[Freesurfer] Errors when testing freesurfer installation

[Peng Zan]

Dear freesurfer experts,

I am new to freesurfer and I met this problem when I was testing freesurfer
installation following the instructions on the 'Testing Freesurfer'
website. I got the problems as follows when I tested command, 'tkmedit bert
orig.mgz' on heavy data from tutorial web.

Couldn't create output file
.xdebug_tkmedit--

ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.

  If you are outside the NMR-Martinos Center,

  go to http://surfer.nmr.mgh.harvard.edu to

  get a valid license file (it's free).

  If you are inside the NMR-Martinos Center,

  make sure to source the standard environment.
I have had the 'license.txt' file under FREESURFER_HOME folder, and the
freeview works fine. I also created a 'fs.license' file under the home
folder and copied the license info into it, but it still did not work. May
you give any suggestions to fix this problem?

Thank you! Looking forward to your reply!

Sincerely,
Peng
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[Freesurfer] ABCD postdoctoral position at Florida International University

[Anthony Dick]

Dear Colleagues,

Please find below an advertisement for our Postdoctoral position at 
Florida International University, Miami, FL. Details are also provided 
in the attached pdf. Thank you!


Anthony
>>>

The Cognitive Neuroscience and Imaging Center at Florida International 
University (FIU) in Miami is seeking a full-time, benefits-earning 
Visiting Postdoctoral Fellow with expertise in magnetic resonance 
imaging (MRI) physics, with emphasis on functional MRI and diffusion- 
weighted MRI. The successful candidate will join a team of investigators 
to develop, support, facilitate, and coordinate daily data collection 
activities for the Adolescent Brain Cognitive Development (ABCD) Study: 
a landmark multi-site NIH study to assess the short- and long-term 
impact of substance use on brain development 
(http://addictionresearch.nih.gov).


The successful candidate will develop, deploy, and optimize multiband 
fMRI and high angular resolution diffusion imaging (HARDI) acquisition 
protocols for use at 3T. She/he will contribute to deploying these MRI 
techniques, as well as prospective motion correction (PROMO), and fast, 
integrated distortion correction methods. These methods will be 
collectively applied in a large, longitudinal study designed to advance 
addiction science through a strong focus on developmentally informed 
assessment. The primary duties/responsibilities of the position involve 
direct engagement in magnetic resonance imaging (MRI) data collection 
efforts, including (but not limited to): protocol development and 
management, execution of research plan, implementation of experiments, 
data acquisition, and data management.


Applicants must have a PhD in physics, biomedical engineering, 
radiological sciences, computer science, or a related field. Candidates 
must have a strong background in MR physics, as well as strong skills in 
computer programming (e.g., python, MATLAB). Applicants must have 
experience in MR scanner operation and software, image reconstruction, 
advanced data analysis (e.g., FSL, AFNI). Experience in multiband fMRI 
and/or HARDI imaging technology, and familiarity with data harmonization 
across multi-center imaging studies are highly desired. The applicant 
should ideally possess outstanding writing and communication skills as 
demonstrated by a successful publication record.


The starting date for this position is January 1, 2016, and the salary 
will be commensurate with experience. To apply, please include all 
documents in one PDF file: cover letter, CV, a one-page statement 
describing your qualifications and research interests, contact 
information for two references, and copies of up to two of your 
publications. Applications should be sent via email to: c...@fiu.edu. 
Review of applications will begin immediately.


For informal enquiries regarding this position, please contact Dr. 
Angela Laird (ala...@fiu.edu).


Additional information about the Center can be found at 
http://cnic.fiu.edu, and more information about the ABCD Project can be 
found at http://www.drugabuse.gov/news- 
events/news-releases/2015/09/nih-launches-landmark-study-substance-use-adolescent-brain- 
development.


--
Anthony Steven Dick, Ph.D.
Assistant Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: ad...@fiu.edu
Webpage: faculty.fiu.edu/~adick; Lab Webpage: http://dcn.fiu.edu
Join the Society for the Study of Human Development: http://www.sshdonline.org

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[Freesurfer] mri_label2vol --fill-ribbon argument

[Arnaud Boré]

Dear Freesurfer's expert,

I want to create a 3d volume using an annot file and I'm using
mri_label2vol command.

When running this command line:

mri_label2vol --annot sub1/label/lh.Yeo2011_7Networks_N1000.annot
--identity --subject sub1 --hemi lh --o sub1/mri/lh.Yeo.nii.gz --temp
sub1/mri/T1.mgz --proj frac 0 5 0.1

I get a 3d volume but the ribbon is not well filled so I wanted to use
--fill-ribbon available with Freesurfer 6 but then I get a binary volume 3d
of the ribbon without any information I had from my annot file.

Is there an error with this  --fill-ribbon option ?
How can I get this 3d volume of the ribbon from annot file ?

