[Freesurfer] Post Doc Position

[Fabrice Crivello]

The Neurofunctional Imaging Group (GIN) is a CNRS-CEA joint research unit of 
the Bordeaux University (UMR 5296, dir. Bernard Mazoyer) and a core member of 
the TRAIL Laboratory of Excellence. The GIN is a multidisciplinary research 
unit gathering scientists with initial training in mathematics and 
instrumentation, cognitive neurosciences, signal processing and databasing.

One objective of the current GIN research project is to develop new tools to 
characterize and describe the gray matter anatomical connectivity networks. 
Within this area we have a position for a 2 years Post Doc.

Description of the position

Recent work on brain connectivity modeling revealed that the topographic 
organization of this connectivity is not limited to large-scale anatomical 
pathways generally observable in diffusion MRI, thus reinforcing the interest 
of studies focusing on the characterization of cortical structural connectivity 
and its variability. Therefore, the estimation of relevant grey matter 
connectomes strongly relies on the choice of an ad'hoc cerebral parcellisation.

We propose a post doc project to first implement a probabilistic cortical atlas 
derived from cortical parcellisations defined individually to optimally extract 
cortical thickness and volume of each individual. The second aim of the post 
doc project is to compute cortical structural connectivity to quantify the 
inter-individual variability of brain organization together with the effects of 
specific factors such as gender, manual preference, functional lateralization 
or cognitive skills. The strength of the present project is that it will 
benefits from the already acquired BIL&GIN database composed of 453 healthy 
volunteers balanced for gender and handedness. Hence, the first probabilistic 
cortical atlas will be operated over a large sample, the 453 participants 
having been previously pre-processed.

Qualification and experience

The qualified applicant should have a PhD in neuro-image analysis, cognitive 
neuroscience, computer science or related field and a background in neuroimage 
processing. Applicants should have experience with existing tools for analysis 
of neuroimaging data (SPM, FSL, Freesurfer.) and a relevant programming 
experience (MATLAB). 

For further information, please contact Dr. Fabrice Crivello 
(fabrice.crive...@u-bordeaux2.fr).

Employment and payment are determined by Bordeaux University (2 400 € per 
month, net salary). Job location is in Bordeaux, France. Interested candidates 
should send their applications including CV with full publication list, the 
names and contact information and a summary of research interests to 
fabrice.crive...@u-bordeaux2.fr.

Dr. Fabrice CRIVELLO
Groupe d'Imagerie Neurofonctionnelle
UMR 5296 - CNRS CEA Université Bordeaux

Université de Bordeaux
146, rue Léo Saignat
CS 61292
33076 Bordeaux Cedex

Mob : +33 618 064 753
Tel : +33 547 304 402
Fax : +33 547 304 394
www.gin.cnrs.fr

See my publications : https://www.researchgate.net/profile/Fabrice_Crivello

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[Freesurfer] Lost toolbar in freeview

[김영국]

	
	



	
	
Dear, I lost the toolbar above control panel in the freeview window. How could I reload the toolbar? Thank you for your consideration.Sincerely yours, Youngkook Kim






 





 			Youngkook Kim, M.D.Clinical Fellow of Department of Physical Medicine & RehabilitationSeoul St. Mary's HospitalThe Catholic University of Korea, College of MedicineE-mail : engla...@hanmail.netMobile phone : +82-10-9963-5820  


 

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[Freesurfer] bbregister with T2 in trac-preproc

[Barbara Kreilkamp]

Dear Freesurfers,

I would like to alter the trac-preproc to include an EPI to T2 registration
(diffeomorphic) as I do not have a field map, is there a way of doing this?
I saw that bbregister actually only uses 6 doF.

