[Freesurfer] mri_watershed for infants or NHP

2016-01-05 Thread Mahmoud 
Dear experts,

I'm trying to adopt the HCP pipeline to our own data but at it is
originally developed for human adults it fails frequently on my data. A big
chunk of the pipeline is based on FreeSurfer so I thought it should be most
relevant to ask my question here.

the main problem I have here is that mri_watershed fails so the rest of the
pipeline cannot proceed. The errors are usually like below:

TEMPLATE DEFORMATION

  second estimation of the COG coord: x=128,y=131, z=124, r=39161
iterations
 couldn't find WM with original limits - expanding ^^

   GLOBAL  CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 38180
  RIGHT_CERCSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1043712479
  LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1117744481
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1064196139
 LEFT_BRAINCSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1050954328
OTHER  CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1062732290
mri_watershed Error:
 GLOBAL region of the brain empty !
##

or

*WATERSHED**
Sorting...
mri_watershed Error:
Problem in the COG calculation:
T1.mgz may not contain properly normalized white-matter.
Confirm that T1.mgz has enough white-matter voxels of value 110.
If white-matter contains few if any voxels of value 110,
try adding wm control-points to nu.mgz, and re-run recon-all.
#

I really appreciate any help or direction.

Thank you!
Mahmoud
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Re: [Freesurfer] Data differ depending on OSX version

2016-01-05 Thread Martin Reuter 


It is mainly the OS version, yet, sometimes the same OS can run on very 
different architectures (eg. on 32bit or 64 bit systems, or even tablets 
and phones), which could affect results. Starting with Lion, OSX only 
runs on 64 bit systems though.


Best, Martin

On 01/05/2016 02:09 AM, Kasper Jessen wrote:

Thank you for your reply.

Okay - so if i understand it correctly, then both the OS version and 
the computer system (i.e processor) has to be the same.


What is the reason for the processer has to be the same?

Best regards,
Kasper Jessen


2016-01-04 15:31 GMT+01:00 Martin Reuter >:


Hi Kasper,

this is because you use two different version of the OS (each
coming with different sets of libraries). 11.4.2 is Lion from
2012. 13.4.0 is Mavericks from 2014.

You don't need to keep the computer fixed, but the OS should be
the same (= here same means same version) and the system (ie
processor).

Cheers, Martin



On 01/04/2016 05:58 AM, Kasper Jessen wrote:

Dear freesurfer,

As i understand from a previous forum thread, it is recommended
that all the data is run on the same computer with the same
operating system.

However, what is the reason for the differing results when I am
running the same 10 subjects on a MacPro and iMac respectively
(please see below):

*MacPro:*
build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0
13.4.0 Darwin Kernel Version 13.4.0

*iMac: *
build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0
11.4.2 Darwin Kernel Version 11.4.2

All the values are different. For example, the
lh_caudalmiddlefrontal_thickness is on the iMac 2.472 and on the
MacPro 2.537.

Is it because of a randomization generator in FreeSurfer?

Best regards,
Kasper Jessen


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Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone:+1-617-724-5652 
Web  :http://reuter.mit.edu  



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MD, PhD student
Center for neuropsychiatric Schizophrenia Research (CNSR)
Mental Health Centre Glostrup
Nordre Ringvej 29-67
2600 Glostrup
Tlf.: 24430136
E-mail: kaspe...@cnsr.dk  eller 
kasper.jes...@regionh.dk 



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Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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[Freesurfer] Is the x-component of the b vectors extracted by mri_convert inverted?

2016-01-05 Thread Emad Ahmadi 
Hi FreeSurfer Experts,

Happy New Year!

I am using mri_convert to extract b vectors (bvecs) from diffusion images 
obtained at Bay 4. Then I use TRACULA for reconstructing white-matter pathways. 
The shape of the reconstructed pathways are odd, so I checked if the extracted 
bvecs are correct. 