Thank you

Arnaud
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[Freesurfer] Freesurfer 6 exits with errors after recon edits on skullstrip

[Tuominen, Lauri Johannes]

Dear Freesurfer experts,

I ran recon-all on launchpad using /usr/local/freesurfer/stable6/bin/recon-all. 
This command worked nicely, but part of the occipital cortex was missing and I 
therefore ran the following command ( both in freesurfer6 ):

  recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -s atib

This took care of the brain mask problem that I had with the previous recon. So 
I then ran on launchpad:

 recon-all -s atib -autorecon2 -autorecon3 -hippocampal-subfields-T1'

The last command exits with errors. Please find the log-files attached.

Thank you for your help!

Best,
Lauri Tuominen

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Re: [Freesurfer] Brainstem Substructures in Freesurfer 6.0 - how to calculate left/right volumes

[Eugenio Iglesias]

Hi Chris, 
at this point, the software does not split the SCP into its left and right 
parts. 
But, you definitely gave me something to think about. When I have the time, 
I'll try to work on this and release a patch. 
Cheers, 
Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Chris Steward"  
To: "Freesurfer support list"  
Sent: Thursday, December 10, 2015 1:53:58 AM 
Subject: [Freesurfer] Brainstem Substructures in Freesurfer 6.0 - how to 
calculate left/right volumes 

Hello, 

I've installed Freesurfer 6.0 beta, and run the -brainstem-structures option to 
recon-all. 

The results look ok, but I'd like the left/right volumes for the superior 
cerebellar peduncle (SCP), rather than the total volume. Is there any easy way 
to do this? 

Thanks, 
Chris 

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[Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

[Matthieu Vanhoutte]

Dear FS experts,

1) First Is it possible to use the partial volume correction provided in
the v6 beta version of FreeSurfer despite the fact that recon-all have been
done for all subjects with the v5.3 ?

2) Does this method supply an intensity normalisation for PET images ?

Best regards,
Matthieu
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Re: [Freesurfer] Shifted surface after gyrification index is calculated

[Bruce Fischl]

and how do you determine they are shifted? In freeview? The surface 
geometry/position should be preserved in the smoothing but appears to not 
to be. Perhaps Marie can comment? Or you can try mris_copy_header to see if 
that does the trick


cheers
Bruce


On Thu, 10 Dec 2015, 
Chris Holdgraf wrote:



Hey Bruce - thus far I have used pretty default parameters. I first ran
recon-all on each subject, then simply ran `recon-all -s s_name -localGI`. 
Here are the transforms for the original vs. inflated surface

On lh.pial:
talairch.xfm: 
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
surfaceRAS to talaraiched surfaceRAS: 
 1.103   0.015  -0.002   4.752;
-0.032   1.064   0.063  -15.999;
 0.015  -0.008   1.170   1.733;
 0.000   0.000   0.000   1.000;
talairached surfaceRAS to surfaceRAS: 
 0.906  -0.013   0.002  -4.519;
 0.028   0.939  -0.051   14.976;
-0.012   0.007   0.854  -1.320;
 0.000   0.000   0.000   1.000;
volume geometry:
extent  : (256, 256, 256)
voxel   : ( 1.,  1.,  1.)
x_(ras) : (-1.,  0.,  0.)
y_(ras) : ( 0.,  0., -1.)
z_(ras) : ( 0.,  1.,  0.)
c_(ras) : ( 0.5078,  2.0802, 23.0431)


On lh.pial-outer-smoothed:

talairch.xfm: 
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
surfaceRAS to talaraiched surfaceRAS: 
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
talairached surfaceRAS to surfaceRAS: 
 0.906  -0.013   0.002  -4.011;
 0.028   0.939  -0.051   17.057;
-0.012   0.007   0.854   21.723;
 0.000   0.000   0.000   1.000;
volume geometry info is either not contained or not valid.

---

I highlight that last bit because maybe it's important? Looks like some
information goes missing in there...

Chris



On Thu, Dec 10, 2015 at 10:27 AM, Bruce Fischl 
wrote:
  Hi Chris

  how do you smooth the surface? Are you sure that you retain the
  surface
  header information? Try looking at the header with mris_info
  before and
  after smoothing

  cheers
  Bruce
  On Thu, 10 Dec 2015, Chris Holdgraf wrote:

  > Hey Freesurfer folks - I'm looking into using Freesurfer for
  doing electrode
  > reconstruction / co-registration in electrocorticography.
  We're making good
  > progress on figuring out recon-all for surfaces and doing
  co-registration to
  > CTs. However, I think I've encountered a strange bug.
  > I'm trying to create a smoothed pial surface so that I project
  electrodes
  > onto this surface. The code seems to run correctly, however,
  the smoothed
  > surface looks translated relative to the original pial surface
  that it was
  > created from.
  >
  > For example, see this issue I opened on github:
  >
  > https://github.com/aestrivex/gselu/issues/7
  >
  > Anyone have an idea why this is happening? I'm not sure why
  the pial surface
  > would be correct, while the smoothed surface would be shifted.
  >
  > Chris
  >
  >
  > --
  > _
  >
  > PhD Candidate in Neuroscience | UC Berkeley
  > Editor and Web Director | Berkeley Science Review
  > _
  >
  >
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--
_

