Re: [Freesurfer] Hippocampal Segmentation

[Iglesias Gonzalez, Eugenio]

Hi Jessica,
I believe that those are the old labels. What version of FreeSurfer are you 
using? 5.1 - 5.3? If so, you should upgrade to 6.0.
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 24 Feb 2017, at 19:18, Jessica Sevick 
> wrote:

Hello FreeSurfer Team ,

I was wondering if you could explain to me what the “Left-Hippocampus” and 
“Right-Hippocampus” labels in the subfield segmentation are? Are they the tail 
of the hippocampi? Or everything that is not assigned to one of the other seven 
labels?

Additionally I am wondering how the hippocampal subfields are ordered in terms 
of their determination? Is it a particular order or is it randomized?

Thanks,

Jessica Sevick
MRI Research Assistant
Seaman Family MR Research Centre
T: 403.944.8652
C: 587.576.
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Re: [Freesurfer] Disastrous Soft Error

[Rockers, Elijah D.]

OK, sorry for spamming the list. I fixed the the faulty skullstrip by using

recon-all -skullstrip -clean-bm -no-wsgcaatlas -subjid 

Currently redoing the surface reconstructions, but it should be OK now.
Thanks for the nice documentation.
Eli


On Fri, 2017-02-24 at 15:30 -0600, Elijah Rockers wrote:


As far as I can tell, everything looks OK up until brainmask.mgz. The
skullstrip step seems to have cropped out the brain and left the neck...

On Fri, 2017-02-24 at 12:58 -0600, Elijah Rockers wrote:
> Hello all,
>
> I recon-all'd ~40 different subjects. I have been going through all the
> images to make sure they were processed correctly. Most required no no
> editing and recon-all did a very good job.
>
> But for one scan in particular, it looks like Freesurfer thinks the top
> of the spinal cord is the brain. Several vertebrae are very nicely
> segmented... :P
>
> Just wondering if you have any suggestions for reprocessing this
> subject? The error is reproducible with default recon-all settings.
>
> Subject has some pathology in the white matter which might be causing
> the problem?
>
> Screenshot of T1.mgz + lh.pial at the following link:
> http://imgur.com/a/uwyaq
>
> Thanks,
> Eli




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Re: [Freesurfer] Disastrous Soft Error

[Rockers, Elijah D.]

As far as I can tell, everything looks OK up until brainmask.mgz. The
skullstrip step seems to have cropped out the brain and left the neck...

On Fri, 2017-02-24 at 12:58 -0600, Elijah Rockers wrote:
> Hello all,
> 
> I recon-all'd ~40 different subjects. I have been going through all the
> images to make sure they were processed correctly. Most required no no
> editing and recon-all did a very good job.
> 
> But for one scan in particular, it looks like Freesurfer thinks the top
> of the spinal cord is the brain. Several vertebrae are very nicely
> segmented... :P
> 
> Just wondering if you have any suggestions for reprocessing this
> subject? The error is reproducible with default recon-all settings.
> 
> Subject has some pathology in the white matter which might be causing
> the problem?
> 
> Screenshot of T1.mgz + lh.pial at the following link:
> http://imgur.com/a/uwyaq
> 
> Thanks,
> Eli


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nation’s top 20 hospitals, placing it for the second time on the magazine’s 
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[Freesurfer] make average subject

[Limachia, Gaurang (NIH/NINDS) [F]]

Hello Freesurfer Experts,

I received this error while running the make_avg_subject script. I would 
greatly appreciate it if you can point me in the right direction.

Also, I do not know how the aparc.annot file is supposed to be created.

not aligning hemispheres before averaging.
zeroing medial wall in aparc
creating new parameterization...

processing subject CON_201 (1 of 98)
reading spherical surface 
/raids/hmcsraid3/silvina/PMD_FATCAT2015/CON_201/surf/lh.sphere.reg...
could not read annot file 
/raids/hmcsraid3/silvina/PMD_FATCAT2015/CON_201/surf/../label/lh.aparc.annot
No such file or directory
mris_make_template: could not read annot file aparc
No such file or directory
ERROR: make_average_surface


Thanks,

Gaurang Shyam Limachia

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[Freesurfer] Hippocampal Segmentation

[Jessica Sevick]

Hello FreeSurfer Team ,

I was wondering if you could explain to me what the “Left-Hippocampus” and 
“Right-Hippocampus” labels in the subfield segmentation are? Are they the tail 
of the hippocampi? Or everything that is not assigned to one of the other seven 
labels?