Thank you very much,
Barbara
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Re: [Freesurfer] Using fieldmap to correct EPI distortions

[Reza Rajimehr]

Hi Doug,

So I am using a command like this:

epidewarp.fsl --mag ~/MonkeyfMRI/oz_fparc/fieldmap/003/fid_mag.nii --dph
~/MonkeyfMRI/oz_fparc/fieldmap/004/fid_phasediff.nii --exf
~/MonkeyfMRI/oz_fparc/bold/template.nii.gz --exfdw
~/MonkeyfMRI/oz_fparc/bold/b0dc.nii.gz --vsm vsm.nii.gz --tediff 2.46
--esp 0.31 --sigma 2 --perev

(note that instead of --o b0dc.nii.gz, I wrote --exfdw b0dc.nii.gz because
this command apparently does not have --o option)

Before running the above command, I have registered the mag and phasediff
volumes to the template volume and I have generated new volumes (fid_mag
and fid_phasediff) that are already in register with the template.

I have two steps remaining in preproc-sess, which are register-sess and
rawfunc2surf-sess. Should I use both -b0dc and -vsm flags for these two
commands? I assume that when I use the above flag(s), my EPI fmc volumes
will be dewarped first, and then they will get registered to the
anatomical and the surface, right? So I hope that when I view/check the
result of registration with tkregister2 (for possible manual
interventions), I will see the dewarped template ...?

Finally what is the effect of specifying -b0dc in mkanalysis-sess?

Thanks,
Reza


> Hi,
>
> I have a basic question, but the answer can be useful for others as well.
>
> I am doing a customized preprocessing of monkey functional data in FS-FAST
> v5.3. After motion correction and before functional-anatomical
> registration, I want to use fieldmap data to correct spatial distortions
> of EPI data. So:
>
> My fieldmap data: dicom files from a fieldmap scan (there are actually two
> series of dicom files for that scan)
>
> My EPI data: fmc.nii.gz files in run folders
>
> Now I have three questions:
>
> 1) How can I unpack the fieldmap data? An example command ...
I think you get two series out, one magnitude and one phase, just
convert those to nifti
>
> 2) How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an
> example command would be very useful.
something like
epidewarp.fsl --mag mag.nii --dph phase.nii --exf template.nii --o
b0dc.nii ...
You have to add --tediff and --esp, but those depend on you sequence
Put the output (b0dc.nii) into session/bold (or session/rest, or where
ever your fmri data are located)
>
> 3) How will the undistorted volumes be used later on in the FS-FAST
> analysis stream?
When you run preproc-sess and mkanalysis-sess add -b0dc to the command line


>
> Your help would be very much appreciated.
>
> Thanks,
> Reza
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Re: [Freesurfer] Lost toolbar in freeview

[Ruopeng Wang]

You will need to reset FreeView’s settings. Make sure freeview is closed, open 
a terminal and run the following command:

defaults delete edu.harvard.mgh.nmr.FreeView

Start freeview again.

Best,
Ruopeng

On Sep 12, 2014, at 4:49 AM, 김영국  wrote:

> 
> Dear, 
> 
> I lost the toolbar above control panel in the freeview window. 
> How could I reload the toolbar? 
> 
> Thank you for your consideration.
> 
> Sincerely yours, 
> Youngkook Kim
> 
> 
> 
> 
> 
> 
> 
> 
> Youngkook Kim, M.D.
> Clinical Fellow of Department of Physical Medicine & Rehabilitation
> Seoul St. Mary's Hospital
> The Catholic University of Korea, College of Medicine
> E-mail : engla...@hanmail.net
> Mobile phone : +82-10-9963-5820 
> 
>   ___
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Re: [Freesurfer] FsFast Functional Connectivity Analysis

[Jiahe Zhang]

Hi Doug,

I was able to get the surface connectivity analysis to run successfully for
the L.Cingulate example that you posted online (
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
). For my own analysis, I'm hoping to use my own functionally defined ROIs
instead of freesurfer segmented regions. For that, do I pass a vol2surf
command on my spherical ROIs and then run the same analysis? I saw that to
prepare a ROI for this kind of analysis, I need to create a configuration
file using funcroi-config, but this command seems to use anatomical ROIs
based on freesurfer segmentation again.

Could you advise how to proceed?

