El sáb., 5 oct. 2019 a las 12:00, <freesurfer-request@nmr.mgh.harvard.edu> escribió:

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Today's Topics:

1. Re: Curvature estimation from Hessian (LOSKE, PHILIPP (PGR))
2. Segmentation faule recon-all (Backhausen, Lea)
3. Tracula (Juan Rivas)
4. Re: Tracula (Yendiki, Anastasia)
5. Question on Z-scoring (Nillo, Ryan Michael R)
6. ERROR gtmseg (Marina Fern?ndez)
7. Re: Question on Z-scoring (Greve, Douglas N.,Ph.D.)
8. Re: ERROR gtmseg (Greve, Douglas N.,Ph.D.)
9. Re: Segmentation faule recon-all (Greve, Douglas N.,Ph.D.)
10. Vertex by Vertex Analysis (WON JONG CHWA)
11. Re: question about aparcstats2table (Kiyotaka Nemoto)
12. Brodmann area parcellation (sang ho shin)
13. Errors running TRACULA (data attached) - valid frame numbers
(Mazzetti, C. (Cecilia))
14. Confidence interval for Cohen's d from gamma/rstd
(Caspar M. Schwiedrzik)
15. Re: Errors running TRACULA (data attached) - valid frame
numbers (Yendiki, Anastasia)

----------------------------------------------------------------------

Message: 1
Date: Fri, 4 Oct 2019 16:27:51 +0000
From: "LOSKE, PHILIPP (PGR)" <p.loske.18@abdn.ac.uk>
Subject: Re: [Freesurfer] Curvature estimation from Hessian
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<AM0PR0402MB36506BB2F6A775BE1ACFC1F9E89E0@AM0PR0402MB3650.eurprd04.prod.outlook.com>

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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 cl?raichte ann an Alba, ?ir. SC013683.
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Message: 2
Date: Fri, 4 Oct 2019 17:37:06 +0000
From: "Backhausen, Lea" <Lea.Backhausen@uniklinikum-dresden.de>
Subject: [Freesurfer] Segmentation faule recon-all
To: "'freesurfer@nmr.mgh.harvard.edu'"
<freesurfer@nmr.mgh.harvard.edu>
Message-ID: <b5def0d7eb7f4d06a5b5bb30c28ac4c4@uniklinikum-dresden.de>
Content-Type: text/plain; charset="iso-8859-1"

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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 f?r Kinder- und Jugendpsychiatrie und -psychotherapie

Universit?tsklinikum Carl Gustav Carus
an der Technischen Universit?t Dresden

Fetscherstra?e 74, 01307 Dresden
http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/>

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Message: 3
Date: Fri, 4 Oct 2019 16:13:43 -0400
From: Juan Rivas <jcrn12@gmail.com>
Subject: [Freesurfer] Tracula
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CACYE61DUbhCoPJLDB+HvQdHwpR9UVht6XXeebOa1ZxhndeOcLw@mail.gmail.com>
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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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Message: 4
Date: Fri, 4 Oct 2019 20:30:56 +0000
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BL0PR04MB4833E6489983F5FE9D6C01AA8A9E0@BL0PR04MB4833.namprd04.prod.outlook.com>

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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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Juan Rivas <jcrn12@gmail.com>
Sent: Friday, October 4, 2019 4:13 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Tracula

External Email - Use Caution

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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Message: 5
Date: Fri, 4 Oct 2019 21:39:37 +0000
From: "Nillo, Ryan Michael R" <RyanMichael.Nillo@ucsf.edu>
Subject: [Freesurfer] Question on Z-scoring
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <ED766936-2A59-4361-8BA2-5B59A4AD18FF@ucsf.edu>
Content-Type: text/plain; charset="utf-8"

