Re: [Freesurfer] Error on rawavg

[Bruce Fischl]

Hi Noah
We need the full command you ran, the screen output and the recon-all.log

Cheers
Bruce

> On Nov 3, 2016, at 12:13 AM, Noah Markowitz  wrote:
> 
> Hi all,
> 
> As I’m doing manual edits, one of my subjects stops running due to the 
> following error:
> 
> ERROR: could not read subj1/mri/rawavg.mgz as type 3
> 
> Any ideas how to correct this? Please let me know.
> 
> Noah
> 
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[Freesurfer] Error on rawavg

[Noah Markowitz]

Hi all,

As I’m doing manual edits, one of my subjects stops running due to the 
following error:

ERROR: could not read subj1/mri/rawavg.mgz as type 3

Any ideas how to correct this? Please let me know.

Noah

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Re: [Freesurfer] mri_binarize --gm option unknown

[Douglas N Greve]

try this version

https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize

On 11/02/2016 12:37 PM, HOSSU Gabriela wrote:
>
> Hello everyone,
>
> I am trying to run a mri_binarize command on FS v 5.2, Linux 64bit, 
> but when I use the option —gm (also for –subcort-gm).
>
> I am getting an error that says the —gm option is not recognized.
>
> Here is the command line and the following error (from the mri folder 
> of a subject):
>
> mri_binarize –i aparc+aseg.mgz –gm –o gmmask.mgz
>
> I obtain this:
>
> ERROR: Option –gm unknown
>
> Thanks very much,
>
> Gabriela HOSSU
>
>
>
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-- 
Douglas N. Greve, Ph.D.
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
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] ROI NumVert

[Douglas N Greve]

oh, sorry, it does assume that you have pbsubmit, I had forgotten that. 
You can actually follow the instructions for building your own atlas at 
the bottom of the xhemi web page

http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi

This does the same thing as make_folding_atlas. It takes a long time if 
you don't have a computational cluster to submit it to, which is why I 
wrote make_folding_atlas

doug


On 11/02/2016 01:15 PM, Daya P wrote:
> Hi,
>
> When i try running make_folding_atlas I get
>
> xhemireg Trout2016 Wed Nov  2 13:11:23 EDT 2016
>   #@# xhemireg --s Trout2016
> pbsubmit: Command not found.
> Launched 9 xhemireg processes
> #%# Waiting for 9 xhemireg processes Wed Nov  2 13:11:33 EDT 2016
> #%# Waiting for 9 xhemireg processes Wed Nov  2 13:12:33 EDT 2016
>
> I do not have access to a cluster. is there any way to bypass this?
>
> Thank  you,
>
> Daiana
>
> On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve 
> > wrote:
>
> I've written a script that will come out with version 6, but I've
> put it
> here
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas
> 
>
> I think it should work in 5.3, but I'm not sure. If not, you can
> download the dev version and make the atlas using that. Run it with
> --help to get info on how to run it.
>
>
>
> On 10/28/2016 05:10 PM, Daya P wrote:
> > Hi Doug,
> >
> > I needed to make a registration template and an cortical atlas
> because
> > I am trying to measure cortical thickness, GM and surface area
> on cat
> > brains.
> >
> > What would be the necessary changes?
> > Would it be possible (and appropriate) to use just
> > mris_left_right_register instead?
> >
> > Daiana
> >
> > On Fri, Oct 28, 2016 at 11:34 AM, Douglas Greve
> > 
>  >> wrote:
> >
> > A difference of 10 out of 500 or 1000 does not both me at
> all. Why
> > do you need to create your own atlas? It is doable for the cross
> > hemi stuff, it is just difficult.
> >
> >
> > On 10/26/16 10:16 AM, Daya P wrote:
> >>
> >> Thank you for your help!
> >>
> >> I created a registration template and atlas from scratch
> could I
> >> input that in the interhemispheric registration analysis?
> >>
> >> The ROIs for the diffrerent regions per hemisphere are 50-100
> >> vertices
> >>
> >> On Oct 24, 2016 5:03 PM, "Douglas N Greve"
> >>  
>  >> wrote:
> >>
> >> It would depend on how big the ROI is to begin with. Do you
> >> know that we
> >> have our own interhemispheric analysis that might be better
> >> for this?
> >> Check out
> >>
> >> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
> 
> >>  >
> >>
> >>
> >> On 10/24/2016 12:33 PM, Daya P wrote:
> >> > Hi Bruce,
> >> >
> >> > I drew ROIs on an initial subject and then after
> >> registering all other
> >> > subjects to the initial one, used mri_label2label to map
> >> the ROIs from
> >> > the initial subject to subsequent ones.
> >> > I am interested in looking at asymmetry between left and
> >> right regions.
> >> >
> >> > I had two concerns, one that the ROIs have different #
> >> vertices on
> >> > different subjects, but as you mentioned the nonlinear
> >> process makes
> >> > sense, since each subject does not have the exact same
> >> brain size and
> >> > curvature.
> >> >
> >> > Another concern was that the ROIs on the left and right
> >> hemisphere in
> >> > a subject do not have the exact same number of vertices.
> >> Would a
> >> > difference of 10 vertices max bias results?
> >> >
> >> > Thank you for your help,
> >> >
> >> > Daiana R. Pur
> >> > Research Assistant
> >> > Canadian Surgical Technologies & Advanced Robotics
> >> > Brain and Mind Institute
> >> > Western University
> >> > London, ON, N6A 5B7
> >> > Canada
> >> >
> >> > On Mon, 

