Re: [Freesurfer] Doubts in hippocampal subfields labeling {Disarmed}

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks, Antonin.
The ASEG has definitely oversegmented the hippo. Those large regions were ASEG 
and the subfield module disagree are mostly partial voluming of the lateral 
ventricle and the cerebral white matter or the fimbria, and are thus NOT 
hippocampus. Having said that, it is also true that the subfield module 
undersegments the fimbria a bit; I’m pretty sure this is because some of the 
fimbria voxels (the most lateral ones) get assigned to the  alveus instead 
(which we don’t shown in the segmentation, as it’s not very reliable…)
I hope this helps,
/Eugenio


--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Antonin Skoch 

Reply-To: Antonin Skoch , Freesurfer support list 

Date: Thursday, 4 July 2019 at 07:31
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Doubts in hippocampal subfields labeling


External Email - Use Caution

Dear Eugenio,

I have uploaded the subject as file hippocampal_subfields_labeling.tar.gz to 
your server surfer.nmr.mgh.harvard.edu.
RAS coordinates of the unlabeled area are -31,-27,-9.
Thank you in advance,

Antonin



Dear Antonin,

It is difficult to see what’s going on in the images you sent. Would you mind

uploading the subject, or at least sending us the image without the

segmentation overlaid (and ideally, a sagittal view as well)?

Cheers,

/Eugenio

--

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com





From:  on behalf of Antonin Skoch



Reply-To: Antonin Skoch , Freesurfer support list



Date: Tuesday, 2 July 2019 at 21:43

To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: [Freesurfer] Doubts in hippocampal subfields labeling





External Email - Use Caution

Dear experts,



I noticed that systematically in most of my subjects there is area in

hippocampal region, labeled in aseg as hippocampus, but NOT labeled as

hippocampus in hippocampal subfields segmentation (it has zero value there).

See screenshots with norm.mgz overlaid by 1) aseg, 2) hippocampal subfields

segmentation.



According to T1 and T2 signal, it should neither be white matter and also

probably not a ventricle/CSF. Neocortex is not located here.

It has similar signal intensity as hippocampus, so I think that it should be

hippocampus, but I am puzzled by hippocampal subfields segmentation results

there. Why it is not labeled?



Could you please help me to clarify this? My concern is to correctly label this

area.

I could upload the example subject if it is of any help.



Regards,



Antonin Skoch
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[Freesurfer] How to Divide the Surface Parcellations of the Brain

[Mahshid Fouladivanda]

External Email - Use Caution


Dear Bruce,


All the outputs are .nii and .gii
I do not know if it is possible to convert it to the annotation!
By the way, what is needed for creation of the annotation file? I mean what 
information, it needs?


Regards
Mahshid
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Re: [Freesurfer] Freesurfer Digest, Vol 185, Issue 11

[Mahshid Fouladivanda]

External Email - Use Caution

Dear Bruce,


All the outputs are .nii and .gii
I do not know if it is possible to convert it to the annotation!
By the way, what is needed for creation of the annotation file? I mean what 
information, it needs?


Regards
Mahshid






From: freesurfer-requ...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Date: Mon, 08 Jul 2019 11:34:24 -0400
Subject: Freesurfer Digest, Vol 185, Issue 11


Send Freesurfer mailing list submissions to
   freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit
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or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
   freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

   1. Re: Skull Strip (Bruce Fischl)
   2. How to Divide the Surface Parcellations of the Brain
  (Mahshid Fouladivanda)
   3. Re: How to Divide the Surface Parcellations of the Brain
  (Bruce Fischl)
   4. Assigning voxels different intensity values (Fotiadis, Panagiotis)
   5. Re: Assigning voxels different intensity values (Bruce Fischl)
   6. Re: Assigning voxels different intensity values
  (Fotiadis, Panagiotis)
   7. Re: Assigning voxels different intensity values (Bruce Fischl)
   8. Re: Assigning voxels different intensity values
  (Fotiadis, Panagiotis)
   9. how to map regional t values on surface (fengmei fan)
  10. Skull Strip (Admin)
  11. Error in analyze (Qdec) (Abby tang)
  12. Re: Freesurfer Digest, Vol 185, Issue 9 (vittal korann)
  13. Postdoctoral Position opening at the University of Pittsburgh
  in neuroimaging of mood disorders (Anna Manelis)
  14. Re: make_average_subject error: could not load norm volume
  from (null) (Greve, Douglas N.,Ph.D.)
  15. Re: Skull Strip (Hoopes, Andrew)
  16. Re: recon-all error: Correcting defect (Diamond, Bram Ryder)
  17. Re: recon-all error: Correcting defect
  (Miguel ?ngel Rivas Fern?ndez)