Additionally I am wondering how the hippocampal subfields are ordered in terms 
of their determination? Is it a particular order or is it randomized?

Thanks,

Jessica Sevick
MRI Research Assistant
Seaman Family MR Research Centre
T: 403.944.8652
C: 587.576.
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[Freesurfer] Disastrous Soft Error

[Rockers, Elijah D.]

Hello all,

I recon-all'd ~40 different subjects. I have been going through all the
images to make sure they were processed correctly. Most required no no
editing and recon-all did a very good job.

But for one scan in particular, it looks like Freesurfer thinks the top
of the spinal cord is the brain. Several vertebrae are very nicely
segmented... :P

Just wondering if you have any suggestions for reprocessing this
subject? The error is reproducible with default recon-all settings.

Subject has some pathology in the white matter which might be causing
the problem?

Screenshot of T1.mgz + lh.pial at the following link:
http://imgur.com/a/uwyaq

Thanks,
Eli

Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
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privileged material for the sole use of the intended recipient(s). Any review, 
use, distribution or disclosure by others is strictly prohibited. If you are 
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[Freesurfer] XL defect detected

[Shane Schofield]

Hi Freesurfer Team,

I am running recon-all on Freesurfer version 6. A few of my subjects have “XL 
defect detected …” and their recon-all have been running for more than 20 
hours. I hope this is not a silly question, but will this XL defect be 
corrected eventually…? 

Another question, what are “defects”? Is there anything I could do to the raw 
T1 before recon-all?

Thanks!

Shane

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[Freesurfer] TRACULA and priors problem

[Juergen Haenggi]

Dear TRACULA experts

I run TRACULA FS 6.0 on a Mac and get the following error:

#@# Priors Fri Feb 24 17:11:18 CET 2017
/tmp/subj33.interpreter_control_01/.15208.txt: No such file or directory.


In the FS archive I found the following email

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50778.html

However, in my situation, the directories of the FS preprocessed subjects are 
in /Applications/freesurfer/subjects folder, and therefore to solution proposed 
in the email (make symbolic links) does not make sense for me.

Is there another work around?

Thanks in advance
Regards
Jürgen

-
University of Zurich
Dr. Jürgen Hänggi, Ph.D.
Department of Psychology
Division Neuropsychology
Binzmuehlestrasse 14, PO Box 25 
8050 Zurich, Switzerland

0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)   
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Re: [Freesurfer] recon-all error (6.0)

[Trisanna Sprung-Much]

Hi Bruce

I tried and still get the same error. Would this mean a space issue? I'm
not sure how this is possible as I'm working off a 2Tb drive

trisanna@kaplan:~$ mri_convert ./tmp.mri_nu_correct.mni.1798/nu1.mnc
orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.1798/nu1.mnc orig_nu.mgz --like
orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.1798/nu1.mnc...
mincRead(): can't find file ./tmp.mri_nu_correct.mni.1798/nu1.mnc


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Feb 24, 2017 at 9:45 AM, Bruce Fischl 
wrote:

> Hi Trisanna
>
> are you  sure you aren't running out of disk space? If not, what happens
> when you run the mri_convert command directly on the command line?
>
> cheers
> Bruce
> On Thu, 23 Feb 2017,
> Trisanna Sprung-Much wrote:
>
> > Hi All
> >
> > I am trying to run a subject in 6.0 (it ran perfectly well in 5.3) and
> it stops when
> > trying to transform to the "conformed" space. I get the following error
> after about a
> > minute. I have not seen this error before.
> >
> > mri_convert ./tmp.mri_nu_correct.mni.2860/nu1.mnc orig_nu.mgz --like
> orig.mgz
> > --conform
> > mri_convert.bin ./tmp.mri_nu_correct.mni.2860/nu1.mnc orig_nu.mgz
> --like orig.mgz
> > --conform
> > ncopen: filename "./tmp.mri_nu_correct.mni.2860/nu1.mnc": Not a netCDF
> file
> > miopen: MINC package entry point
> > Error opening ./tmp.mri_nu_correct.mni.2860/nu1.mnc
> > mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.2860/
> nu1.mnc
> > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> > reading from ./tmp.mri_nu_correct.mni.2860/nu1.mnc...
> > Linux kaplan 3.13.0-105-generic #152-Ubuntu SMP Fri Dec 2 15:37:11 UTC
> 2016 x86_64
> > x86_64 x86_64 GNU/Linux
> >
> > recon-all -s icbm-131 exited with ERRORS at Thu Feb 23 11:40:53 EST 2017
> >
> > To report a problem, see http://surfer.nmr.mgh.harvard.
> edu/fswiki/BugReporting
> >
> >
> > Any ideas?
> >
> > Best
> >
> > Trisanna
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> >
> >
> >
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Re: [Freesurfer] Mindboggle official software release and publication!

