[Freesurfer] Mixed Block Event-related Design Optseq Question

[Yu Han]

External Email - Use Caution

Hello Experts,
I am wondering if any of you are aware of any commands of optseq for a mixed 
design? We are specifically not sure how to specify block duration. It seems 
like optseq is designed for event related design according to the help page, 
but I checked some community blogs and it looks like there should be some 
commands for mixed block event related design.
There are four blocks of 6 images each.
1) Surprise/Embarrassment faces
2) Happy/Sad faces
3) Identify gender of faces
4) Match shapes

We planned to have the Match shapes blocks to interleave all other blocks. 
Thank you in advance!

Best,
Yu
optseq2 --ntp 160 --tr 2 --psdwin 0 20 2 --ev disgustingPic 2 20 --ev 
attractivePic 2 15 --ev neutalPic 2 30 --evc 1 -1 0 --nkeep 3 --o IAPS 
--tnullmin 2 --tnullmax 8 --nsearch 1000

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Re: [Freesurfer] Ex vivo segmentations

[Fotiadis, Panagiotis]

Cool. Thanks again!


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869

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

Sent: Monday, July 30, 2018 4:29:35 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Ex vivo segmentations

as I said, I don't think I would trust the ex vivo thicknesses. Definitely
not in an absolute sense
On Mon, 30 Jul 2018,
Fotiadis, Panagiotis wrote:

>
> Hi Bruce,
>
>
> Thanks, that is actually really helpful.
>
> Also, I realized I misspoke earlier when I was talking about the cortical 
> thickness range. The
> 3.7-3.9 mm range that I mentioned was referring to global cortical thickness 
> across (not within) the
> different brains I have processed. The range of cortical thickness within 
> individual brains was
> indeed wider ( between 2 - 5mm). I was just curious about why the average 
> cortical thickness across
> brains was higher than what I've seen in the in vivo brains.
>
>
> Best,
>
> Panos
>
>
> Panagiotis Fotiadis
> Senior Imaging Research Technologist
> J. P. Kistler Stroke Research Center, Department of Neurology
> Massachusetts General Hospital, Boston, MA
> T: (617) 643-3869
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of
> Bruce Fischl 
> Sent: Monday, July 30, 2018 4:07:48 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Ex vivo segmentations
> Hi Panos
>
> I think you can trust the white surface (more or less), it's the pial
> that is tougher. So you might sample say 1mm out from the white and not
> use the pial at all
> cheers
> Bruce
> On Mon, 30 Jul 2018, Fotiadis, Panagiotis wrote:
>
> >
> > Hi Bruce,
> >
> >
> > Thanks for your prompt response! I see, in that case I will disregard 
> > cortical thickness for
> now. I
> > was also interested in measuring the average signal intensities of the gray 
> > and white matter in
> > those ex vivo brains. Do you think it would be prudent to use the resulting 
> > surfaces from the ex
> > vivo pipeline (after of course checking their accuracy and making sure the 
> > gray/white
> segmentations
> > look accurate) to measure said intensities, or would you recommend another 
> > way?
> >
> >
> > Thanks,
> > Panos
> >
> >
> > Panagiotis Fotiadis
> > Senior Imaging Research Technologist
> > J. P. Kistler Stroke Research Center, Department of Neurology
> > Massachusetts General Hospital, Boston, MA
> > T: (617) 643-3869
> >
> >___
> _
> > From: freesurfer-boun...@nmr.mgh.harvard.edu 
> >  on behalf of
> > Bruce Fischl 
> > Sent: Monday, July 30, 2018 3:56:33 PM
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] Ex vivo segmentations
> > Hi Panos
> >
> > I wouldn't trust the thickness from the ex vivo pipeline, and in any case
> > those number are way to narrow a range. The normal cortex thickness ranges
> > from about 1.5mm to 4 or 4.5mm. Getting reasonable thickness from ex vivo
> > data is high on our to-do list
> >
> > cheers
> > Bruce
> >
> > On Mon, 30 Jul 2018, Fotiadis, Panagiotis wrote:
> >
> > >
> > > Hi Bruce and Doug,
> > >
> > >
> > > I have processed a few ex vivo brains with the help of the ex vivo 
> > > freesurfer pipeline (outlined
> > > in https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon), and have 
> > > extracted their cortical
> > > thickness. So far the range of the cortical thicknesses have been 
> > > approximately between
> > > 3.70-3.90 mm. Does that number sound reasonable for ex vivo brains? I am 
> > > asking because the
> > typical
> > > cortical thickness that I would expect to find on an in vivo brain would 
> > > be between 2.05 - 2.35
> > mm.
> > >
> > > Thanks in advance for any advice!
> > >
> > > Best,
> > >
> > > Panos
> > >
> > >
> > > Panagiotis Fotiadis
> > > Senior Imaging Research Technologist
> > > J. P. Kistler Stroke Research Center, Department of Neurology
> > > Massachusetts General Hospital, Boston, MA
> > > T: (617) 643-3869
> > >
> > >
> >
> >
>
>
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Re: [Freesurfer] Ex vivo segmentations