--

Message: 1
Date: Sun, 7 Jul 2019 13:33:35 -0400 (EDT)
From: Bruce Fischl 
Subject: Re: [Freesurfer] Skull Strip
To: Freesurfer support list 
Message-ID:
   
Content-Type: text/plain; charset="utf-8"

I believe I already answered this. I don't understand what amplified
noise you mean. The brainmask.mgz can be used with mri_mask to apply to
any input volume you want.

cheers
Bruce
On Sun, 7 Jul 2019, Admin wrote:

>
> External Email - Use Caution
>
> Dear Freesurfer group? Now,I want ?generated a brain mask including the 
brain but excluding the
> amplified noise regions after skull strip, but I can't find the 
corresponding command line, so I
> send this email to you,?hoping to get your help.?
> My English is poor, if?I make mistakes ,?I hope you can understand me. 
Thanks for your help?
>
>
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
? ? ? ? ? ? ? ? ? ? ? ? ?
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
? Sincerely: Meng Nan Lin
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
? ? ? ? ? ? ? ? ? ? ? ? ?
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
? Date: 07/04/2019
>
>
>
>
> ?
>
>
>
>
> ?
>
>
>

--

Message: 2
Date: Mon, 08 Jul 2019 01:06:44 +0430
From: "Mahshid Fouladivanda" 
Subject: [Freesurfer] How to Divide the Surface Parcellations of the
   Brain
To: "freesurfer@nmr.mgh.harvard.edu" 
Message-ID: 
Content-Type: text/plain; charset="us-ascii"

External Email - Use Caution

Dear Freesurfer Experts,


I would like to divide the surface parcellations of the neonatal brain. The
parcells were extracted using Draw_EM (Developing brain Region Annotation
With Expectation-Maximization), an atlas based segmentation, from cortical
and sub-cortical. As I understand from help comments,
mris_divide_parcellation would help, but it needs annotation file to be
imported as input. I do not have the annotation file. I would appreciate it
if you could help me how to divide my parcells in more regions?



Regards,
Mahshid
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Message: 3
Date: Sun, 7 Jul 2019 18:27:49 -0400 (EDT)
From: Bruce Fischl 
Subject: Re: [Freesurfer] How to Divide the Surface Parcellations of
   the Brain
To: Freesurfer support list 
Message-ID:
   
Content-Type: text/plain; charset="iso-8859-15"

Hi Mahshid

what forma

Re: [Freesurfer] recon-all error: Correcting defect

[Miguel Ángel Rivas Fernández]

External Email - Use Caution

Dear Bram,

Thanks for your help, yes I tried to fix this issue following Bruce´s
suggestions and everything worked fine. I manually filled the brain lesions
in the wm.mgz and now the recon-all did not stop in the correcting defect.


Best regards,

El lun., 8 jul. 2019 a las 17:17, Diamond, Bram Ryder (<
brdiam...@mgh.harvard.edu>) escribió:

