Re: [Freesurfer] Question about OptSeq

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

No, there  is not. optseq assumes you will be doing an FIR analysis (=finite 
impulse response = not assuming a shape to the hemodynamic response). In this 
analysis, this must be the relationship. If you assume a shape, then this 
relationship is not necessary. In your case, you can set the dPSD=1.

On 7/1/2019 7:19 AM, Davide Nardo wrote:

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Dear Prof Greve,

I hope you don’t mind if I ask you a question about OptSeq.

It looks like a constraint in using OptSeq is that any event duration must be 
an integer multiple of the dPSD, which in turn needs to be an integer multiple 
of the TR, and seemingly there is no exception to this rule.

I am in a situation in which my TR = 2 sec, and my event duration = 3 sec, 
therefore I get an error message when running OptSeq.

However, I am puzzled by this, as in my experience with fMRI an event duration 
does not necessarily need to be a multiple of the TR…

Is there any way I can circumvent this requirement in OptSeq?

Best.

Davide Nardo

--
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MRC Cognition and Brain Sciences Unit
University of Cambridge
15 Chaucer Road
Cambridge, CB2 7EF
davide.na...@mrc-cbu.cam.ac.uk


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

[Bruce Fischl]

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

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

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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[Freesurfer] Error opening Freeview

[Zeng,Victor (BIDMC - Psychiatry)]

?Hi all,


I'm having issues opening Freeview (The most recent version): it loads .mgz and 
labels correctly, but then after 5 seconds it shuts off, giving off this error:



qt_xcb_createCursorXRender: query_pict_formats failed
[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named beta by nick Mon Jul  1 
16:25:24 2019
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault

?
I was wondering if there's anything I can do to debug, or whether it's just a 
lack of computer capacity on our end.

Best,


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
ph: 617 754 1237
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Re: [Freesurfer] mri_gtmpvc -- Failed tissue type check

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

Hi Cristina, can you send more info? Eg, your command line and terminal output. 
Do you do anything special (eg, your own annotation)?

On 7/1/2019 5:57 PM, Lois Gomez, Cristina wrote:
Hi Freesurfers,

I am having trouble with one subject's PVC (we process many cases and never had 
this issue before).
When running mri_gtmpvc I get a 'Failed tissue type check' error.

I've seen that other people have reported similar errors in the past, but I 
haven't found any advice on how to trouble-shoot this.
We have longitudinal PET data with two tracers for this subject, so it is very 
important for us to get this fixed. Any advice?

Thank you,
Cristina



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

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

That is the problem. It is not a cortical surface (ie, white or pial); isn't 
this LGI surface just a surface shrink wrapped around cortex? Not sure how to 
map that across subject.

On 7/1/2019 2:53 PM, Nillo, Ryan Michael R wrote:
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. 
mailto:dgr...@mgh.harvard.edu>> 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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Re: [Freesurfer] Surfaces with different numbers of vertices. {Disarmed}

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

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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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  > 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] Citing the development version for use of hippocampal/amygdala sub-field segmentation

[Daniel Callow]

External Email - Use Caution

Hello,

I used the longitudinal HippocampalSubfieldsAndNucleiOfAmygdala

pipeline to create subject-specific hippocampal ROI's for a paper I am
preparing for submission. I would like to know what the best way to cite
this technique is.

This is what I currently have in my methods section.

Subjects T1-weighted anatomical images were processed with the FreeSurfer
image analysis suite (http://surfer.nmr.mgh.harvard.edu/, version 6.0)
and
Automated hippocampal subfield segmentation was performed for each subjects
T1 weighted image using the Freesurfer longitudinal hippocampal subfield
segmentation program(Iglesias et al., 2015, 2016).

Do I need to cite my use of the development version? And if so how is the
best way to go about doing this?

Best,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
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Re: [Freesurfer] Surfaces with different numbers of vertices.

[Bruce Fischl]

can you send the entire output?
On Mon, 1 Jul 2019, 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  
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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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 >> > 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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Re: [Freesurfer] Error opening Freeview

[Ruopeng Wang]

Hi Victor,


Would it be possible to send me the data files and the freeview command 
you ran? You can upload them from here:



https://gate.nmr.mgh.harvard.edu/filedrop2/


Thanks,

Ruopeng


On 7/1/19 4:29 PM, Zeng,Victor (BIDMC - Psychiatry) wrote:


​Hi all,


I'm having issues opening Freeview (The most recent version): it loads 
.mgz and labels correctly, but then after 5 seconds it shuts off, 
giving off this error:




qt_xcb_createCursorXRender: query_pict_formats failed
[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
probably memory access out of range

[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC 
ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple 
to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, 
and run

[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 


[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 
17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124

[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named beta by nick Mon Jul 
 1 16:25:24 2019
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt

[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 
--with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 
COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory 
unknown file

[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault

​
I was wondering if there's anything I can do to debug, or whether it's 
just a lack of computer capacity on our end.


Best,


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
ph: 617 754 1237
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[Freesurfer] mri_gtmpvc -- Failed tissue type check

[Lois Gomez, Cristina]

Hi Freesurfers,

I am having trouble with one subject's PVC (we process many cases and never had 
this issue before).
When running mri_gtmpvc I get a 'Failed tissue type check' error.

I've seen that other people have reported similar errors in the past, but I 
haven't found any advice on how to trouble-shoot this.
We have longitudinal PET data with two tracers for this subject, so it is very 
important for us to get this fixed. Any advice?

Thank you,
Cristina
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[Freesurfer] LME - Monte Carlo

[tom parker]

External Email - Use Caution

Dear FreeSurfers,

I was reading the wiki documents about how to run LME analyses in
FreeSurfer.
I found that one of the disadvantages is that, at the moment, it only
allows FDR corrections to be applied for multiple comparisons.

I have 2 patient groups that show cortical thinning compared to controls at
baseline when I correct with Monte Carlo but nothing survives with FDR.
Now, I would like to see if these cortical thinning patterns change over
time so I thought I should keep things consistent and use Monte Carlo for
the longitudinal analysis as well.

Is there any way of using Monte Carlo for LME? I read some suggestions in
emails that were sent 2 years ago but I was wondering if there are any
updates or if there is a guide with recommended steps?

Thank you so much!
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