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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Message: 6
Date: Sat, 5 Oct 2019 00:28:40 +0200
From: Marina Fern?ndez <marina.fdez.alvarez@gmail.com>
Subject: [Freesurfer] ERROR gtmseg
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAALjZmfhoo2kK=Bo0YJpSrdRmaYaO1RYgg83rNSqL6w84Yz2CA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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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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Message: 7
Date: Fri, 4 Oct 2019 22:31:11 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] Question on Z-scoring
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <df908adc-8792-d058-706b-338e456110aa@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

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

External Email - Use Caution

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Message: 8
Date: Fri, 4 Oct 2019 22:32:56 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] ERROR gtmseg
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <7aa65757-83cb-f53c-b2f3-35ba69ab11b8@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

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 Fern?ndez wrote:

External Email - Use Caution

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.

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Message: 9
Date: Fri, 4 Oct 2019 22:39:06 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] Segmentation faule recon-all
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <8f822bb5-c5c1-c420-f79f-2d4e6729ec68@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

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:

External Email - Use Caution
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 f?r Kinder- und Jugendpsychiatrie und ?psychotherapie

Universit?tsklinikum Carl Gustav Carus
an der Technischen Universit?t Dresden

Fetscherstra?e 74, 01307 Dresden
http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/>

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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Message: 10
Date: Fri, 4 Oct 2019 15:44:23 -0700
From: WON JONG CHWA <williamchwa@ucla.edu>
Subject: [Freesurfer] Vertex by Vertex Analysis
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CACj1kb=0wXV81-bzK3qPiccBzSDoA7P36m-QyHo9VfMf_HfkEw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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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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Message: 11
Date: Sat, 5 Oct 2019 12:13:35 +0900
From: Kiyotaka Nemoto <kiyotaka@nemotos.net>
Subject: Re: [Freesurfer] question about aparcstats2table
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAHvOE4FBh3YQJWhWR1QTHPsg5NyfWbmTYAW86gVTYw1uc_=Xnw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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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

External Email - Use Caution
>
> 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
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
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: kiyotaka@nemotos.net
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Message: 12
Date: Sat, 5 Oct 2019 06:31:45 +0100
From: sang ho shin <happysaram20@gmail.com>
Subject: [Freesurfer] Brodmann area parcellation
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CANnEPJL1HKMTLD+jA3LwkNT6t5uYaHyTAovB==H12LTmbpQREQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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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

?
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Message: 13
Date: Sat, 5 Oct 2019 07:23:23 +0000
From: "Mazzetti, C. (Cecilia)" <C.Mazzetti@donders.ru.nl>
Subject: [Freesurfer] Errors running TRACULA (data attached) - valid
frame numbers
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <1570260203487.17811@donders.ru.nl>
Content-Type: text/plain; charset="iso-8859-1"

External Email - Use Caution

Dear members,

I've tried troubleshooting but can't wrap my head around this. Trying to run TRACULA after recon-all the subjects, but I keep getting:

################

[...]

R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
(a bunch of these)

TR=3670.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.989717, -0.110817, -0.0904434)
j_ras = (-0.128995, 0.964706, 0.22957)
k_ras = (-0.0618111, -0.238876, 0.969081)

keeping frames 0 1 12 23 34 45 56 67 78 89 100
ERROR: valid frame numbers are between 0 and 0

trac-preproc exited with ERRORS
#####

I checked the # of bvals and bvecs in the dorm folder compared to orig ones, same.

I don't know what's wrong

below config file:

set subjlist = ( subject02_C )
set dcmlist = ( /myfolder/freesurfer/subject02_C/dmri/data.nii.gz )

set bveclist = ( /myfolder/freesurfer/subject02_C/dmri/bvecs )
set bvallist = ( /myfolder/freesurfer/subject02_C/dmri/bvals )

set doeddy = 1
set dorotbvecs = 1
set usemaskanat = 1
set thrbet = 0.3
set doregflt = 0
set doregbbr = 1
?set doregmni = 1
set doregcvs = 0

set pathlist = ( lh.cst_AS rh.cst_AS \
lh.ilf_AS rh.ilf_AS \
lh.unc_AS rh.unc_AS \
fmajor_PP fminor_PP \
lh.atr_PP rh.atr_PP \
lh.cab_PP rh.cab_PP \
lh.ccg_PP rh.ccg_PP \
lh.slfp_PP rh.slfp_PP \
lh.slft_PP rh.slft_PP )

set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)

Please any sort of input/help is super appreciated.