> Hi Miguel!
>
> I'll be happy to help with your issue, but I'm having trouble finding your
> subject's directory on our server. Could you please try and upload the data
> via FTP, again? Also, have you tried either of Bruce's suggestions?
>
> Thanks,
> Bram
>
> Bram R. Diamond, BSc
> Research Technician II
> Laboratory for Computational Neuroimaging
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 13th Street
> Charlestown, MA 02129
> (p): 617-726-6598
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas
> Fernández 
> Sent: Wednesday, June 26, 2019 11:37 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] recon-all error: Correcting defect
>
> External Email - Use Caution
>
> Hello Bruce,
>
> Ok, I have sent to you the subject via FileDrop if you want to take a
> look. Thanks.
>
> Best regards,
>
> El mié., 26 jun. 2019 a las 17:04, Bruce Fischl (<
> fis...@nmr.mgh.harvard.edu>) escribió:
> Hi Miguel
>
> depending on the lesions it may not be fixable (since they may change the
> topology of the cortex). If you upload the subject we will take a look, or
> you can try manually filling in the lesion in the wm.mgz (or marking it as
> lesion in the aseg.mgz) and seeing if that helps
>
> cheers
> Bruce
> On Wed, 26 Jun 2019, Miguel Ángel Rivas
> Fernández wrote:
>
> >
> > External Email - Use Caution
> >
> >
> >  I ran the recon-all in one subject and and this process was stopped in
> the topology correction. In
> > particular during the
> >
> >  "CORRECTING DEFECT 36 (vertices=19847, convex hull=5892, v0=94733)".
> >
> > I reviewed the lh.inflated.nofix and the lh.orig.nofix files in Freeview
> and I noticed that the this
> > error would be located in the lh.inflated.nofix file. I am not
> completely sure but I suspect that
> > this error may be due to the fact that there is a large amount of brain
> lesion and this would
> > difficult the topology correction. How can I fix this problem?
> >
> > Thanks in advance.
> >
> > Best regards,
> >
> > --
> > Miguel Ángel Rivas Fernández
> >
> >___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
> Miguel Ángel Rivas Fernández
>
> ___
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>


-- 
*Miguel Ángel Rivas Fernández*
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Re: [Freesurfer] recon-all error: Correcting defect

[Diamond, Bram Ryder]

Hi Miguel!

I'll be happy to help with your issue, but I'm having trouble finding your 
subject's directory on our server. Could you please try and upload the data via 
FTP, again? Also, have you tried either of Bruce's suggestions?

Thanks,
Bram

Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Miguel Ángel Rivas 
Fernández 
Sent: Wednesday, June 26, 2019 11:37 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error: Correcting defect

External Email - Use Caution

Hello Bruce,

Ok, I have sent to you the subject via FileDrop if you want to take a look. 
Thanks.

Best regards,

El mié., 26 jun. 2019 a las 17:04, Bruce Fischl 
(mailto:fis...@nmr.mgh.harvard.edu>>) escribió:
Hi Miguel

depending on the lesions it may not be fixable (since they may change the
topology of the cortex). If you upload the subject we will take a look, or
you can try manually filling in the lesion in the wm.mgz (or marking it as
lesion in the aseg.mgz) and seeing if that helps

cheers
Bruce
On Wed, 26 Jun 2019, Miguel Ángel Rivas
Fernández wrote:

>
> External Email - Use Caution
>
>
>  I ran the recon-all in one subject and and this process was stopped in the 
> topology correction. In
> particular during the
>
>  "CORRECTING DEFECT 36 (vertices=19847, convex hull=5892, v0=94733)".
>
> I reviewed the lh.inflated.nofix and the lh.orig.nofix files in Freeview and 
> I noticed that the this
> error would be located in the lh.inflated.nofix file. I am not completely 
> sure but I suspect that
> this error may be due to the fact that there is a large amount of brain 
> lesion and this would
> difficult the topology correction. How can I fix this problem?
>
> Thanks in advance.
>
> Best regards,
>
> --
> Miguel Ángel Rivas Fernández
>
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--
Miguel Ángel Rivas Fernández

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Re: [Freesurfer] Skull Strip

[Hoopes, Andrew]

Hi, unless you build the binaries yourself, I believe the stable freesurfer 
versions only support cuda 5. However, cuda support has been completely removed 
in the current development version. The dev version that you’re referencing is 
from 2016.
Andrew


From:  on behalf of Admin 
<15140248...@163.com>
Reply-To: FS Help 
Date: Monday, July 8, 2019 at 2:07 AM
To: FS Help 
Subject: [Freesurfer] Skull Strip


External Email - Use Caution
Dear Freesurfer group：
just tried recon-all with the -use-gpu flag from the current development 
version of freesurfer (freesurfer-Linux-centos6_x86_64-dev-20161123-bb356e0), 
but it fail with the message that is cannot open libcudart.so.5.0.
I have the current cuda version install(8.0). Does Freesurfer only work 
with cuda 5.0?