PhD Candidate in Neuroscience | UC Berkeley
Editor and Web Director | Berkeley Science Review
_

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Re: [Freesurfer] Freesurfer 6 exits with errors after recon edits on skullstrip

[Bruce Fischl]

Hi Lauri

I think you forgot to attach the logs

Bruce


On Thu, 10 Dec 2015, Tuominen, Lauri Johannes wrote:


Dear Freesurfer experts,

I ran recon-all on launchpad using
/usr/local/freesurfer/stable6/bin/recon-all. This command worked nicely, but
part of the occipital cortex was missing and I therefore ran the following
command ( both in freesurfer6 ):

  recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -s atib

This took care of the brain mask problem that I had with the previous recon.
So I then ran on launchpad:

 recon-all -s atib -autorecon2 -autorecon3 -hippocampal-subfields-T1'

The last command exits with errors. Please find the log-files attached.

Thank you for your help!

Best,
Lauri Tuominen
 

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Re: [Freesurfer] Shifted surface after gyrification index is calculated

[Chris Holdgraf]

Yep - sorry, here's a pic:
https://cloud.githubusercontent.com/assets/1839645/11702154/263fb152-9e89-11e5-8485-dc97c8ca2ca7.png

You can see the smoothed version is shifted lower.

I couldn't find mris_copy_header on my path. Is it only included in the
beta version? I'm running 5.3. Could try beta as well, just not sure how
stable it is...

On Thu, Dec 10, 2015 at 12:38 PM, Bruce Fischl 
wrote:

> and how do you determine they are shifted? In freeview? The surface
> geometry/position should be preserved in the smoothing but appears to not
> to be. Perhaps Marie can comment? Or you can try mris_copy_header to see if
> that does the trick
>
>
> cheers
> Bruce
>
>
> On Thu, 10 Dec 2015, Chris Holdgraf wrote:
>
> Hey Bruce - thus far I have used pretty default parameters. I first ran
>> recon-all on each subject, then simply ran `recon-all -s s_name
>> -localGI`.
>> Here are the transforms for the original vs. inflated surface
>>
>> On lh.pial:
>> talairch.xfm:
>>  1.103   0.015  -0.002   4.202;
>> -0.032   1.064   0.063  -19.651;
>>  0.015  -0.008   1.170  -25.227;
>>  0.000   0.000   0.000   1.000;
>> surfaceRAS to talaraiched surfaceRAS:
>>  1.103   0.015  -0.002   4.752;
>> -0.032   1.064   0.063  -15.999;
>>  0.015  -0.008   1.170   1.733;
>>  0.000   0.000   0.000   1.000;
>> talairached surfaceRAS to surfaceRAS:
>>  0.906  -0.013   0.002  -4.519;
>>  0.028   0.939  -0.051   14.976;
>> -0.012   0.007   0.854  -1.320;
>>  0.000   0.000   0.000   1.000;
>> volume geometry:
>> extent  : (256, 256, 256)
>> voxel   : ( 1.,  1.,  1.)
>> x_(ras) : (-1.,  0.,  0.)
>> y_(ras) : ( 0.,  0., -1.)
>> z_(ras) : ( 0.,  1.,  0.)
>> c_(ras) : ( 0.5078,  2.0802, 23.0431)
>>
>>
>> On lh.pial-outer-smoothed:
>>
>> talairch.xfm:
>>  1.103   0.015  -0.002   4.202;
>> -0.032   1.064   0.063  -19.651;
>>  0.015  -0.008   1.170  -25.227;
>>  0.000   0.000   0.000   1.000;
>> surfaceRAS to talaraiched surfaceRAS:
>>  1.103   0.015  -0.002   4.202;
>> -0.032   1.064   0.063  -19.651;
>>  0.015  -0.008   1.170  -25.227;
>>  0.000   0.000   0.000   1.000;
>> talairached surfaceRAS to surfaceRAS:
>>  0.906  -0.013   0.002  -4.011;
>>  0.028   0.939  -0.051   17.057;
>> -0.012   0.007   0.854   21.723;
>>  0.000   0.000   0.000   1.000;
>> volume geometry info is either not contained or not valid.
>>
>> ---
>>
>> I highlight that last bit because maybe it's important? Looks like some
>> information goes missing in there...
>>
>> Chris
>>
>>
>>
>> On Thu, Dec 10, 2015 at 10:27 AM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Chris
>>
>>   how do you smooth the surface? Are you sure that you retain the
>>   surface
>>   header information? Try looking at the header with mris_info
>>   before and
>>   after smoothing
>>
>>   cheers
>>   Bruce
>>   On Thu, 10 Dec 2015, Chris Holdgraf wrote:
>>
>>   > Hey Freesurfer folks - I'm looking into using Freesurfer for
>>   doing electrode
>>   > reconstruction / co-registration in electrocorticography.
>>   We're making good
>>   > progress on figuring out recon-all for surfaces and doing
>>   co-registration to
>>   > CTs. However, I think I've encountered a strange bug.
>>   > I'm trying to create a smoothed pial surface so that I project
>>   electrodes
>>   > onto this surface. The code seems to run correctly, however,
>>   the smoothed
>>   > surface looks translated relative to the original pial surface
>>   that it was
>>   > created from.
>>   >
>>   > For example, see this issue I opened on github:
>>   >
>>   > https://github.com/aestrivex/gselu/issues/7
>>   >
>>   > Anyone have an idea why this is happening? I'm not sure why
>>   the pial surface
>>   > would be correct, while the smoothed surface would be shifted.
>>   >
>>   > Chris
>>   >
>>   >
>>   > --
>>   > _
>>   >
>>   > PhD Candidate in Neuroscience | UC Berkeley
>>   > Editor and Web Director | Berkeley Science Review
>>   > _
>>   >
>>   >
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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.
>>
>>
>>
>>
>> --
>> _
>>
>> PhD Candidate in Neuroscience | UC Berkeley
>> Editor and Web 