Thanks,
Jiahe


On Mon, Aug 11, 2014 at 5:18 PM, Douglas N Greve 
wrote:

> How did you look at fmcpr.up.sm6.fsaverage.lh.nii.gz? If you did not do
> this, try it
>
> tksurfer fsaverage lh inflated -ov fmcpr.up.sm6.fsaverage.lh.nii.gz -t
> fmcpr.up.sm6.fsaverage.lh.nii.gz
>
> This will bring up an overlay as well as a time course
>
>
> On 08/11/2014 05:05 PM, Jiahe Zhang wrote:
> > Both looked fine. First value in .mincost is .45
> >
> >
> > On Mon, Aug 11, 2014 at 4:51 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > two ways:
> >
> > 1. run tkregister-sess to visually check them
> > 2. look at the first value in register.dof6.dat.mincost. It is hard
> to
> > say what a threshold is for a good registration, but typical
> > values are
> > about .5 or so. If it is .8 or more, it is probably a problem (and
> > probably the initialization is not good)
> >
> >
> > On 08/11/2014 04:35 PM, Jiahe Zhang wrote:
> > > I'm not sure how to check the registration. I see a
> > register.dof6.dat
> > > being produced for each run but I can't tell if it contains the
> > > correct parameters. How can I tell if the registration was
> accurate?
> > >
> > >
> > > On Mon, Aug 11, 2014 at 4:01 PM, Douglas N Greve
> > > mailto:gr...@nmr.mgh.harvard.edu>
> >  > >> wrote:
> > >
> > > did you check the registration?
> > >
> > > On 08/11/2014 03:53 PM, Jiahe Zhang wrote:
> > > > There's nothing even when the threshold is set to 0.
> > > >
> > > > I just checked the preprocessing outputs. I can see
> > normal-looking
> > > > volumes
> > > > fmcpr.nii.gz
> > > > fmcpr.up.nii.gz
> > > > fmcpr.up.sm6.mni305.2mm.nii.gz
> > > >
> > > > But there is nothing when I open
> > fmcpr.up.sm6.fsaverage.lh.nii.gz or
> > > > fmcpr.up.sm6.fsaverage.rh.nii.gz
> > > >
> > > >
> > > >
> > > >
> > > > On Wed, Aug 6, 2014 at 6:40 PM, Douglas N Greve
> > > >  > 
> >  >>
> > >  > 
> > >  >  > > >
> > > >
> > > > When you say that they are "empty" what do you mean? That
> > > there is
> > > > nothing above threshold or that there is nothing
> > regardless
> > > of how low
> > > > the threshold is? See if you get something if you set the
> > > thresh close
> > > > to 0. Does this happen in the volume and the surface?
> Have
> > > you checked
> > > > the registration to assure that it is accurate?
> > > >
> > > > On 08/06/2014 06:33 PM, Jiahe Zhang wrote:
> > > > > Hi Doug,
> > > > >
> > > > > I was trying to run functional connectivity analysis
> > following
> > > > > instructions on the FreeSurferWiki
> > > > >
> > > >
> > >
> > (
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
> ).
> > > > > I was able to successfully run the following
> > commands (nothing
> > > > errored
> > > > > as far as I can tell) but the resulting partial
> > > correlation and
> > > > > significance maps turned out to be empty. Could you
> > take a
> > > look
> > > > at the
> > > > > commands and let me know if anything can be improved?
> > > > >
> > > > > 1. PREPROC
> > > > > preproc-sess -s subject_001 -fwhm 6 -surface
> > fsaverage lhrh
> > > > > -mni305-2mm -fsd bold -per-run -stc up
> > > > >
> > > > > 2. SEED CONFIG
> > > > > fcseed-config -segid 1010 -fcname
> > L_Posteriorcingulate.dat
> > > -fsd bold
> > > > > -mean -cfg mean.L_Posteriorcingulate.config
> > > > >
> >   

Re: [Freesurfer] Segmentation failure

[Martin Reuter]

Hi Patrick,

no images were attached.