[Bruce Fischl]

as I said, I don't think I would trust the ex vivo thicknesses. Definitely 
not in an absolute sense
On Mon, 30 Jul 2018, 
Fotiadis, Panagiotis wrote:




Hi Bruce,


Thanks, that is actually really helpful. 

Also, I realized I misspoke earlier when I was talking about the cortical 
thickness range. The
3.7-3.9 mm range that I mentioned was referring to global cortical thickness 
across (not within) the
different brains I have processed. The range of cortical thickness within 
individual brains was
indeed wider ( between 2 - 5mm). I was just curious about why the average 
cortical thickness across
brains was higher than what I've seen in the in vivo brains. 


Best,

Panos 


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of
Bruce Fischl 
Sent: Monday, July 30, 2018 4:07:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Ex vivo segmentations  
Hi Panos

I think you can trust the white surface (more or less), it's the pial
that is tougher. So you might sample say 1mm out from the white and not
use the pial at all
cheers
Bruce
On Mon, 30 Jul 2018, Fotiadis, Panagiotis wrote:

>
> Hi Bruce,
>
>
> Thanks for your prompt response! I see, in that case I will disregard 
cortical thickness for
now. I
> was also interested in measuring the average signal intensities of the gray 
and white matter in
> those ex vivo brains. Do you think it would be prudent to use the resulting 
surfaces from the ex
> vivo pipeline (after of course checking their accuracy and making sure the 
gray/white
segmentations
> look accurate) to measure said intensities, or would you recommend another 
way?
>
>
> Thanks,
> Panos
>
>
> Panagiotis Fotiadis
> Senior Imaging Research Technologist
> J. P. Kistler Stroke Research Center, Department of Neurology
> Massachusetts General Hospital, Boston, MA
> T: (617) 643-3869
>
>___
_
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of
> Bruce Fischl 
> Sent: Monday, July 30, 2018 3:56:33 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Ex vivo segmentations  
> Hi Panos
>
> I wouldn't trust the thickness from the ex vivo pipeline, and in any case
> those number are way to narrow a range. The normal cortex thickness ranges
> from about 1.5mm to 4 or 4.5mm. Getting reasonable thickness from ex vivo
> data is high on our to-do list
>
> cheers
> Bruce
>
> On Mon, 30 Jul 2018, Fotiadis, Panagiotis wrote:
>
> >
> > Hi Bruce and Doug,
> >
> >
> > I have processed a few ex vivo brains with the help of the ex vivo 
freesurfer pipeline (outlined
> > in https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon), and have 
extracted their cortical
> > thickness. So far the range of the cortical thicknesses have been 
approximately between
> > 3.70-3.90 mm. Does that number sound reasonable for ex vivo brains? I am 
asking because the
> typical
> > cortical thickness that I would expect to find on an in vivo brain would be 
between 2.05 - 2.35
> mm. 
> >
> > Thanks in advance for any advice!
> >
> > Best,
> >
> > Panos
> >
> >
> > Panagiotis Fotiadis
> > Senior Imaging Research Technologist
> > J. P. Kistler Stroke Research Center, Department of Neurology
> > Massachusetts General Hospital, Boston, MA
> > T: (617) 643-3869
> >
> >
>
>

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Re: [Freesurfer] Ex vivo segmentations

[Fotiadis, Panagiotis]

Hi Bruce,


Thanks, that is actually really helpful.

Also, I realized I misspoke earlier when I was talking about the cortical 
thickness range. The 3.7-3.9 mm range that I mentioned was referring to global 
cortical thickness across (not within) the different brains I have processed. 
The range of cortical thickness within individual brains was indeed wider ( 
between 2 - 5mm). I was just curious about why the average cortical thickness 
across brains was higher than what I've seen in the in vivo brains.