Re: [Freesurfer] Shifted surface after gyrification index is calculated

[Bruce Fischl]

what hardware are you running on? We can send you a version of 
mris_copy_header. Or you can can send me the two surfaces (before and 
after smoothing) and I can see if it fixes the problem


cheers
Bruce
On Thu, 10 Dec 2015, 
Chris Holdgraf wrote:



Yep - sorry, here's apic: 
https://cloud.githubusercontent.com/assets/1839645/11702154/263fb152-9
e89-11e5-8485-dc97c8ca2ca7.png
You can see the smoothed version is shifted lower. 

I couldn't find mris_copy_header on my path. Is it only included in the beta
version? I'm running 5.3. Could try beta as well, just not sure how stable
it is...

On Thu, Dec 10, 2015 at 12:38 PM, Bruce Fischl 
wrote:
  and how do you determine they are shifted? In freeview? The
  surface geometry/position should be preserved in the smoothing
  but appears to not to be. Perhaps Marie can comment? Or you can
  try mris_copy_header to see if that does the trick

  cheers
  Bruce


  On Thu, 10 Dec 2015, Chris Holdgraf wrote:

Hey Bruce - thus far I have used pretty default
parameters. I first ran
recon-all on each subject, then simply ran
`recon-all -s s_name -localGI`. 
Here are the transforms for the original vs.
inflated surface

On lh.pial:
talairch.xfm: 
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
surfaceRAS to talaraiched surfaceRAS: 
 1.103   0.015  -0.002   4.752;
-0.032   1.064   0.063  -15.999;
 0.015  -0.008   1.170   1.733;
 0.000   0.000   0.000   1.000;
talairached surfaceRAS to surfaceRAS: 
 0.906  -0.013   0.002  -4.519;
 0.028   0.939  -0.051   14.976;
-0.012   0.007   0.854  -1.320;
 0.000   0.000   0.000   1.000;
volume geometry:
extent  : (256, 256, 256)
voxel   : ( 1.,  1.,  1.)
x_(ras) : (-1.,  0.,  0.)
y_(ras) : ( 0.,  0., -1.)
z_(ras) : ( 0.,  1.,  0.)
c_(ras) : ( 0.5078,  2.0802, 23.0431)


On lh.pial-outer-smoothed:

talairch.xfm: 
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
surfaceRAS to talaraiched surfaceRAS: 
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
talairached surfaceRAS to surfaceRAS: 
 0.906  -0.013   0.002  -4.011;
 0.028   0.939  -0.051   17.057;
-0.012   0.007   0.854   21.723;
 0.000   0.000   0.000   1.000;
volume geometry info is either not contained or not
valid.

---

I highlight that last bit because maybe it's
important? Looks like some
information goes missing in there...

Chris



On Thu, Dec 10, 2015 at 10:27 AM, Bruce Fischl

wrote:
      Hi Chris

      how do you smooth the surface? Are you sure
that you retain the
      surface
      header information? Try looking at the header
with mris_info
      before and
      after smoothing

      cheers
      Bruce
      On Thu, 10 Dec 2015, Chris Holdgraf wrote:

      > Hey Freesurfer folks - I'm looking into
using Freesurfer for
      doing electrode
      > reconstruction / co-registration in
electrocorticography.
      We're making good
      > progress on figuring out recon-all for
surfaces and doing
      co-registration to
      > CTs. However, I think I've encountered a
strange bug.
      > I'm trying to create a smoothed pial surface
so that I project
      electrodes
      > onto this surface. The code seems to run
correctly, however,
      the smoothed
      > surface looks translated relative to the
original pial surface
      that it was
      > created from.
      >
      > For example, see this issue I opened on
github:
      >
      > https://github.com/aestrivex/gselu/issues/7
      >
      > Anyone have an idea why this is happening?
I'm not sure why
      

[Freesurfer] reg-feat2anat error ("mri_convert ERROR: could not determine file")

[Emily Coffey]

Hello,

I am having a similar problem to that posted several times previously. I 
get an error when running reg-feat2anat to register FSL feat files to 
the freesurfer reconstruction, see:

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-June/038437.html

because the 
subjectsfeatfolder.feat/reg/freesurfer/tmp/refvol.fslregister.nii file 
does not seem to make itself.