To check if the extracted bvecs are correct, I used Diffusion Toolkit together 
with the extracted bvecs to do deterministic tractography. Then I checked the 
shape of the extracted nerve fibers. I have put a slide deck in the following 
dropbox folder showing that the shape of the extracted nerve fibers don’t look 
right:

https://www.dropbox.com/s/1bt6on0rwm9url6/x_inversion.pptx?dl=0 


Then I inverted the x-components of the extracted bvecs, and did the 
tractography again. This corrected the shape of the extracted nerve fibers (see 
the slide deck).

I additionally had a look at the extracted dtift_V1 vectors under the two 
conditions, i.e. before and after x-component inversion. The results showed the 
same thing: x inversion corrects the images.

I just wanted to see if others have had the same problem and confirm that I 
should invert the x-component of the bvecs extracted via mri_convert (I had the 
same experience with dcm2nii tool, where I had to invert the z-component of the 
extracted bvecs). 

I hope a wonderful new year for everyone!
Emad

Emad Ahmadi, MD
---
Research Fellow in Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
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Re: [Freesurfer] Freesurfer 6.0 -hires mri_segment potential issue

2016-01-05 Thread Bruce Fischl 

Hi Ajay

it's kind of dicey to use an arbitrary nightly build as we have no idea 
what was in that that might have been fixed the next day. I would wait 
for a beta, or at the very least try a new version as I don't think our 
current version exhibits the behavior you are experiencing.


cheers
Bruce
On Tue, 29 Dec 
2015, Ajay Kurani wrote:



Hello Freesurfer experts,

   I am using the nightly build of Freesurfer 6.0 (Dec 18, 2015) on Ubuntu
14.04 with a high resolution image (0.5mm isotropic).  I set
OMP_NUM_THREADS=16 and then passed the -openmp 16 and -itkthreads 16 flags
in my autorecon 2 line command.  Autorecon1 and the beginning parts of
Autorecon2 ran in a reasonable amount of time. 

Currently the program is running the mri_segment -keep -mprage brain.mgz
wm.seg.mgz line command however it has been at this step for approximately 5
days!  I used top line command to verify that the program is still running
and it seems to be still running.  I wasn't sure if this time for this step
is typical for a high-res image (as this is my first time processing data
higher than 1mm iso), or if there is a potential bug.

I ran this same subject on another computer using the same version of
Freesurfer and Ubuntu (8 core machine) and mri_segment (~ step 15) has been
running for over a day so far.  Any feedback would be appreciated as to if
this amount of processing time is typical for this type of resolution, or if
it could be a potential bug and that I should wait for a new beta release?

Thanks,
Ajay

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Re: [Freesurfer] Individual regions of CorticalParcellation_Yeo2011

2016-01-05 Thread Parker, Richard 
Hi Professor Yeo,


Sorry for the late reply.


In the end I ended up giving in and performing my functional connectivity 
analysis in MNI space, like any rational person would. As a result, I ended up 
using the MNI152 versions of network masks you provided.


Thanks for all your help, and for providing the split region ROI files!


Best wishes,


Richard Parker


Richard Parker
Postgraduate Research Student

Maurice Wohl Clinical Neuroscience Institute
King's College London

Telephone: 07943515208
Email: richard.r.par...@kcl.ac.uk
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Re: [Freesurfer] .Img format

2016-01-05 Thread Douglas N Greve 
please see surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



On 01/05/2016 12:51 PM, Hassan bakhshi wrote:
>
> Hello ,
>
> I have an image with .img format and an image with .hdr format.
>
> Freesurfer cant run them. What im suppose to di0o??? I just want to 
> view the image.
>
>
>
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Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] .Img format

2016-01-05 Thread Hassan bakhshi 
Hello ,

I have an image with .img format and an image with .hdr format.

Freesurfer cant run them. What im suppose to di0o??? I just want to view
the image.
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Re: [Freesurfer] how to display individual Desikan parcels?

2016-01-05 Thread Douglas N Greve 
How does it look in tksurfer?