If the skull strip removes any brain, you edit the brainmask and fill 
the voxels back (or adjust the watershed parameter if lot's of brain is 
missing). In you case it sounds like the brain is not missing from the 
brainmask, but the surfaces don't grab all of it. Is the white matter 
surface also undersegmented in that area? Then try adding control points 
in white matter that should help with both surfaces.


Best, Martin


On 09/10/2014 05:40 AM, Jan-Patrick Stellmann wrote:

Dear all,

we observe some segmentation faults in the temporal lobe in single patients. 
Gyri are within the brain mask but outside the pail boundaries. Editing brain 
mask.mgz or wm.mgz does not resolves the problem.
Examples are attached.

How can we add missing brain? we are using free surfer v5.3.0 on a linux mint 
workstation.

Thanks in advance.

Best regards,
Patrick


--

DANKE FÜR 125 JAHRE ENGAGEMENT UND VERTRAUEN.
www.uke.de/125
_

Besuchen Sie uns auf: www.uke.de
_

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; 
Gerichtsstand: Hamburg
Vorstandsmitglieder: Prof. Dr. Christian Gerloff (Vertreter des Vorsitzenden), 
Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik
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SAVE PAPER - THINK BEFORE PRINTING


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--
Dr. Martin Reuter

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu

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[Freesurfer] social media: Facebook, Twitter and now LinkedIn

[Martin Reuter]

Hi,

many of you are aware of (yes, even excited about) our social media 
presence at
Facebook: http://facebook.com/FreeSurferMRI
Twitter: http://www.twitter.com/FreeSurferMRI

and so we have just added a group on
LinkedIn: https://www.linkedin.com/groups/FreeSurfer-8173404
(it's hard to believe, but it's true!)

While these are all social media, they each have their special focus. 
While facebook is more personal with pictures of courses, social events 
etc, Twitter focuses on sharing news, and LinkedIn is a professional 
network group which will allow you to connect with other professionals 
in your field, browse and post related job offers, and even start your 
own discussions (Wow -  they're all great).

So, head over to any or all of these and 'follow', 'like' or 'join' us ...

Cheers,
Martin

(how I love social media, it works completely without eye-contact ;-) )

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Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

[Eryilmaz, Huseyin Hamdi]

Hi Doug, 

I tested this new script on volume data and it did create the file 
'sig.masked.mgh', which shows the significance map masked by Monte Carlo 
surviving clusters. So, I guess you can update the current file now. 

Thanks!
Hamdi



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, September 11, 2014 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

I think it must have gotten contaminated as an attachement. Try using
this one

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim


On 09/10/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
> Yes I could save the file from my email into '/homes/8/hhe0/Documents'. Under 
> 'Permissions' tab of this file, 'Allow executing file as program' option is 
> checked.
>
> I can try cd'ing into that folder then run the command as :
>
>>> mri_glmfit-sim --glmdir  --sim mc-z 1 1.3 mcz1_1.3 
>>> --sim-sign abs --cwpvalthresh .05
> but I'm not sure if it will then use the new mri_glmfit-sim file you sent or 
> the original file under '/usr/local/freesurfer/stable5_0_0/bin/'.
>
> Hamdi
>
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, September 10, 2014 4:10 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh
>
> Not sure what is wrong. Is it executable? Were you able to save the file
> from your email or did you cut and paste it into a file and save the file?
>
>
> On 09/10/2014 04:03 PM, Eryilmaz, Huseyin Hamdi wrote:
>> Hi Doug,
>>
>> Running it as you suggested didn't work either. I tried it as follows:
>>
>> 1) /homes/8/hhe0/Documents/mri_glmfit-sim --glmdir  --sim mc-z 
>> 1 1.3 mcz1_1.3 --sim-sign abs --cwpvalthresh .05
>>
>> It says:
>>
>> 'nknown option: `-
>> Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].
>>
>> Then I thought maybe this is a c shell script so I need to use ./ before the 
>> command. I tried that but it gave the same error as above.
>>
>> Any ideas?
>>
>> Thanks!
>> Hamdi
>>
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, September 09, 2014 6:14 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh
>>
>> Yes, you can just run
>>
>> /path/to/your/local/copy/mri_glmfit-sim
>>
>>
>>
>> On 09/09/2014 05:49 PM, Eryilmaz, Huseyin Hamdi wrote:
>>> Hi Doug,
>>>
>>> I don't seem to have the permission to change the contents of that folder. 
>>> So I can't really copy it over. Is it possible to run this locally? I'm 
>>> working on a linux workstation at Martinos and when I ask the source, it 
>>> gives me that folder:
>>>
> which mri_glmfit-sim
>>> /usr/local/freesurfer/stable5_0_0/bin/mri_glmfit-sim
>>>
>>>
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Tuesday, September 09, 2014 5:24 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh
>>>
>>> You can just copy it over the old one (but make  a backup of it first)
>>>
>>> On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 Thanks for your reply. I can certainly test it. Could you tell me how I 
 can run this new 'mri_glmfit-sim' you sent me? The original 
 'mri_glmfit-sim' that I use is under 
 '/usr/local/freesurfer/stable5_0_0/bin/'