Re: [Freesurfer] ROI NumVert

[Daya P]

Hi,

When i try running make_folding_atlas I get

xhemireg Trout2016 Wed Nov  2 13:11:23 EDT 2016
  #@# xhemireg --s Trout2016
pbsubmit: Command not found.
Launched 9 xhemireg processes
#%# Waiting for 9 xhemireg processes Wed Nov  2 13:11:33 EDT 2016
#%# Waiting for 9 xhemireg processes Wed Nov  2 13:12:33 EDT 2016

I do not have access to a cluster. is there any way to bypass this?

Thank  you,

Daiana

On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve 
wrote:

> I've written a script that will come out with version 6, but I've put it
> here
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas
>
> I think it should work in 5.3, but I'm not sure. If not, you can
> download the dev version and make the atlas using that. Run it with
> --help to get info on how to run it.
>
>
>
> On 10/28/2016 05:10 PM, Daya P wrote:
> > Hi Doug,
> >
> > I needed to make a registration template and an cortical atlas because
> > I am trying to measure cortical thickness, GM and surface area on cat
> > brains.
> >
> > What would be the necessary changes?
> > Would it be possible (and appropriate) to use just
> > mris_left_right_register instead?
> >
> > Daiana
> >
> > On Fri, Oct 28, 2016 at 11:34 AM, Douglas Greve
> > > wrote:
> >
> > A difference of 10 out of 500 or 1000 does not both me at all. Why
> > do you need to create your own atlas? It is doable for the cross
> > hemi stuff, it is just difficult.
> >
> >
> > On 10/26/16 10:16 AM, Daya P wrote:
> >>
> >> Thank you for your help!
> >>
> >> I created a registration template and atlas from scratch could I
> >> input that in the interhemispheric registration analysis?
> >>
> >> The ROIs for the diffrerent regions per hemisphere are 50-100
> >> vertices
> >>
> >> On Oct 24, 2016 5:03 PM, "Douglas N Greve"
> >> >
> wrote:
> >>
> >> It would depend on how big the ROI is to begin with. Do you
> >> know that we
> >> have our own interhemispheric analysis that might be better
> >> for this?
> >> Check out
> >>
> >> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
> >> 
> >>
> >>
> >> On 10/24/2016 12:33 PM, Daya P wrote:
> >> > Hi Bruce,
> >> >
> >> > I drew ROIs on an initial subject and then after
> >> registering all other
> >> > subjects to the initial one, used mri_label2label to map
> >> the ROIs from
> >> > the initial subject to subsequent ones.
> >> > I am interested in looking at asymmetry between left and
> >> right regions.
> >> >
> >> > I had two concerns, one that the ROIs have different #
> >> vertices on
> >> > different subjects, but as you mentioned the nonlinear
> >> process makes
> >> > sense, since each subject does not have the exact same
> >> brain size and
> >> > curvature.
> >> >
> >> > Another concern was that the ROIs on the left and right
> >> hemisphere in
> >> > a subject do not have the exact same number of vertices.
> >> Would a
> >> > difference of 10 vertices max bias results?
> >> >
> >> > Thank you for your help,
> >> >
> >> > Daiana R. Pur
> >> > Research Assistant
> >> > Canadian Surgical Technologies & Advanced Robotics
> >> > Brain and Mind Institute
> >> > Western University
> >> > London, ON, N6A 5B7
> >> > Canada
> >> >