I'm wondering where I can find an active link to an updated 
reg-feat2anat, as all the links I find in threads are not working.

I did find a potential workaround: if I create the /mri/tmp directory 
and convert the .mgz file from the freesurfer output to .nii here, as 
explained on this website 
(http://wikis.la.utexas.edu/imagelab/book/how-convert-mgz-structural-files-nii-structural-files)
 
I can create the missing nii file and rerun the registration, however, 
I'm uncertain about the orientation parameters as although the 
orientation of the nii matches that of my original T1, the resulting 
registration in freesurer is nonsense.

Example of the command I am using to manually convert the .mgz to nii:

mri_convert --in_type mgz --out_type nii 
subjectsfreesurferfolder/mri/brainmask.mgz --out_orientation RAS 
subjectsfeatfolder.feat/reg/freesurfer/tmp/refvol.fslregister.nii


Any suggestions on either the updated file location or the workaround 
much appreciated!


Notes:

I am running this version of FreeSurfer:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
On Linux: Ubuntu 12.04.5 LTS

Emily
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Re: [Freesurfer] Shifted surface after gyrification index is calculated

[Chris Holdgraf]

It's a cluster running Linux CentOS 64-bit. If it's as simple as getting
the file and adding it to my path I'm happy to give it a try...

Chris

On Thu, Dec 10, 2015 at 1:47 PM, Bruce Fischl 
wrote:

> what hardware are you running on? We can send you a version of
> mris_copy_header. Or you can can send me the two surfaces (before and after
> smoothing) and I can see if it fixes the problem
>
> cheers
> Bruce
> On Thu, 10 Dec 2015, Chris Holdgraf wrote:
>
> Yep - sorry, here's apic:
>> https://cloud.githubusercontent.com/assets/1839645/11702154/263fb152-9
>> e89-11e5-8485-dc97c8ca2ca7.png
>> You can see the smoothed version is shifted lower.
>>
>> I couldn't find mris_copy_header on my path. Is it only included in the
>> beta
>> version? I'm running 5.3. Could try beta as well, just not sure how stable
>> it is...
>>
>> On Thu, Dec 10, 2015 at 12:38 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   and how do you determine they are shifted? In freeview? The
>>   surface geometry/position should be preserved in the smoothing
>>   but appears to not to be. Perhaps Marie can comment? Or you can
>>   try mris_copy_header to see if that does the trick
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Thu, 10 Dec 2015, Chris Holdgraf wrote:
>>
>> Hey Bruce - thus far I have used pretty default
>> parameters. I first ran
>> recon-all on each subject, then simply ran
>> `recon-all -s s_name -localGI`.
>> Here are the transforms for the original vs.
>> inflated surface
>>
>> On lh.pial:
>> talairch.xfm:
>>  1.103   0.015  -0.002   4.202;
>> -0.032   1.064   0.063  -19.651;
>>  0.015  -0.008   1.170  -25.227;
>>  0.000   0.000   0.000   1.000;
>> surfaceRAS to talaraiched surfaceRAS:
>>  1.103   0.015  -0.002   4.752;
>> -0.032   1.064   0.063  -15.999;
>>  0.015  -0.008   1.170   1.733;
>>  0.000   0.000   0.000   1.000;
>> talairached surfaceRAS to surfaceRAS:
>>  0.906  -0.013   0.002  -4.519;
>>  0.028   0.939  -0.051   14.976;
>> -0.012   0.007   0.854  -1.320;
>>  0.000   0.000   0.000   1.000;
>> volume geometry:
>> extent  : (256, 256, 256)
>> voxel   : ( 1.,  1.,  1.)
>> x_(ras) : (-1.,  0.,  0.)
>> y_(ras) : ( 0.,  0., -1.)
>> z_(ras) : ( 0.,  1.,  0.)
>> c_(ras) : ( 0.5078,  2.0802, 23.0431)
>>
>>
>> On lh.pial-outer-smoothed:
>>
>> talairch.xfm:
>>  1.103   0.015  -0.002   4.202;
>> -0.032   1.064   0.063  -19.651;
>>  0.015  -0.008   1.170  -25.227;
>>  0.000   0.000   0.000   1.000;
>> surfaceRAS to talaraiched surfaceRAS:
>>  1.103   0.015  -0.002   4.202;
>> -0.032   1.064   0.063  -19.651;
>>  0.015  -0.008   1.170  -25.227;
>>  0.000   0.000   0.000   1.000;
>> talairached surfaceRAS to surfaceRAS:
>>  0.906  -0.013   0.002  -4.011;
>>  0.028   0.939  -0.051   17.057;
>> -0.012   0.007   0.854   21.723;
>>  0.000   0.000   0.000   1.000;
>> volume geometry info is either not contained or not
>> valid.
>>
>> ---
>>
>> I highlight that last bit because maybe it's
>> important? Looks like some
>> information goes missing in there...
>>
>> Chris
>>
>>
>>
>> On Thu, Dec 10, 2015 at 10:27 AM, Bruce Fischl
>> 
>> wrote:
>>   Hi Chris
>>
>>   how do you smooth the surface? Are you sure
>> that you retain the
>>   surface
>>   header information? Try looking at the header
>> with mris_info
>>   before and
>>   after smoothing
>>
>>   cheers
>>   Bruce
>>   On Thu, 10 Dec 2015, Chris Holdgraf wrote:
>>
>>   > Hey Freesurfer folks - I'm looking into
>> using Freesurfer for
>>   doing electrode
>>   > reconstruction / co-registration in
>> electrocorticography.
>>   We're making good
>>   > progress on figuring out recon-all for
>> surfaces and doing
>>   co-registration to
>>   > CTs. However, I think I've encountered a
>> strange bug.
>>   > I'm trying to create a smoothed pial surface
>> so that I project
>>   electrodes
>>   > onto this 