On 01/04/2016 03:29 PM, Mihaela Stefan wrote:
> Hi Doug,
>
> I am going back to this old email.
> I was able to brake the annot file into separate labels and I created 
> a new annotation file with only the labels that I was interested in. 
> However, the inflated surface disappears when I upload my own 
> annotation in freeview. Only the labels are shown (see attachment). If 
> I select "show outline only", then the inflated surface remains 
> displayed. How can I keep the inflated surface displayed while I am 
> loading the annotation file?
>
> On a different note, I could upload multiple labels in the same time 
> in freeview in the past. Now I can only upload one label at the time. 
> I wonder if there is some setting that I am missing.
>
> Thanks!
> Mihaela
>
> On Wed, Oct 28, 2015 at 1:29 PM, Douglas N Greve 
> > wrote:
>
> Break up the annot into separate labels then recombine the ones
> you want
> into a new annotation. Use mri_annotation2label for the first step
> then
> mris_label2annot for the second.
>
>
> On 10/27/2015 02:35 PM, Mihaela Stefan wrote:
> > Hello Freesurfers,
> >
> > I would like to be able to display just a few parcels from the
> Desikan
> > atlas on the fsaverage inflated surface. For example, I would
> like to
> > display only the superiorfrontal and the posteriorcingulate. I tried
> > to recreate the parcels myself by drawing labels, but they don't
> look
> > pretty (see the attachment).
> > I traced the labels in qdec (based on the Annotation/Opacity
> tab) and
> > then I mapped them to fsaverage and visualized them with freeview.
> >
> > There's probably a better way to do that but I couldn't figure
> it out.
> > Can anyone help me with this?
> >
> > Thanks!
> > Mihaela
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> 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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> 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.
>
>
>
>
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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] how to display individual Desikan parcels?

2016-01-05 Thread Douglas N Greve 
ok, that means a bug in freeview.

On 01/05/2016 02:15 PM, Mihaela Stefan wrote:
> It worked in tksurfer!
> Thanks!
> Mihaela
>
> On Tue, Jan 5, 2016 at 1:13 PM, Douglas N Greve 
> > wrote:
>
> How does it look in tksurfer?
>
> On 01/04/2016 03:29 PM, Mihaela Stefan wrote:
> > Hi Doug,
> >
> > I am going back to this old email.
> > I was able to brake the annot file into separate labels and I
> created
> > a new annotation file with only the labels that I was interested in.
> > However, the inflated surface disappears when I upload my own
> > annotation in freeview. Only the labels are shown (see
> attachment). If
> > I select "show outline only", then the inflated surface remains
> > displayed. How can I keep the inflated surface displayed while I am
> > loading the annotation file?
> >
> > On a different note, I could upload multiple labels in the same time
> > in freeview in the past. Now I can only upload one label at the
> time.
> > I wonder if there is some setting that I am missing.
> >
> > Thanks!
> > Mihaela
> >
> > On Wed, Oct 28, 2015 at 1:29 PM, Douglas N Greve
> > 
>  >> wrote:
> >
> > Break up the annot into separate labels then recombine the ones
> > you want
> > into a new annotation. Use mri_annotation2label for the
> first step
> > then
> > mris_label2annot for the second.
> >
> >
> > On 10/27/2015 02:35 PM, Mihaela Stefan wrote:
> > > Hello Freesurfers,
> > >
> > > I would like to be able to display just a few parcels from the
> > Desikan
> > > atlas on the fsaverage inflated surface. For example, I would
> > like to
> > > display only the superiorfrontal and the
> posteriorcingulate. I tried
> > > to recreate the parcels myself by drawing labels, but they
> don't
> > look
> > > pretty (see the attachment).
> > > I traced the labels in qdec (based on the Annotation/Opacity
> > tab) and
> > > then I mapped them to fsaverage and visualized them with
> freeview.
> > >
> > > There's probably a better way to do that but I couldn't figure
> > it out.
> > > Can anyone help me with this?
> > >
> > > Thanks!
> > > Mihaela
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> 
> >  >
> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > 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/
> >
> > ___
> > 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.
> >
> >
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
>

Re: [Freesurfer] how to display individual Desikan parcels?