[Arno Klein]

Great question!  You can certainly run Mindboggle on FreeSurfer output for
earlier versions of FreeSurfer.  In fact, we did this for part of the work
described in the PLoS Computational Biology article:

"For this study we used FreeSurfer v5.1-derived labels and meshes, but the
recently released FreeSurfer version 6 is recommended because it uses
Mindboggle’s DKT-100 surface-based atlas (with the DKT31 labeling protocol)
by default to generate labels on the cortical surfaces, and generates
corresponding labeled cortical and non-cortical volumes (wmparc.mgz) [75

]."

I am certain you can run a FreeSurfer command to update the cortical labels
to be in accord with the DKT-31 labeling protocol (
http://journal.frontiersin.org/article/10.3389/fnins.2012.00171/full) and
the new DKT-100 atlas used in FreeSurfer.  I will leave it to others on
this list who have greater FreeSurfer expertise than I to recommend the
appropriate command.

Cheers,
Arno

On Fri, Feb 24, 2017 at 6:55 AM Ritobrato Datta 
wrote:

> Hi Arno,
>
> This is fascinating stuff. In my research, I have come across instances
> when I felt that a hybrid of ANTS and freesurfer would be very useful. Is
> this pipeline possible for data processed with the earlier versions of
> freesurfer say 5.1 ? FS6 just got released in Jan 2017 and I am sure for
> most ongoing studies, the data have already been processed in earlier
> versions of freesurfer.
>
> If there is a patch or script to update the data processed using earlier
> versions of freesurfer, that will save a lot of time than running
> everything from scratch in FS6.
>
> Please let us know.
>
> Best
>
> Rito
>
> - Original Message -
> From: Arno Klein 
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Thu, 23 Feb 2017 20:37:44 -0500 (EST)
> Subject: [Freesurfer] Mindboggle official software release and publication!
>
> Announcing the official release of Mindboggle (http://mindboggle.info),
> open source software  and data
>  for analyzing the shapes of brain structures from
> human MRI data (processed through FreeSurfer and optionally through ANTs).
> The release coincides with a publication in PLoS Computational Biology that
> documents and evaluates the software:
>
> Klein A, Ghosh SS, Bao FS, Giard J, Hame Y, Stavsky E, Lee N, Rossa B,
> Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human
> brains. PLoS Computational Biology 13(3): e1005350.
> doi:10.1371/journal.pcbi.1005350
> 
>
> Cheers,
> @rno
>
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Re: [Freesurfer] Intensity information of Hippocampal Subfields

[Douglas N Greve]

The basic command is

mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz

where seg is the hippo sub field seg and input is the input where you 
want to get the intensities from (probably norm.mgz). Note that you need 
to use the hipp sub field output that is 1mm (not the high res one)


On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote:
> Dear FreeSurfer Experts,
> I want to compute some intensity information (e.g., mean and std) of each 
> Hippocampal subfields (similar to aseg.stats file).
> I think one option could be mri_segstats command, but I am not sure.
> If it works, what are the inputs of this command?
>
> Thank you in advance for any help.
> Alireza
>
>
>
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>

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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] mri_segstats

[Douglas N Greve]

That is everything that has a segmentation number = 0. You can exclude 
it with, --excludeid 0


On 02/24/2017 10:08 AM, John Anderson wrote:
> Dear Freesurfer experts,
> I have used the following commandline to generate the final statistics 
> in my analysis:
> mri_segstats --seg aseg.mgz  --ctab-default --i suvr.nii --mask 
> mask.nii --sum stats.dat
>
> The final output of this command is (attached). Depedning on 
> the anatomical location of the mask, I expect that I will get two 
> structures in the stats file. What is the "unknown" label means? is it 
> CSF? Do I need to include it in my next statistcal analses?
>
> I highly appreciate your input!
>
> Best,
> John
>
>
> Sent with ProtonMail  Secure Email.
>
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Mindboggle official software release and publication!