[Freesurfer] Gray matter intensity

[Sabrina Yu]

Hello,



I have been following the instructions in this email thread: 
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html.
 And have successfully gotten the wm-gm signal intensity contrast, but now have 
a few questions regarding signal intensity for white matter and gray matter 
intensity.


1) Does the wmparc.stats contain mean white matter intensity values for each 
ROI?

2) Is it possible to extract these same mean intensity values for gray matter? 
There is no gmparc.stats file. We know that it's possible to calculate these 
from the WM/GM ratio from pctsurfcon, but it'd be great if there was a more 
direct way to get this data.


Thank you,

Sabrina Yu
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[Freesurfer] Question about running recon-all with deface

[Mishra, Virendra]

Hello,

We are currently in the process of analyzing some data that was defaced using 
mri_deface command of freesurfer. This defaced data was then used as an input 
to recon-all and the volume and thickness was computed. These results were then 
compared against the same subject's recon-all with the face but with and 
without the deface flag within recon-all. All of the steps were done on version 
5.3.0. We have got some differences and we are unable to explain why. Some of 
the regions have error greater than 20% when the input was a defaced brain. We 
would appreciate if you could advise as to how to approach to the same results 
as we were running the data with the face .

To summarize: (The commands are not precise below but we ensured the commands 
are run correctly per the command help)

1)  Step 1: mri_deface -i original_T1 -o deface_T1

2)  Step 2: recon-all -i deface_T1

3)  Step 3: recon-all -i original_T1 -deface

4)  Step 4: recon-all -i original_T1

5)  The results from Step 3 is exactly equal to Step 4

6)  The results from Step 2 and Step3/4 have errors >20% in certain regions.

7)  Step 1-4 are done with version 5.3.0

Any response will be greatly appreciated.

Thanks

Regards

Virendra

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[Freesurfer] Freeview PETSC Error

[Udunna Anazodo]

Hi,

I downloaded and installed Freesurfer stable release 5.3 distribution 
linux_centos4_x86_64 on an Ubuntu 12.04 system. However freeview crashes 
with a PETSC error. I read the freesurfer archives and followed the 
instructions found on 
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-November/041243.html.
 
I downloaded the most recent version of freeview.bin using wget as 
suggested but I still get the same error message. Any ideas how to work 
around this. Thanks

[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 udunna-work by udunna 
Thu Dec 10 17:42:30 2015
[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

-- 
Udunna
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[Freesurfer] Shifted surface after gyrification index is calculated

[Chris Holdgraf]

Hey Freesurfer folks - I'm looking into using Freesurfer for doing
electrode reconstruction / co-registration in electrocorticography. We're
making good progress on figuring out recon-all for surfaces and doing
co-registration to CTs. However, I think I've encountered a strange bug.

I'm trying to create a smoothed pial surface so that I project electrodes
onto this surface. The code seems to run correctly, however, the smoothed
surface looks translated relative to the original pial surface that it was
created from.

For example, see this issue I opened on github:

https://github.com/aestrivex/gselu/issues/7

Anyone have an idea why this is happening? I'm not sure why the pial
surface would be correct, while the smoothed surface would be shifted.

Chris


-- 
_

PhD Candidate in Neuroscience | UC Berkeley 
Editor and Web Director | Berkeley Science Review

_
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Re: [Freesurfer] Shifted surface after gyrification index is calculated

[Bruce Fischl]

Hi Chris

how do you smooth the surface? Are you sure that you retain the surface 
header information? Try looking at the header with mris_info before and 
after smoothing

cheers
Bruce
On Thu, 10 Dec 2015, Chris Holdgraf wrote:

> Hey Freesurfer folks - I'm looking into using Freesurfer for doing electrode
> reconstruction / co-registration in electrocorticography. We're making good
> progress on figuring out recon-all for surfaces and doing co-registration to
> CTs. However, I think I've encountered a strange bug.
> I'm trying to create a smoothed pial surface so that I project electrodes
> onto this surface. The code seems to run correctly, however, the smoothed
> surface looks translated relative to the original pial surface that it was
> created from.
> 
> For example, see this issue I opened on github:
> 
> https://github.com/aestrivex/gselu/issues/7
> 
> Anyone have an idea why this is happening? I'm not sure why the pial surface
> would be correct, while the smoothed surface would be shifted.
> 
> Chris
> 
> 
> --
> _
> 
> PhD Candidate in Neuroscience | UC Berkeley
> Editor and Web Director | Berkeley Science Review
> _
> 
>
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Re: [Freesurfer] Individual regions of CorticalParcellation_Yeo2011

[Parker, Richard]

Hi Professor Yeo,

Thanks for providing a link to your split region MNI space files.