> >> > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl
> >> >  >> 
> >>  >> >> wrote:
> >> >
> >> > Hi Daiana
> >> >
> >> > yes, that is to be expected given the nonlinear nature
> >> of the
> >> > cross-subject registration. It shouldn't bias things,
> >> although
> >> > you'll need to give us more details if you want a more
> >> definitive
> >> > answer.
> >> >
> >> > cheers
> >> > Bruce
> >> >
> >> >
> >> >
> >> > On Mon, 24 Oct 2016, Daya P wrote:
> >> >
> >> > Hi All,
> >> >
> >> > My question is about using mri_label2label. When
> >> mapping the
> >> > labels from one
> >> > subject to another the number of vertices of each
> >> ROI is
> >> > different. Is that
> >> > something to be expected?
> >> >
> >> > How much of a difference does a number 

[Freesurfer] mri_binarize --gm option unknown

[HOSSU Gabriela]

Hello everyone,

I am trying to run a mri_binarize command on FS v 5.2, Linux 64bit, but when I 
use the option -gm (also for -subcort-gm).
I am getting an error that says the -gm option is not recognized.

Here is the command line and the following error (from the mri folder of a 
subject):
mri_binarize -i aparc+aseg.mgz -gm -o gmmask.mgz

I obtain this:
ERROR: Option -gm unknown

Thanks very much,

Gabriela HOSSU

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Re: [Freesurfer] mapping ROI to surface space

[Andrews, Derek]

Hello Freesurfer Developers,

I have gotten ahold of the dev version of mri_label2label.

Currently I have a .w file that I need to “fill in the holes” on. Could
you please specify the steps I will need to take to make my .w file an
acceptable input for mri_label2label, and any recommendations you may have
for the value of N for the —close flag.

Thank you.

Best, Derek 




Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk





On 28/10/2016 15:53, "Bruce Fischl"  wrote:

>Hi Derek
>
>I think the dev version of mri_label2label supports
>open/close/dilate/erode
>operations:
>
>mri_label2label --help
>USAGE: mri_label2label.bin
>
>--srclabel input label file
>
>--erode  N erode the label N times before writing
>--open   N open the label N times before writing
>--close  N close the label N times before writing
>--dilate  Ndilate the label N times before writing
>  .
>.
>.
>
>if your version doesn't have these operations let us know and we can get
>you an updated one
>
>cheers
>Bruce
>
>
>
>On Fri, 28 Oct 2016,
>Andrews, Derek wrote:
>
>> Hi Bruce,
>>
>> As always thank you for your prompt reply.
>>
>> For the morphological close operation, would you suggest using mris_fill
>> on the surface ROI I created and then running mri_vol2surf again on the
>> volume output by mris_fill?
>>
>> Best, Derek
>>
>>
>> 
>> Derek Sayre Andrews, MSc
>> PhD Candidate
>>
>> The Sackler Institute for Translational Neurodevelopment
>> Department of Forensic and Neurodevelopmental Sciences
>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>>London
>>
>> Telephone: +44 (0)20 7848 5701
>> Email: derek.andr...@kcl.ac.uk
>>
>>
>>
>>
>>
>> On 28/10/2016 14:54, "Bruce Fischl"  wrote:
>>
>>> p.s. you could remove many/most of these holes using a morphological
>>> close operation
>>> On Fri, 28 Oct 2016, Andrews, Derek wrote:
>>>
 Hello Freesurfer Developers and Community,