[Olivier Coulon]

Thanks to Docker, you can run it on a mac, it's all explained on the 
Mindboggle website.


Olivier

Shane Schofield a écrit :

Hello,

Thanks. Seems very interesting!
Is there any way to run this on Mac?

Cheers


--
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[Freesurfer] mri_segstats

[John Anderson]

Dear Freesurfer experts,

I have used the following commandline to generate the final statistics in my 
analysis:
mri_segstats --seg aseg.mgz --ctab-default --i suvr.nii --mask mask.nii --sum 
stats.dat

The final output of this command is (attached). Depedning on the anatomical 
location of the mask, I expect that I will get two structures in the stats 
file. What is the "unknown" label means? is it CSF? Do I need to include it in 
my next statistcal analses?

I highly appreciate your input!


Best,
John



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[Freesurfer] Intensity information of Hippocampal Subfields

[ali reza mohammadi nejad]

Dear FreeSurfer Experts,
I want to compute some intensity information (e.g., mean and std) of each 
Hippocampal subfields (similar to aseg.stats file).
I think one option could be mri_segstats command, but I am not sure. 
If it works, what are the inputs of this command?

Thank you in advance for any help.
Alireza



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Re: [Freesurfer] Segmentation question

[Bruce Fischl]

HI Yusif

you can read our 1999 paper (Anders Dale first author) for the basics, 
although it has evolved considerably since then

cheers
Bruce
On Thu, 23 Feb 2017, yusif 
Al-kheder wrote:

> Hello,
> I was wondering how does Freesurfer segment the white matter from the grey 
> matter.
>
>
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Re: [Freesurfer] recon-all error (6.0)

[Bruce Fischl]

Hi Trisanna

are you  sure you aren't running out of disk space? If not, what happens 
when you run the mri_convert command directly on the command line?

cheers
Bruce
On Thu, 23 Feb 2017, 
Trisanna Sprung-Much wrote:

> Hi All
> 
> I am trying to run a subject in 6.0 (it ran perfectly well in 5.3) and it 
> stops when
> trying to transform to the "conformed" space. I get the following error after 
> about a
> minute. I have not seen this error before.
> 
> mri_convert ./tmp.mri_nu_correct.mni.2860/nu1.mnc orig_nu.mgz --like orig.mgz
> --conform
> mri_convert.bin ./tmp.mri_nu_correct.mni.2860/nu1.mnc orig_nu.mgz --like 
> orig.mgz
> --conform
> ncopen: filename "./tmp.mri_nu_correct.mni.2860/nu1.mnc": Not a netCDF file
> miopen: MINC package entry point
> Error opening ./tmp.mri_nu_correct.mni.2860/nu1.mnc
> mincRead(): error reading volume from file 
> ./tmp.mri_nu_correct.mni.2860/nu1.mnc
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from ./tmp.mri_nu_correct.mni.2860/nu1.mnc...
> Linux kaplan 3.13.0-105-generic #152-Ubuntu SMP Fri Dec 2 15:37:11 UTC 2016 
> x86_64
> x86_64 x86_64 GNU/Linux
> 
> recon-all -s icbm-131 exited with ERRORS at Thu Feb 23 11:40:53 EST 2017
> 
> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> 
> Any ideas?
> 
> Best
> 
> Trisanna
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
> 
> 
>
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Re: [Freesurfer] help error RB_ALL_2008-03-26

[Bruce Fischl]

Hi Flavia

can you send us the reon-all.log and also what version you are trying to 
run?

cheers
Bruce
On Wed, 22 Feb 2017, Flavia Arduini wrote:

> Hi,
> I try tu run this code:
> recon-all -s CAROFILO -i
> /home/matlab/Scrivania/SEGMENTAZIONE/CAROFILO/T2/Phase2/c2scCAROFILO.nii
> -autorecon2-wm
> but compare this error
> ERROR: cannot find /usr/local/freesurfer/average/RB_all_2008-03-26.gca
> How can I fix this problem?
> 
> Thanks
> 
> Flavia Arduini
> 
> 
>
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Re: [Freesurfer] Virtualbox for FS v6.0 ?