Could you please advise on how to get these labels into subject native space?

If using the standard version of the network labels that comes packaged with 
Freesurfer 5.3.0, I can get the annotation file into native space quite easily 
with the following command:


mri_surf2surf --srcsubject fsaverage --trgsubject $SUBJECT_NAME --hemi lh 
--sval-annot 
$FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot 
--tval $SUBJECT_NAME/label/lh.Yeo2011_17Networks_N1000.annot

However, in the dropbox link you posted, it doesn't seem that there is a .annot 
file compatible with fsaverage. The fsaverage5 version is present, but if I try 
slotting the fsaverage5 .annot file into the above call to mri_surf2surf, I get 
disastrous results.

Do you perhaps have a .annot file for the upsampled (and split) network labels? 
Or perhaps there's an easier way to achieve what I'm after. I notice that you 
have provided a .nii file for the network ROIs that is in the same space as 
fsaverage, perhaps this file can be warped to native space somehow?

Best wishes,

Richard Parker
King's College London








Hi Erica,



You can try this link:

https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_SplitLabels.zip



Regards,

Thomas



On Wed, Oct 7, 2015 at 2:45 AM, Yi-Chia Erica Kung  wrote:

> Dear Prof. Yeo,

>

> I would like to extract the brain regions of the functional canonical

> network, such as DMN, SAL, or CEN, withFreesurfer. And I found that you have

> provided the split regions of 7&17 Network in previous discussion string.

> (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41288.html

>  )

>

> However, the dropbox download link you offered has expired.

> Would you mind uploading it again?

>

> Thank you very much.

>

> Erica

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Re: [Freesurfer] Recon-all get stucked without error during processing

[Matthieu Vanhoutte]

Hi Bruce,

Do you have an idea of how to solve this problem of skull stripping (below)
?

Best regards,
Matthieu

2015-12-09 16:25 GMT+01:00 Matthieu Vanhoutte :

> Hi Bruce,
>
> In fact T1.mgz is ok, but the skull stripping failed and seemed to have
> taken only the jawbone and the neck.
>
> Best regards,
> Matthieu
>
>
> 2015-12-09 16:16 GMT+01:00 Bruce Fischl :
>
>> Hi Matthieu
>>
>> you need to track backwards and see where the problem started. Why is the
>> norm warped? Actaully, it shouldn't be warped, although it might be
>> truncated if the skull stripping failed.
>>
>>
>> cheers
>> Bruce
>> On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote:
>>
>> Hi Bruce,
>>>
>>> Indeed norm.mgz isn't empty but doesn't look well (truncated and warped).
>>>
>>> Is this bug fixed in the v6 beta release ?
>>>
>>> If this is the case :
>>> 1) Would you advise me to try on the v6 ?
>>> 2) Should I so relaunch all recon-all process on my subjects computed
>>> with v5.3  and work only with the v6 beta ?
>>>
>>> Best regards,
>>> Matthieu
>>>
>>> 2015-12-09 15:55 GMT+01:00 Bruce Fischl :
>>>   Hi Matthieu
>>>
>>>   this might be a bug that is fixed in 6.0. Can you cehck the input
>>> to
>>>   mri_cc (norm.mgz) and make sure it is not empty? In older versions
>>> if the
>>>   skull stripping failed and generated an empty
>>>   norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang.
>>>
>>>   cheers
>>>   Bruce
>>>
>>>   On Wed, 9 Dec 2015,
>>>   Matthieu Vanhoutte wrote:
>>>
>>>   > Dear FS epxerts,
>>>   >
>>>   > I have launched a recon-all process on a subject. Unfortunately,
>>> I tried two times but the process get stucked at
>>>   the same step
>>>   > without error.
>>>   >
>>>   > Please found the recon-all.log associated attached to this mail.
>>>   >
>>>   > Thanks in advance for helping !
>>>   >
>>>   > Best regards,
>>>   > Matthieu
>>>   >
>>>   >
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Re: [Freesurfer] Shifted surface after gyrification index is calculated

[Chris Holdgraf]

Hey Bruce - thus far I have used pretty default parameters. I first ran
recon-all on each subject, then simply ran `recon-all -s s_name -localGI`.