2016-01-05 Thread Mihaela Stefan 
It worked in tksurfer!
Thanks!
Mihaela

On Tue, Jan 5, 2016 at 1:13 PM, Douglas N Greve 
wrote:

> How does it look in tksurfer?
>
> On 01/04/2016 03:29 PM, Mihaela Stefan wrote:
> > Hi Doug,
> >
> > I am going back to this old email.
> > I was able to brake the annot file into separate labels and I created
> > a new annotation file with only the labels that I was interested in.
> > However, the inflated surface disappears when I upload my own
> > annotation in freeview. Only the labels are shown (see attachment). If
> > I select "show outline only", then the inflated surface remains
> > displayed. How can I keep the inflated surface displayed while I am
> > loading the annotation file?
> >
> > On a different note, I could upload multiple labels in the same time
> > in freeview in the past. Now I can only upload one label at the time.
> > I wonder if there is some setting that I am missing.
> >
> > Thanks!
> > Mihaela
> >
> > On Wed, Oct 28, 2015 at 1:29 PM, Douglas N Greve
> > > wrote:
> >
> > Break up the annot into separate labels then recombine the ones
> > you want
> > into a new annotation. Use mri_annotation2label for the first step
> > then
> > mris_label2annot for the second.
> >
> >
> > On 10/27/2015 02:35 PM, Mihaela Stefan wrote:
> > > Hello Freesurfers,
> > >
> > > I would like to be able to display just a few parcels from the
> > Desikan
> > > atlas on the fsaverage inflated surface. For example, I would
> > like to
> > > display only the superiorfrontal and the posteriorcingulate. I
> tried
> > > to recreate the parcels myself by drawing labels, but they don't
> > look
> > > pretty (see the attachment).
> > > I traced the labels in qdec (based on the Annotation/Opacity
> > tab) and
> > > then I mapped them to fsaverage and visualized them with freeview.
> > >
> > > There's probably a better way to do that but I couldn't figure
> > it out.
> > > Can anyone help me with this?
> > >
> > > Thanks!
> > > Mihaela
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > 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/
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  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
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Re: [Freesurfer] recon-all get stucked

2016-01-05 Thread Bruce Fischl 
Hi Salvatore

that is a very large defect - about 1/4 the size of a typical surface. 
Usually that means something big is wrong and you'll need to correct it 
manually. You can visualize the defects on the ?h.orig.nofix and 
?h.inflated.nofix surfaces and use them to figure out what is causing the 
defect in the wm.mgz and correct it with either manual editing or control 
points.

cheers
Bruce


On Tue, 5 Jan 2016, 
salvatoreandrea...@libero.it wrote:

> Hi Freesurfer experts!
> 
> I am running recon-all with a Toshiba Satellite (16 Gb RAM and 4 CPU). My OS
> is Ubuntu 14.04 LTS (Trusty). Unfortunately recon-all gets stucked at the
> following:
> 
> CORRECTING DEFECT 0 (vertices=30357, convex hull=5730)
> XL defect detected...
> 
> 
> I am using the Freesurfer development version, because I need to use Recon
> Edit. Attached you find the recon-all log.
> 
> 
> Best regards,
> 
> Salvatore
> 
> 
>
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[Freesurfer] Need help finding minimum number of vertices for monte carlo correction

2016-01-05 Thread Tara Miskovich 
Hello Freesurfer experts,

I need help me finding how to get the minimum number of vertices required
to pass the cluster-corrected threshold with monte carlo simulations used
in qdec for a surface based analysis?

This is per a reviewer request, but I cannot find anything on the wiki or
in the mail archives on how to get this value.

Can someone please help me with this issue?

-- 
Thank you,

Tara
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