Let me know if I can give more information

Cheers,

Cecilia

?

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------------------------------

Message: 14
Date: Sat, 5 Oct 2019 16:43:53 +0200
From: "Caspar M. Schwiedrzik" <cschwiedrz@mail.rockefeller.edu>
Subject: [Freesurfer] Confidence interval for Cohen's d from
gamma/rstd
To: "Freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CA+bX-38E-qLV47fWjYdJyqwLdUF8f_HTWxvW+U=ZJj2-PpZNNA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Hi!
I have an OSGM from a fixed effects group analysis with mri_glmfit. I would
like to calculate the effect size and the 95% confidence intervals. I see
from various threads on the mailing list that Cohen's d can easily be
obtained from the outputs of mri_glmfit by dividing gamma by rstd.

I am wondering now how to compute the 95% CIs for Cohen's d from the
outputs of mri_glmfit?

Thank you very much!
Caspar
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------------------------------

Message: 15
Date: Sat, 5 Oct 2019 15:03:47 +0000
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] Errors running TRACULA (data attached) -
valid frame numbers
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BL0PR04MB483384C04DB2A55C0451616C8A990@BL0PR04MB4833.namprd04.prod.outlook.com>

Content-Type: text/plain; charset="utf-8"

Hi Cecilia - Does the number of entries in the bvals and bvecs files match the number of volumes in data.nii.gz?

a.y
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mazzetti, C. (Cecilia) <C.Mazzetti@donders.ru.nl>
Sent: Saturday, October 5, 2019 3:23:23 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Errors running TRACULA (data attached) - valid frame numbers

External Email - Use Caution

Dear members,

I've tried troubleshooting but can't wrap my head around this. Trying to run TRACULA after recon-all the subjects, but I keep getting:

################

[...]

R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
(a bunch of these)

TR=3670.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.989717, -0.110817, -0.0904434)
j_ras = (-0.128995, 0.964706, 0.22957)
k_ras = (-0.0618111, -0.238876, 0.969081)

keeping frames 0 1 12 23 34 45 56 67 78 89 100
ERROR: valid frame numbers are between 0 and 0

trac-preproc exited with ERRORS
#####

I checked the # of bvals and bvecs in the dorm folder compared to orig ones, same.

I don't know what's wrong

below config file:

set subjlist = ( subject02_C )
set dcmlist = ( /myfolder/freesurfer/subject02_C/dmri/data.nii.gz )

set bveclist = ( /myfolder/freesurfer/subject02_C/dmri/bvecs )
set bvallist = ( /myfolder/freesurfer/subject02_C/dmri/bvals )

set doeddy = 1
set dorotbvecs = 1
set usemaskanat = 1
set thrbet = 0.3
set doregflt = 0
set doregbbr = 1
?set doregmni = 1
set doregcvs = 0

set pathlist = ( lh.cst_AS rh.cst_AS \
lh.ilf_AS rh.ilf_AS \
lh.unc_AS rh.unc_AS \
fmajor_PP fminor_PP \
lh.atr_PP rh.atr_PP \
lh.cab_PP rh.cab_PP \
lh.ccg_PP rh.ccg_PP \
lh.slfp_PP rh.slfp_PP \
lh.slft_PP rh.slft_PP )

set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)

Please any sort of input/help is super appreciated.

Let me know if I can give more information

Cheers,

Cecilia

?

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------------------------------

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End of Freesurfer Digest, Vol 188, Issue 7
******************************************