Here are the transforms for the original vs. inflated surface

On lh.pial:
talairch.xfm:
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
surfaceRAS to talaraiched surfaceRAS:
 1.103   0.015  -0.002   4.752;
-0.032   1.064   0.063  -15.999;
 0.015  -0.008   1.170   1.733;
 0.000   0.000   0.000   1.000;
talairached surfaceRAS to surfaceRAS:
 0.906  -0.013   0.002  -4.519;
 0.028   0.939  -0.051   14.976;
-0.012   0.007   0.854  -1.320;
 0.000   0.000   0.000   1.000;
volume geometry:
extent  : (256, 256, 256)
voxel   : ( 1.,  1.,  1.)
x_(ras) : (-1.,  0.,  0.)
y_(ras) : ( 0.,  0., -1.)
z_(ras) : ( 0.,  1.,  0.)
c_(ras) : ( 0.5078,  2.0802, 23.0431)


On lh.pial-outer-smoothed:

talairch.xfm:
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
surfaceRAS to talaraiched surfaceRAS:
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
talairached surfaceRAS to surfaceRAS:
 0.906  -0.013   0.002  -4.011;
 0.028   0.939  -0.051   17.057;
-0.012   0.007   0.854   21.723;
 0.000   0.000   0.000   1.000;
*volume geometry info is either not contained or not valid.*

---

I highlight that last bit because maybe it's important? Looks like some
information goes missing in there...

Chris



On Thu, Dec 10, 2015 at 10:27 AM, Bruce Fischl 
wrote:

> Hi Chris
>
> how do you smooth the surface? Are you sure that you retain the surface
> header information? Try looking at the header with mris_info before and
> after smoothing
>
> cheers
> Bruce
> On Thu, 10 Dec 2015, Chris Holdgraf wrote:
>
> > Hey Freesurfer folks - I'm looking into using Freesurfer for doing
> electrode
> > reconstruction / co-registration in electrocorticography. We're making
> good
> > progress on figuring out recon-all for surfaces and doing
> co-registration to
> > CTs. However, I think I've encountered a strange bug.
> > I'm trying to create a smoothed pial surface so that I project electrodes
> > onto this surface. The code seems to run correctly, however, the smoothed
> > surface looks translated relative to the original pial surface that it
> was
> > created from.
> >
> > For example, see this issue I opened on github:
> >
> > https://github.com/aestrivex/gselu/issues/7
> >
> > Anyone have an idea why this is happening? I'm not sure why the pial
> surface
> > would be correct, while the smoothed surface would be shifted.
> >
> > Chris
> >
> >
> > --
> > _
> >
> > PhD Candidate in Neuroscience | UC Berkeley
> > Editor and Web Director | Berkeley Science Review
> > _
> >
> >
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-- 
_

PhD Candidate in Neuroscience | UC Berkeley 
Editor and Web Director | Berkeley Science Review

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[Freesurfer] summary files and figures from Monte Carlo simulation

[Karl Liu]

Dear Experts,


After running  Monte Carlo simulation from the command line,
I noticed two cluster summary files are produced for each contrast:  
cache.th20.neg.sig.cluster.summary and mc-z.neg.th20.sig.cluster.summary.
They are quite similar, with different number of surviving clusters in some
cases. I am wondering which is the one to report final results. Will you
explain a bit more about the differences between them?


Also, after reading the summary
file, we still have to visualize the results. If the MC simulation is done in
QDEC GUI, then the QDEC automatically presents the outcome from 
mc-z.neg.th20.sig.cluster.mgh,
but I am not sure if this is the right file. I am using FS version 5.3 without
tksurferfv. I found the tksurfer is running quite slow and unresponsive. Any
other suggestions?


Thank you very much!



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[Freesurfer] Qdec question

[sabin khadka]

Hi all - When you get a significant cluster after doing monte-carlo simulation, 
we get peak vertex/Talairach coordinates and also saved in *summary files. Is 
there a way to find all the parcellated regions (Desikan, or, Destriuex) in the 
significant clusters?

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Re: [Freesurfer] FreeSurfer 6 recon-all exiting with errors at -cortparc step

[Zaretskaya, Natalia]

Hi Bruce,

I re-ran the -cortparc step with the current dev version
freesurfer-Linux-centos6_x86_64-dev-20151209

It took ~6 hours and the error is still the same. It seems to run through the 
left hemisphere, but crashes on the right one.

Cheers!
Natalia

On 09 Dec 2015, at 14:37, Bruce Fischl 
> wrote:

HI Natalia

can you try the dev version? I'm pretty sure I fixed this. You can just rerun 
mris_ca_label. We'll hopefully be cutting a new stable 6 sometime soon

cheers
Bruce


On Wed, 9 Dec 2015, Zaretskaya, Natalia wrote:

Dear all,
I am running recon-all with FreeSurfer 6 stable version on launchpad and
have it exiting with errors with all of my 43 brains, always at the same
stage (-cortparc). The same brains used to run through recon-all smoothly
with the dev version just a month or so ago, and I am not doing anything
essentially different than before, except using FreeSurfer 6, so I am
wondering what’s wrong. The output of recon-all before the error looks o.k.
I attached an example recon-all.log file.
Many thanks in advance for your help!
Natalia
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