 Best,
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, September 08, 2014 11:48 AM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 That was an oversight. I've attached a version that should work. Can you
 test it for me? Once I know it works I'll check it in to tree.
 doug




 On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote:
> Dear FS experts,
>
> I have a question about a MC output file. When I run the MC sim
> (using mri_glmfit-sim) on the surface, it generates a bunch of files
> including a 'sig.masked.mgh', which is nice for displaying the
> significance map limited to the clusters that survive the MC
> correction. However, when I run it on the volume, it doesn't genera

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

[Douglas N Greve]

great, I'll check it in to the source so it will be part of the next version
thanks
doug
On 09/12/2014 10:31 AM, Eryilmaz, Huseyin Hamdi wrote:
> Hi Doug,
>
> I tested this new script on volume data and it did create the file 
> 'sig.masked.mgh', which shows the significance map masked by Monte Carlo 
> surviving clusters. So, I guess you can update the current file now.
>
> Thanks!
> Hamdi
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, September 11, 2014 1:55 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh
>
> I think it must have gotten contaminated as an attachement. Try using
> this one
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim
>
>
> On 09/10/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
>> Yes I could save the file from my email into '/homes/8/hhe0/Documents'. 
>> Under 'Permissions' tab of this file, 'Allow executing file as program' 
>> option is checked.
>>
>> I can try cd'ing into that folder then run the command as :
>>
 mri_glmfit-sim --glmdir  --sim mc-z 1 1.3 mcz1_1.3 
 --sim-sign abs --cwpvalthresh .05
>> but I'm not sure if it will then use the new mri_glmfit-sim file you sent or 
>> the original file under '/usr/local/freesurfer/stable5_0_0/bin/'.
>>
>> Hamdi
>>
>>
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Wednesday, September 10, 2014 4:10 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh
>>
>> Not sure what is wrong. Is it executable? Were you able to save the file
>> from your email or did you cut and paste it into a file and save the file?
>>
>>
>> On 09/10/2014 04:03 PM, Eryilmaz, Huseyin Hamdi wrote:
>>> Hi Doug,
>>>
>>> Running it as you suggested didn't work either. I tried it as follows:
>>>
>>> 1) /homes/8/hhe0/Documents/mri_glmfit-sim --glmdir  --sim 
>>> mc-z 1 1.3 mcz1_1.3 --sim-sign abs --cwpvalthresh .05
>>>
>>> It says:
>>>
>>> 'nknown option: `-
>>> Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].
>>>
>>> Then I thought maybe this is a c shell script so I need to use ./ before 
>>> the command. I tried that but it gave the same error as above.
>>>
>>> Any ideas?
>>>
>>> Thanks!
>>> Hamdi
>>>
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Tuesday, September 09, 2014 6:14 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh
>>>
>>> Yes, you can just run
>>>
>>> /path/to/your/local/copy/mri_glmfit-sim
>>>
>>>
>>>
>>> On 09/09/2014 05:49 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 I don't seem to have the permission to change the contents of that folder. 
 So I can't really copy it over. Is it possible to run this locally? I'm 
 working on a linux workstation at Martinos and when I ask the source, it 
 gives me that folder:

>> which mri_glmfit-sim
 /usr/local/freesurfer/stable5_0_0/bin/mri_glmfit-sim



 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, September 09, 2014 5:24 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 You can just copy it over the old one (but make  a backup of it first)

 On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
> Hi Doug,
>
> Thanks for your reply. I can certainly test it. Could you tell me how I 
> can run this new 'mri_glmfit-sim' you sent me? The original 
> 'mri_glmfit-sim' that I use is under 
> '/usr/local/freesurfer/stable5_0_0/bin/'
>
> Best,
> Hamdi
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, September 08, 2014 11:48 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh
>
> That was an oversight. I've attached a version that should work. Can you
> test it for me? Once I know it works I'll check it in to tree.
> doug
>
>
>
>
> On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote:
>> Dear FS experts,
>>
>> I have a question about a MC output file. When 

Re: [Freesurfer] FsFast Functional Connectivity Analysis

[Douglas N Greve]

You need to have your ROI as a segmentation in the anatomical 
(conformed) space. If it is a label on the surface, you can use 
mri_label2vol to turn it into a volume (make sure to use --proj frac 0 1 
.1  to fill the ribbon). When you run funcroi-config specify -seg 
yourseg.mgz 1 where yourseg.mgz is the output of mri_label2vol and "1" 
refers to the fact that the output volume is a binary mask where your 
ROI is 1 and everything else is 0

doug


On 09/12/2014 09:05 AM, Jiahe Zhang wrote:
> Hi Doug,
>
> I was able to get the surface connectivity analysis to run 
> successfully for the L.Cingulate example that you posted online 
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough).
>  
> For my own analysis, I'm hoping to use my own functionally defined 
> ROIs instead of freesurfer segmented regions. For that, do I pass a 
> vol2surf command on my spherical ROIs and then run the same analysis? 
> I saw that to prepare a ROI for this kind of analysis, I need to 
> create a configuration file using funcroi-config, but this command 
> seems to use anatomical ROIs based on freesurfer segmentation again.
>
> Could you advise how to proceed?
>
> Thanks,
> Jiahe
>
>
> On Mon, Aug 11, 2014 at 5:18 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> How did you look at fmcpr.up.sm6.fsaverage.lh.nii.gz? If you did
> not do
> this, try it
>
> tksurfer fsaverage lh inflated -ov fmcpr.up.sm6.fsaverage.lh.nii.gz -t
> fmcpr.up.sm6.fsaverage.lh.nii.gz
>
> This will bring up an overlay as well as a time course
>
>
> On 08/11/2014 05:05 PM, Jiahe Zhang wrote:
> > Both looked fine. First value in .mincost is .45
> >
> >
> > On Mon, Aug 11, 2014 at 4:51 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
> >
> > two ways:
> >
> > 1. run tkregister-sess to visually check them
> > 2. look at the first value in register.dof6.dat.mincost. It
> is hard to
> > say what a threshold is for a good registration, but typical
> > values are
> > about .5 or so. If it is .8 or more, it is probably a
> problem (and
> > probably the initialization is not good)
> >
> >
> > On 08/11/2014 04:35 PM, Jiahe Zhang wrote:
> > > I'm not sure how to check the registration. I see a
> > register.dof6.dat
> > > being produced for each run but I can't tell if it
> contains the
> > > correct parameters. How can I tell if the registration was
> accurate?
> > >
> > >
> > > On Mon, Aug 11, 2014 at 4:01 PM, Douglas N Greve
> > >  
> >
> >  
> >   > >
> > > did you check the registration?
> > >
> > > On 08/11/2014 03:53 PM, Jiahe Zhang wrote:
> > > > There's nothing even when the threshold is set to 0.
> > > >
> > > > I just checked the preprocessing outputs. I can see
> > normal-looking
> > > > volumes
> > > > fmcpr.nii.gz
> > > > fmcpr.up.nii.gz
> > > > fmcpr.up.sm6.mni305.2mm.nii.gz
> > > >
> > > > But there is nothing when I open
> > fmcpr.up.sm6.fsaverage.lh.nii.gz or
> > > > fmcpr.up.sm6.fsaverage.rh.nii.gz
> > > >
> > > >
> > > >
> > > >
> > > > On Wed, Aug 6, 2014 at 6:40 PM, Douglas N Greve
> > > >  
> >  >
> >  
> >>
> > >  
> >  >
> > >  
> >   wrote:
> > > >
> > > >
> > > > When you say that they are "empty" what do you
> mean? That
> > > there is
> > > > nothing above threshold or that there is nothing
> > regardless
> > > of how low
> > > > the threshold is? See if you get something if
> you set the
> > > thresh close
> > > > to 0. Does this 