[Z K]

Based on the subtle issues that arose with previous releases of VirtualBox FS 
images, it was decided that a better solution was to simply have users install 
a Linux VirtualBox image themselves (e.g. Ubuntu 16) and let them install the 
Linux release of FS in that image. This is a much more flexible solution. 

> On Feb 23, 2017, at 9:33 AM, Randolph Andrews  wrote:
> 
> In past releases of FreeSurfer, there had been a version of the software 
> suite contained in a VirtualBox (alongside the MacOS and Linux versions).  
> Currently, I only see Mac & Linux.  Is there a plan to release a VirtualBox 
> edition of 6.0 ?
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Re: [Freesurfer] mri_binarize --gm

[Douglas Greve]

try making it executable,

chmod a+x mri_binarize

then run rehash and see if it work


On 2/24/17 12:13 AM, Jinsong Tang wrote:

Dear all,

I am trying to run a mri_binarize command on FS 5.3

   mri_binarize --i aparc+aseg.mgz --gm --o gmmask.mgz
   I obtain this:
ERROR: Option –gm unknown

I found there was a previous post suggest to use the new mri_binarize from
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize

I download this one, and replace the old one with this new one.

however, I obtian this:
mri_binarize : command  not found.

How to fix this?

Thanks and best,

Jinsong


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Re: [Freesurfer] Mindboggle official software release and publication!

[Shane Schofield]

Hello, 

Thanks. Seems very interesting! 
 
Is there any way to run this on Mac? 

Cheers 


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Re: [Freesurfer] Mindboggle official software release and publication!

[Ritobrato Datta]

Hi Arno,

This is fascinating stuff. In my research, I have come across instances when I 
felt that a hybrid of ANTS and freesurfer would be very useful. Is this 
pipeline possible for data processed with the earlier versions of freesurfer 
say 5.1 ? FS6 just got released in Jan 2017 and I am sure for most ongoing 
studies, the data have already been processed in earlier versions of 
freesurfer. 

If there is a patch or script to update the data processed using earlier 
versions of freesurfer, that will save a lot of time than running everything 
from scratch in FS6. 

Please let us know. 

Best

Rito
 
- Original Message -
From: Arno Klein 
To: freesurfer@nmr.mgh.harvard.edu
Sent: Thu, 23 Feb 2017 20:37:44 -0500 (EST)
Subject: [Freesurfer] Mindboggle official software release and publication!

Announcing the official release of Mindboggle (http://mindboggle.info),
open source software  and data
 for analyzing the shapes of brain structures from
human MRI data (processed through FreeSurfer and optionally through ANTs).
The release coincides with a publication in PLoS Computational Biology that
documents and evaluates the software:

Klein A, Ghosh SS, Bao FS, Giard J, Hame Y, Stavsky E, Lee N, Rossa B,
Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human
brains. PLoS Computational Biology 13(3): e1005350.
doi:10.1371/journal.pcbi.1005350


Cheers,
@rno
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Re: [Freesurfer] LGI data for each region?

[Antonin Skoch]

Dear Shane,

use this command:

mri_segstats --annot my_subject_id lh aparc --i 
$SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats

Look at the info on FreeSurfer wiki:

https://surfer.nmr.mgh.harvard.edu/fswiki/LGI

Antonin Skoch

Hi Freesurfer,

How can I get the LGI measurements for each brain region in Desikan atlas? 
Instead of getting thickness with aparcstats2table, I want the gyrification 
instead.Thank you.

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[Freesurfer] LGI data for each region?

[Shane Schofield]

Hi Freesurfer,

How can I get the LGI measurements for each brain region in Desikan atlas? 
Instead of getting thickness with aparcstats2table, I want the gyrification 
instead.

Thank you.

Cheers,
Shane

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