Best,

Panos


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869

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

Sent: Monday, July 30, 2018 4:07:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Ex vivo segmentations

Hi Panos

I think you can trust the white surface (more or less), it's the pial
that is tougher. So you might sample say 1mm out from the white and not
use the pial at all
cheers
Bruce
On Mon, 30 Jul 2018, Fotiadis, Panagiotis wrote:

>
> Hi Bruce,
>
>
> Thanks for your prompt response! I see, in that case I will disregard 
> cortical thickness for now. I
> was also interested in measuring the average signal intensities of the gray 
> and white matter in
> those ex vivo brains. Do you think it would be prudent to use the resulting 
> surfaces from the ex
> vivo pipeline (after of course checking their accuracy and making sure the 
> gray/white segmentations
> look accurate) to measure said intensities, or would you recommend another 
> way?
>
>
> Thanks,
> Panos
>
>
> Panagiotis Fotiadis
> Senior Imaging Research Technologist
> J. P. Kistler Stroke Research Center, Department of Neurology
> Massachusetts General Hospital, Boston, MA
> T: (617) 643-3869
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of
> Bruce Fischl 
> Sent: Monday, July 30, 2018 3:56:33 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Ex vivo segmentations
> Hi Panos
>
> I wouldn't trust the thickness from the ex vivo pipeline, and in any case
> those number are way to narrow a range. The normal cortex thickness ranges
> from about 1.5mm to 4 or 4.5mm. Getting reasonable thickness from ex vivo
> data is high on our to-do list
>
> cheers
> Bruce
>
> On Mon, 30 Jul 2018, Fotiadis, Panagiotis wrote:
>
> >
> > Hi Bruce and Doug,
> >
> >
> > I have processed a few ex vivo brains with the help of the ex vivo 
> > freesurfer pipeline (outlined
> > in https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon), and have 
> > extracted their cortical
> > thickness. So far the range of the cortical thicknesses have been 
> > approximately between
> > 3.70-3.90 mm. Does that number sound reasonable for ex vivo brains? I am 
> > asking because the
> typical
> > cortical thickness that I would expect to find on an in vivo brain would be 
> > between 2.05 - 2.35
> mm.
> >
> > Thanks in advance for any advice!
> >
> > Best,
> >
> > Panos
> >
> >
> > Panagiotis Fotiadis
> > Senior Imaging Research Technologist
> > J. P. Kistler Stroke Research Center, Department of Neurology
> > Massachusetts General Hospital, Boston, MA
> > T: (617) 643-3869
> >
> >
>
>
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Re: [Freesurfer] Ex vivo segmentations

[Bruce Fischl]

Hi Panos

I think you can trust the white surface (more or less), it's the pial 
that is tougher. So you might sample say 1mm out from the white and not 
use the pial at all

cheers
Bruce
On Mon, 30 Jul 2018, Fotiadis, Panagiotis wrote:



Hi Bruce,


Thanks for your prompt response! I see, in that case I will disregard cortical 
thickness for now. I
was also interested in measuring the average signal intensities of the gray and 
white matter in
those ex vivo brains. Do you think it would be prudent to use the resulting 
surfaces from the ex
vivo pipeline (after of course checking their accuracy and making sure the 
gray/white segmentations
look accurate) to measure said intensities, or would you recommend another way?


Thanks,
Panos


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of
Bruce Fischl 
Sent: Monday, July 30, 2018 3:56:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Ex vivo segmentations  
Hi Panos

I wouldn't trust the thickness from the ex vivo pipeline, and in any case
those number are way to narrow a range. The normal cortex thickness ranges
from about 1.5mm to 4 or 4.5mm. Getting reasonable thickness from ex vivo
data is high on our to-do list

cheers
Bruce

On Mon, 30 Jul 2018, Fotiadis, Panagiotis wrote:

>
> Hi Bruce and Doug,
>
>
> I have processed a few ex vivo brains with the help of the ex vivo freesurfer 
pipeline (outlined
> in https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon), and have extracted 
their cortical
> thickness. So far the range of the cortical thicknesses have been 
approximately between
> 3.70-3.90 mm. Does that number sound reasonable for ex vivo brains? I am 
asking because the
typical
> cortical thickness that I would expect to find on an in vivo brain would be 
between 2.05 - 2.35
mm. 
>
> Thanks in advance for any advice!
>
> Best,
>
> Panos
>
>
> Panagiotis Fotiadis
> Senior Imaging Research Technologist
> J. P. Kistler Stroke Research Center, Department of Neurology
> Massachusetts General Hospital, Boston, MA
> T: (617) 643-3869
>
>