Date: 07/08/2019
















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Re: [Freesurfer] make_average_subject error: could not load norm volume from (null)

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

Can you send the full terminal output of make_average_subject? There should 
also be some log files (make_average_volume.log and make_average_surface.log) 
in the average subject that would be helpful

On 7/4/2019 4:36 AM, Mads Jensen wrote:

External Email - Use Caution

HI FreeSurfer Developers,

I'm attempting to create an average subject make_average_subject but I
get the error message the following error when I run the
make_average_command:

Loading aseg from REMOVED-PATH/avg_elder/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from (null)

Linux 4.4.0-130-generic #156-Ubuntu SMP Thu Jun 14 08:53:28 UTC 2018
x86_64 x86_64 x86_64 GNU/Linux

I cannot find anything similar on the mailing list. I hope anyone have
any thoughts on how to trouble-shoot this one? Also, Ive attached the
recon-all.log in case it's of any use.

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Ubuntu 16.04.4 LTS
3) uname -a: Linux hyades02 4.4.0-130-generic #156-Ubuntu SMP Thu Jun
14 08:53:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached




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[Freesurfer] Postdoctoral Position opening at the University of Pittsburgh in neuroimaging of mood disorders

[Anna Manelis]

External Email - Use Caution

Candidates are being considered for a post-doctoral associate position in
the Anticipation, Cognition and Emotion lab ( www.ace.pitt.edu ) at the
University of Pittsburgh (http://www.pitt.edu) to work with Dr. Anna
Manelis and her team. A successful candidate will work on the NIMH funded
research project that uses multimodal neuroimaging (fMRI, MRI, DTI and
fNIRS) to understand the contribution of anticipatory processing to
cognitive and emotional dysfunction in individuals with mood disorders.

Pittsburgh is a vibrant community which promotes diversity and
collaboration within its university and medical systems. Our lab works in
conjunction with the University of Pittsburgh Medical Center to perform
neuroimaging studies which will help us to better understand mood
disorders, including major depressive disorder and bipolar disorders.

*Required Qualification*s: we are seeking a highly motivated candidate with
a PhD degree (or anticipated PhD degree) in psychology, cognitive
neuroscience, computational neuroscience or a related discipline. A strong
research background in the analysis and interpretation of neuroimaging data
is required. A successful candidate will have excellent writing and
communication skills. Candidates with a strong computational background are
encouraged to apply. Experience with FSL, Freesurfer and E-prime is
preferred. The ability to program in Shell, Matlab, Python and/or R is
preferred.  Experience with fNIRS, graph modeling and pattern
classification analyses is a plus. While prior experience with clinical
populations is not necessary, we expect candidates to be interested in
neuroimaging research of working and episodic memory and/or anticipatory
and emotional processing in individuals with mood disorders.

*Responsibilities*:

· Help to run fMRI/fNIRS experiments
· Analyze fMRI, MRI, DTI and fNIRS neuroimaging data
· Write manuscripts
· Present findings from studies at conferences

This is a full-time position that can be extended to 3 years. We are
looking for someone to join our lab in Fall 2019 (with some flexibility).
This position is funded by the NIMH and salary will vary based on
experience.

If you are interested in this position, please send a CV, research
statement, preprints/reprints of papers, and the names and contact
information for two references to *Anna Manelis (manel...@upmc.edu
).*
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Re: [Freesurfer] Freesurfer Digest, Vol 185, Issue 9

[vittal korann]

External Email - Use Caution

Thanks, Tim for your reply.

No, there is only "lh.pial" file exists not 'lh.pial_lgi.
What might be the problem?