 I am looking to map a ROI.nii based on the MNI152 template to the
 fsaverage
 pial surface.

 I have used the following commands

 Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat ‹init-fsl
‹12
 ‹t1

 Then

 mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi lh

 The ROI appears to be in the right place however is very blotchy.
Have I
 missed a step? Or is this correct?

 See bellow a picture of the ROI highlighted in FSL and in tksurfer
after
 mapped using the above.

 Thank you for your support,

 Best, Derek

 [IMAGE]




 
___
__
 ___

 Derek Sayre Andrews, MSc
 PhD Candidate

 The Sackler Institute for Translational Neurodevelopment

 Department of Forensic and Neurodevelopmental Sciences

 Institute of Psychiatry, Psychology & Neuroscience, King's College
 London

 Telephone: +44 (0)20 7848 5701
 Email: derek.andr...@kcl.ac.uk



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[Freesurfer] Fw: recon-all steps question

[miracooloz]

  Sent from my BlackBerry 10 smartphone.From: miracle ozzoude Sent: Monday, October 31, 2016 8:39 AMTo: Douglas N GreveSubject: recon-all steps questionHello Freesurfer, I have couple of questions. While going through the frequently asked questions on your page http://freesurfer.net/fswiki/UserContributions/FAQ I came across a question regarding how to integrate a skull stripped from another problem into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid > create a symbolic link from T1.mgz to brainmask.auto.mgz and another like from brainmask.auto.mgz to brainmask.mgz --> after run the finall stages of recon-all: recon-all -autorecon2 -autorecon3 -s subjid). First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created during skull stripping? why are they present if I included the "-no skullstrip" flag? Second question, where do I insert my already skull stripped data in the symbolic link? Last question, the final stages of recon-all doesn't include skull stripping, how can I be sure my skull stripped data was incorporated into the freesurfer recon-all process? Best, Paul

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Re: [Freesurfer] morphometric stats and global measure of volume

[Bruce Fischl]

Hi Naveed

the atlas is composed of 40 subjects distributed in age and pathology 
(AD), following the CMA conventions that we cite in our  Neuron paper.


cheers
Bruce
On 
Wed, 2 Nov 2016, Muhammad Naveed Iqbal Qureshi wrote:




I want to know which atlas is used by Freesurfer to calculate morphometric 
stats and
global measure of volume.
Specifically for the sub-cortical regions.
Thank you.
 Best,
 Naveed




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Re: [Freesurfer] Is there any way to measure the volume of substantia nigra and red nucleus via FS?

[Bruce Fischl]

HI Nellie

not really. We have some prototype tools for this, but nothing we are 
able to distribute at this time (except for the relatively coarse 
brainstem targets that are in V6)


cheers
Bruce
On Wed, 2 Nov 2016, nellie wrote:


Hi, FreeSurfer experts,

I would like to know is there any command to measure the volume of substantia 
nigra,
red nucleus, and anyother nucleis in brainstem by using FS ?

Thanks in advance,
Nellie


 


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[Freesurfer] morphometric stats and global measure of volume

[Muhammad Naveed Iqbal Qureshi]

I want to know which atlas is used by Freesurfer to calculate morphometric 
stats and global measure of volume.
Specifically for the sub-cortical regions.
Thank you.
 Best,
 Naveed



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