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Re: [Freesurfer] Ex vivo segmentations

[Fotiadis, Panagiotis]

Hi Bruce,


Thanks for your prompt response! I see, in that case I will disregard cortical 
thickness for now. I was also interested in measuring the average signal 
intensities of the gray and white matter in those ex vivo brains. Do you think 
it would be prudent to use the resulting surfaces from the ex vivo pipeline 
(after of course checking their accuracy and making sure the gray/white 
segmentations look accurate) to measure said intensities, or would you 
recommend another way?


Thanks,
Panos


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869

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

Sent: Monday, July 30, 2018 3:56:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Ex vivo segmentations

Hi Panos

I wouldn't trust the thickness from the ex vivo pipeline, and in any case
those number are way to narrow a range. The normal cortex thickness ranges
from about 1.5mm to 4 or 4.5mm. Getting reasonable thickness from ex vivo
data is high on our to-do list

cheers
Bruce

On Mon, 30 Jul 2018, Fotiadis, Panagiotis wrote:

>
> Hi Bruce and Doug,
>
>
> I have processed a few ex vivo brains with the help of the ex vivo freesurfer 
> pipeline (outlined
> in https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon), and have extracted 
> their cortical
> thickness. So far the range of the cortical thicknesses have been 
> approximately between
> 3.70-3.90 mm. Does that number sound reasonable for ex vivo brains? I am 
> asking because the typical
> cortical thickness that I would expect to find on an in vivo brain would be 
> between 2.05 - 2.35 mm.
>
> Thanks in advance for any advice!
>
> Best,
>
> Panos
>
>
> Panagiotis Fotiadis
> Senior Imaging Research Technologist
> J. P. Kistler Stroke Research Center, Department of Neurology
> Massachusetts General Hospital, Boston, MA
> T: (617) 643-3869
>
>
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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.

Re: [Freesurfer] Ex vivo segmentations

[Bruce Fischl]

Hi Panos

I wouldn't trust the thickness from the ex vivo pipeline, and in any case 
those number are way to narrow a range. The normal cortex thickness ranges 
from about 1.5mm to 4 or 4.5mm. Getting reasonable thickness from ex vivo 
data is high on our to-do list


cheers
Bruce

On Mon, 30 Jul 2018, Fotiadis, Panagiotis wrote:



Hi Bruce and Doug,


I have processed a few ex vivo brains with the help of the ex vivo freesurfer 
pipeline (outlined
in https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon), and have extracted 
their cortical
thickness. So far the range of the cortical thicknesses have been approximately 
between
3.70-3.90 mm. Does that number sound reasonable for ex vivo brains? I am asking 
because the typical
cortical thickness that I would expect to find on an in vivo brain would be 
between 2.05 - 2.35 mm. 

Thanks in advance for any advice!

Best,

Panos


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869

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contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] Ex vivo segmentations

[Fotiadis, Panagiotis]

Hi Bruce and Doug,


I have processed a few ex vivo brains with the help of the ex vivo freesurfer 
pipeline (outlined in https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon), 
and have extracted their cortical thickness. So far the range of the cortical 
thicknesses have been approximately between 3.70-3.90 mm. Does that number 
sound reasonable for ex vivo brains? I am asking because the typical cortical 
thickness that I would expect to find on an in vivo brain would be between 2.05 
- 2.35 mm.

Thanks in advance for any advice!


Best,

Panos


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869
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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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Re: [Freesurfer] masking cortical thickness

[Douglas N. Greve]

Yes, that should work. You can create a mask by breaking the annotation 
into labels (mri_annotation2label), then converting the label into a 
binary mask (mri_label2label with --mask option), then mri_binarize --i 
lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh


On 07/30/2018 01:47 AM, N Saf wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer Experts,
>
> I wonder how can I show the cortical thickness surface on just one 
> region of my interest in Freeview.  assume that I want to see the 
> thickness surface of one of the regions in DKTatlas. does it work if I 
> make a binary mask of that specific region on aparcDKTatlas.annot and 
> then multiply it to the ?h.thickness surface ?? any help will be 
> appreciated.
>
> Best Regards,
> Nazanin
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Atlases in FreeSurfer

[Bruce Fischl]

