.. If I understood it correctly, those should be
cortical thickness values in mm, making those values implausible. For that
reason I made a label of that cluster using the autofill option from
tksurfer. The idea was to obtain the mean cortical thickness using
mris_anatomical_stats after mapping the label to the subjects.

Now my questions, what would be the best method to map the label created
from the fsaverage_sym space to the subject space? Or just simply, is this
the right way to do this? or should I check why I am obtaining those values
in the *y.ocn.dat file?

Thanks in advance.

Kind Regards

José Graterol
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