Re: [Freesurfer] Using fieldmap to correct EPI distortions

[Douglas N Greve]

Sorry, the b0dc.nii.gz should be the argument of --vsm (no need to use 
--exfdw).


On 09/12/2014 08:28 AM, Reza Rajimehr wrote:
> Hi Doug,
>
> So I am using a command like this:
>
> epidewarp.fsl --mag ~/MonkeyfMRI/oz_fparc/fieldmap/003/fid_mag.nii --dph
> ~/MonkeyfMRI/oz_fparc/fieldmap/004/fid_phasediff.nii --exf
> ~/MonkeyfMRI/oz_fparc/bold/template.nii.gz --exfdw
> ~/MonkeyfMRI/oz_fparc/bold/b0dc.nii.gz --vsm vsm.nii.gz --tediff 2.46
> --esp 0.31 --sigma 2 --perev
>
> (note that instead of --o b0dc.nii.gz, I wrote --exfdw b0dc.nii.gz because
> this command apparently does not have --o option)
>
> Before running the above command, I have registered the mag and phasediff
> volumes to the template volume and I have generated new volumes (fid_mag
> and fid_phasediff) that are already in register with the template.
>
> I have two steps remaining in preproc-sess, which are register-sess and
> rawfunc2surf-sess. Should I use both -b0dc and -vsm flags for these two
> commands?
Both of those options are the same thing (I could not decide what to 
call it).
> I assume that when I use the above flag(s), my EPI fmc volumes
> will be dewarped first, and then they will get registered to the
> anatomical and the surface, right? So I hope that when I view/check the
> result of registration with tkregister2 (for possible manual
> interventions), I will see the dewarped template ...?
Actually, tkregister2 does not take a VSM, so you will be looking at the 
nondewarped. You can use mri_vol2vol with the --vsm option to map the 
template into anatomical space and unwarp, then load that up in tkmedit 
to see the surfaces on the dewarped.
>
> Finally what is the effect of specifying -b0dc in mkanalysis-sess?
It just tells it to use the B0 distortion corrected data.
>
> Thanks,
> Reza
>
>
>> Hi,
>>
>> I have a basic question, but the answer can be useful for others as well.
>>
>> I am doing a customized preprocessing of monkey functional data in FS-FAST
>> v5.3. After motion correction and before functional-anatomical
>> registration, I want to use fieldmap data to correct spatial distortions
>> of EPI data. So:
>>
>> My fieldmap data: dicom files from a fieldmap scan (there are actually two
>> series of dicom files for that scan)
>>
>> My EPI data: fmc.nii.gz files in run folders
>>
>> Now I have three questions:
>>
>> 1) How can I unpack the fieldmap data? An example command ...
> I think you get two series out, one magnitude and one phase, just
> convert those to nifti
>> 2) How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an
>> example command would be very useful.
> something like
> epidewarp.fsl --mag mag.nii --dph phase.nii --exf template.nii --o
> b0dc.nii ...
> You have to add --tediff and --esp, but those depend on you sequence
> Put the output (b0dc.nii) into session/bold (or session/rest, or where
> ever your fmri data are located)
>> 3) How will the undistorted volumes be used later on in the FS-FAST
>> analysis stream?
> When you run preproc-sess and mkanalysis-sess add -b0dc to the command line
>
>
>> Your help would be very much appreciated.
>>
>> Thanks,
>> Reza
> ___
> 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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Re: [Freesurfer] problems with tracula pre-processing (bvecs)