Hi Siti

it is more or less the same protocol, but I exepect there are some 
differences as for example neuromorphometrics used differentt (probably 
better) visualization and editing tools. We rebuild the atlas for every 
release to account for changes in registration, normalization, etc


We have multiple cortical atlases, one described by Christophe Destrieux 
and one by Rahul Desikan.


cheers
Bruce


On Mon, 30 Jul 2018, Yaakub, Siti Nurbaya wrote:



External Email - Use Caution

Hello,

 

I’m working on a comparison of atlas and segmentation methods. One of the
atlas sets I’m using is the subset of Neuromorphometrics data from the
MICCAI 2012 Grand Challenge and Workshop on Multi-Atlas Labeling. From what
I understand, the “general segmentation” of the brains for this atlas was
defined by the MGH Center for Morphometric Analysis, while the cortical
segmentation is similar to the DKT atlas available in FreeSurfer.

 

I have 2 questions about the atlases used in FreeSurfer:

1. Is this MGH sub-cortical segmentation protocol similar to that used in
the default FreeSurfer sub-cortical segmentation?

2. Would it be possible to have more information about the atlas subjects
used in both the FreeSurfer cortical (DK & DKT atlases) and sub-cortical
segmentation and are these manual labels available for download? The only
description I could find on the sub-cortical atlas was from Fischl et al.
2002, but I don’t think this is the atlas set used in the most current
FreeSurfer version.

 

Thank you and best wishes,

Siti

 

-- 

Siti Nurbaya Yaakub, Ph.D.

Research Associate

School of Biomedical Engineering and Imaging Sciences

King’s College London

St. Thomas’ Hospital

London SE1 7EH

 

 


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[Freesurfer] Surface editing: recon-all exited with errors

[Rockers, Elijah D.]

External Email - Use Caution

Hello.


I manually edited the brainmask.mgz file for three subjects. This was done to 
prevent the pial surface from extending into non-cortical areas, in particular 
the soft-tissue near the brain stem, and some cerebellar areas. Usually this 
type of editing (just removing voxels from brianmask.mgz) doesn't give me any 
trouble, and I use the command recon-all -make all -subjid  -sd 
 to then rebuild the surfaces.


However, the tail of the log shows that the pipeline exited with errors, with a 
few commands near the end related to curvstats and jacobian_white failing. The 
new surfaces seem to look fine in freeview. The edits to brainmask were 
registered correctly, but I'm still concerned that the errors might affect an 
mri_glmfit analysis. This is true for all three subjects I edited, which seems 
odd, and I'm not sure what would be causing this.


Below is a pastebin showing the relevant errors. The rest of the pipeline seems 
to execute without errors. I could send entire log if necessary.


https://pastebin.com/raw/b4JX04AT


Thanks,

- Eli

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas for patient care. Houston Methodist 
is nationally ranked in 8 specialties and is designated as a Magnet hospital 
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[Freesurfer] Atlases in FreeSurfer

[Yaakub, Siti Nurbaya]

External Email - Use Caution

Hello,

I’m working on a comparison of atlas and segmentation methods. One of the atlas 
sets I’m using is the subset of Neuromorphometrics data from the MICCAI 2012 
Grand Challenge and Workshop on Multi-Atlas Labeling. From what I understand, 
the “general segmentation” of the brains for this atlas was defined by the MGH 
Center for Morphometric Analysis, while the cortical segmentation is similar to 
the DKT atlas available in FreeSurfer.

I have 2 questions about the atlases used in FreeSurfer:
1. Is this MGH sub-cortical segmentation protocol similar to that used in the 
default FreeSurfer sub-cortical segmentation?
2. Would it be possible to have more information about the atlas subjects used 
in both the FreeSurfer cortical (DK & DKT atlases) and sub-cortical 
segmentation and are these manual labels available for download? The only 
description I could find on the sub-cortical atlas was from Fischl et al. 2002, 
but I don’t think this is the atlas set used in the most current FreeSurfer 
version.

Thank you and best wishes,
Siti

--
Siti Nurbaya Yaakub, Ph.D.
Research Associate
School of Biomedical Engineering and Imaging Sciences
King’s College London
St. Thomas’ Hospital
London SE1 7EH


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Re: [Freesurfer] hippocampal subfields segmentation error

[오진영]

External Email - Use Caution

Dear Eugenio

Thank you for your help.
As I need to segment the nuclei of amygdala, I'll try to download the
development version.

Thanks!!