Any help would be appreciated

Thanks & regards
-Korann




On Sat, Jul 6, 2019 at 9:30 PM 
wrote:

> Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
> freesurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
> freesurfer-ow...@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
>1. Re: [External] Re:  rostral anterior cingulate fix?
>   (Zeng,Victor (BIDMC - Psychiatry))
>2. Re: [External] Re:  rostral anterior cingulate fix? (Bruce Fischl)
>3. Re: recon-all Error : inputs cannot have multiple frames.
>   ( Yueming )
>4. Re: recon-all Error : inputs cannot have multiple frames.
>   (Bruce Fischl)
>5. error while running pial_lgi for gyrification index
>   (vittal korann)
>6. Re: error while running pial_lgi for gyrification index
>   (Tim Sch?fer)
>7. Viewing Uncorrected Significance Map in Freeview (Marie Hill)
>
>
> --
>
> Message: 1
> Date: Fri, 5 Jul 2019 17:42:28 +
> From: "Zeng,Victor (BIDMC - Psychiatry)" 
> Subject: Re: [Freesurfer] [External] Re:  rostral anterior cingulate
> fix?
> To: Freesurfer support list 
> Message-ID: <1562348548910.95...@bidmc.harvard.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Sorry, I thought I attached something
> Victor Zeng
> Beth Israel Deaconess Medical Center
> Keshavan Lab
> ph: 617 754 1237
> --
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> Sent: Friday, July 5, 2019 10:24 AM
> To: Freesurfer support list
> Subject: [External] Re: [Freesurfer] rostral anterior cingulate fix?
>
> Hi Victor
>
> can you render the parcellation in that area on the surface (in freeview)
> and show it to us?
>
> cheers
> Bruce
>
>
> On Fri, 5 Jul 2019, Zeng,Victor (BIDMC - Psychiatry) wrote:
>
> >
> > Hi Freesurfer group -
> >
> >
> > I'm using FS6.0 dev-20190118, and I'm processing a few brain scans. I'm
> seeing a misparcellation of
> > the right rostral anterior cingulate using tkmedit (I know tkmedit is
> sorta deprecated), and it
> > doesn't seem inappropriate to use control point fixes. How would you
> best fix this (I'm open to
> > using freeview), without just editing the aparc+aseg.mgz?
> >
> >
> > Victor Zeng
> > Beth Israel Deaconess Medical Center
> > Keshavan Lab
> > ph: 617 754 1237
> > --
> >
> >
> 
> >
> > This message is intended for the use of the person(s) to whom it may be
> addressed. It may contain
> > information that is privileged, confidential, or otherwise protected
> from disclosure under
> > applicable law. If you are not the intended recipient, any
> dissemination, distribution, copying, or
> > use of this information is prohibited. If you have received this message
> in error, please
> > permanently delete it and immediately notify the sender. Thank you.
> >
> >
> -- next part --
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> Type: image/png
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> Desc: Screenshot from 2019-07-05 13-41-46.png
> Url :
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190705/626cd039/attachment-0001.png
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> --
>
> Message: 2
> Date: Fri, 5 Jul 2019 13:45:40 -0400 (EDT)
> From: Bruce Fischl 
> Subject: Re: [Freesurfer] [External] Re:  rostral anterior cingulate
> fix?
> To: Freesurfer support list 
> Message-ID:
> 
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> you did, but not a surface rendering. Load it with freeview and show it as
> a surface (maybe inflated and white)
>
> On Fri, 5 Jul 2019, Zeng,Victor (BIDMC
> - Psychiatry) wrote:
>
> >
> > Sorry, I thought I attached something
> > Victor Zeng
> > Beth Israel Deaconess Medical Center
> > Keshavan Lab
> > ph: 617 754 1237
> > --
> >
> > 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> > Sent: Friday, July 5, 2019 10:24 AM
> > To: Freesurfer support list
> > Subject: [External] Re: [Freesurfer] rostral anterior cingulate fix?
> >
> > Hi Victor
> >
> > can you render the parcellation in 

[Freesurfer] Skull Strip

[Admin]

External Email - Use Caution

Dear Freesurfer group：
just tried recon-all with the -use-gpu flag from the current development 
version of freesurfer (freesurfer-Linux-centos6_x86_64-dev-20161123-bb356e0), 
but it fail with the message that is cannot open libcudart.so.5.0.
I have the current cuda version install(8.0). Does Freesurfer only work 
with cuda 5.0?
Date: 07/08/2019







 






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