Jinyoung

2018-07-30 17:39 GMT+09:00 Iglesias Gonzalez, Eugenio 
:

> External Email - Use Caution
>
> Dear Jin,
>
> 6.0 does not segment the nuclei of the amygdala; you can ignore that line,
> assuming the code runs to completion (I am assuming it does?)
>
> If you want to segment the nuclei of the amygdala, you’ll have to download
> the development version:
>
> http://freesurfer.net/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of 오진영 <
> jinyoung.oh...@gmail.com>
> *Reply-To: *Freesurfer support list 
> *Date: *Monday, 30 July 2018 at 09:29
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] hippocampal subfields segmentation error
>
>
>
> *External Email - Use Caution*
>
> Dear Eugenio,
>
>
>
> Thanks for your reply.
>
> I am running version "freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" of
> freesurfer.
>
> As the log is so long, I attached whole log as a text file and I just
> copied few lines before the error below:
>
>
>
> WorldToImageTransform after cropping:
>
> AffineTransform (0x128c17790)
>
>   RTTI typeinfo:   itk::AffineTransform
>
>   Reference Count: 1
>
>   Modified Time: 377450804
>
>   Debug: Off
>
>   Object Name:
>
>   Observers:
>
> none
>
>   Matrix:
>
> -3.3 8.73125e-11 2.22045e-16
>
> -8.4821e-14 -2.67186e-12 -3.3
>
> 5.55112e-16 3.3 1.97674e-10
>
>   Offset: [15.4608, 101.71, 117.525]
>
>   Center: [0, 0, 0]
>
>   Translation: [15.4608, 101.71, 117.525]
>
>   Inverse:
>
> -0.3 4.85723e-17 9.7012e-12
>
> 8.32667e-17 2.19633e-11 0.3
>
> 9.42996e-15 -0.3 -2.96735e-13
>
>   Singular: 0
>
> I am WriteImage and I'm running!
>
> Wrote image to file asmr2.mgz
>
> This file does not contain MRI parameters
>
> This file does not contain MRI parameters
>
> numberOfLabels: 25
>
> Rasterizing mesh...here: 25
>
> here2: 25
>
> done
>
> mri_convert.bin discreteLabels.mgz discreteLabelsResampledT1.mgz -rt
> nearest -odt float -rl /Users/mnd_mac/Desktop/JY_
> surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/norm.mgz
>
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
>
> reading from discreteLabels.mgz...
>
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>
> i_ras = (-1, 0, 2.84217e-14)
>
> j_ras = (0, 6.58905e-11, -1)
>
> k_ras = (2.91038e-11, 1, -8.90815e-13)
>
> reading template info from volume /Users/mnd_mac/Desktop/JY_
> surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/norm.mgz...
>
> Reslicing using nearest
>
> writing to discreteLabelsResampledT1.mgz...
>
> mv: rename volumesAmygdala.txt to /Users/mnd_mac/Desktop/JY_
> surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.
> hippoSfVolumes-T1.amygdala.v10.txt: No such file or directory
>
>
>
> Thank you so much.
>
> Hope to hear you soon!
>
>
>
> Jin Young
>
>
>
> 2018-07-30 17:01 GMT+09:00 Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk>:
>
> *External Email - Use Caution*
>
> Dear Jinyoung,
>
> Can you please send us the log, or at least the last few lines before the
> error?
>
> Also, which exact version are you using? 6.0 or dev?
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of 오진영 <
> jinyoung.oh...@gmail.com>
> *Reply-To: *Freesurfer support list 
> *Date: *Monday, 30 July 2018 at 06:41
> *To: *"freesurfer@nmr.mgh.harvard.edu" 
> *Cc: *JongHyun Lee 
> *Subject: *[Freesurfer] hippocampal subfields segmentation error
>
>
>
> *External Email - Use Caution*
>
> Hello, freesurfer experts
>
>
>
> I'm trying to run segmentation of hippocampal subfields and nuclei of
> amygdala by using "segmentSF_T1.sh" command.
>
> I have downloaded the newest development version(freesurfer v.6.0) and
> license, as well as the required matlab runtime.
>
>
>
> However, I am getting the following error:
>
> mv: rename volumesAmygdala.txt to /Users/mnd_mac/Desktop/JY_
> surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.
> hippoSfVolumes-T1.amygdala.v10.txt: No such file or directory
>
>
>
> and I have no idea how to find the text file and solve this problem out.
>
> If you have any idea or recommends, please send me the e-mail back.
>
>
>
> Thanks!
>
>
>
> Jinyoung
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is 

Re: [Freesurfer] hippocampal subfields segmentation error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Jin,
6.0 does not segment the nuclei of the amygdala; you can ignore that line, 
assuming the code runs to completion (I am assuming it does?)
If you want to segment the nuclei of the amygdala, you’ll have to download the 
development version:
http://freesurfer.net/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of 오진영 

Reply-To: Freesurfer support list 
Date: Monday, 30 July 2018 at 09:29
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampal subfields segmentation error


External Email - Use Caution
Dear Eugenio,

Thanks for your reply.
I am running version "freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" of 
freesurfer.
As the log is so long, I attached whole log as a text file and I just copied 
few lines before the error below:


WorldToImageTransform after cropping:

AffineTransform (0x128c17790)

  RTTI typeinfo:   itk::AffineTransform

  Reference Count: 1

  Modified Time: 377450804

  Debug: Off

  Object Name:

  Observers:

none

  Matrix:

-3.3 8.73125e-11 2.22045e-16

-8.4821e-14 -2.67186e-12 -3.3

5.55112e-16 3.3 1.97674e-10

  Offset: [15.4608, 101.71, 117.525]

  Center: [0, 0, 0]

  Translation: [15.4608, 101.71, 117.525]

  Inverse:

-0.3 4.85723e-17 9.7012e-12

8.32667e-17 2.19633e-11 0.3

9.42996e-15 -0.3 -2.96735e-13

  Singular: 0

I am WriteImage and I'm running!

Wrote image to file asmr2.mgz

This file does not contain MRI parameters

This file does not contain MRI parameters

numberOfLabels: 25

Rasterizing mesh...here: 25

here2: 25

done

mri_convert.bin discreteLabels.mgz discreteLabelsResampledT1.mgz -rt nearest 
-odt float -rl 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/norm.mgz

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

reading from discreteLabels.mgz...

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

i_ras = (-1, 0, 2.84217e-14)

j_ras = (0, 6.58905e-11, -1)

k_ras = (2.91038e-11, 1, -8.90815e-13)

reading template info from volume 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/norm.mgz...

Reslicing using nearest

writing to discreteLabelsResampledT1.mgz...

mv: rename volumesAmygdala.txt to 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.hippoSfVolumes-T1.amygdala.v10.txt:
 No such file or directory

Thank you so much.
Hope to hear you soon!

Jin Young

2018-07-30 17:01 GMT+09:00 Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>>:

External Email - Use Caution
Dear Jinyoung,
Can you please send us the log, or at least the last few lines before the error?
Also, which exact version are you using? 6.0 or dev?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 오진영 mailto:jinyoung.oh...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, 30 July 2018 at 06:41
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: JongHyun Lee mailto:jonghyunlee1...@gmail.com>>
Subject: [Freesurfer] hippocampal subfields segmentation error


External Email - Use Caution
Hello, freesurfer experts

I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala 
by using "segmentSF_T1.sh" command.
I have downloaded the newest development version(freesurfer v.6.0) and license, 
as well as the required matlab runtime.

However, I am getting the following error:
mv: rename volumesAmygdala.txt to 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.hippoSfVolumes-T1.amygdala.v10.txt:
 No such file or directory

and I have no idea how to find the text file and solve this problem out.
If you have any idea or recommends, please send me the e-mail back.

Thanks!

Jinyoung


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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] hippocampal subfields segmentation error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Jinyoung,
Can you please send us the log, or at least the last few lines before the error?
Also, which exact version are you using? 6.0 or dev?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of 오진영 

Reply-To: Freesurfer support list 
Date: Monday, 30 July 2018 at 06:41
To: "freesurfer@nmr.mgh.harvard.edu" 
Cc: JongHyun Lee 
Subject: [Freesurfer] hippocampal subfields segmentation error


External Email - Use Caution
Hello, freesurfer experts

I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala 
by using "segmentSF_T1.sh" command.
I have downloaded the newest development version(freesurfer v.6.0) and license, 
as well as the required matlab runtime.

However, I am getting the following error:
mv: rename volumesAmygdala.txt to 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.hippoSfVolumes-T1.amygdala.v10.txt:
 No such file or directory

and I have no idea how to find the text file and solve this problem out.
If you have any idea or recommends, please send me the e-mail back.

Thanks!

Jinyoung

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.