[Michele Cavallari]

Tried...unfortunately it didn't improve

On Thu, Sep 11, 2014 at 4:56 PM, Chris Watson <
christopher.wat...@childrens.harvard.edu> wrote:

>  You can try just re-running "trac-prep -prior" and "trac-paths" for the
> L uncinate and no other tracts
>
>  On 09/11/2014 02:58 PM, Michele Cavallari wrote:
>
> So, I re-ran the case with the set reinit option. It "half" worked!...in
> the sense that the new results show the left uncinate right, but the
> right-side one is still a dot (see screenshot of the brain view from the
> bottom).
> Any further suggestion?
> Thanks.
>
>  [image: Inline image 2]
>
>
>
>
>
> On Thu, Sep 11, 2014 at 1:36 PM, Michele Cavallari <
> cavallari.mich...@gmail.com> wrote:
>
>> Thanks! it's running...
>>
>> On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp <
>> bakk@googlemail.com> wrote:
>>
>>>  Hi Michele,
>>>
>>> Don't think there is anything wrong with the attached dmrirc.tutorial
>>> file.
>>> You definitely need to add the '-c' flag infront of the path to your
>>> configuration file.
>>> Right now it reads the path to your file as a flag, which is of course
>>> not what you want.
>>>
>>> Best,
>>> Barbara
>>>
>>>
>>>
>>>
>>> On 11/09/2014 17:49, Michele Cavallari wrote:
>>>
>>> Hi Anastasia,
>>> I am probably doing something wrong with the syntax of the dmrirc file.
>>> I get this error message
>>>
>>>   trac-all -prior
>>> /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial
>>>
>>> ERROR: flag
>>> /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial
>>> unrecognized
>>>
>>> -prior
>>> /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial
>>>
>>>  Could you please check the attached file?
>>>
>>>
>>> On Wed, Sep 10, 2014 at 1:51 PM, Anastasia Yendiki <
>>> ayend...@nmr.mgh.harvard.edu> wrote:
>>>

 Thanks, Michele. Hard to tell what's causing this, perhaps a bit of
 distortion orbitofrontally. You may be able to fix this type of thing by
 reinitializing the tract reconstruction: Add "set reinit = 1" to your
 configuration file, set the pathlist to include only the left and right
 uncinate, and then rerun the -prior and -path steps of trac-all on this
 subject.

 On Wed, 10 Sep 2014, Michele Cavallari wrote:

  uploaded (and activated).Thanks!
>
>
>
> On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki <
> ayend...@nmr.mgh.harvard.edu> wrote:
>
>   Hi Michele - The anatomical segmentation does look good, but
> from the
>   screenshot the DWI data seems to be noisy in the orbitofrontal
> area, which
>   may be affecting the uncinate. It's hard to tell just from one
> slice.
>
>   If you upload all the tracula output directories of this subject
> (dmri,
>   dmri.bedpostX, dlabel, dpath) for me here, I'll take a look:
>   https://gate.nmr.mgh.harvard.edu/filedrop2/
>
>   Thanks!
>   a.y
>
>   On Wed, 10 Sep 2014, Michele Cavallari wrote:
>
> Hi Anastasia,I completed the tracula processing.
> By looking at the tractography results in the viewer I
> noticed
> that the uncinate
> fasciculus is pretty small (see attached screenshot). It
> actually appears as a small
> blue dot. And the problem is both on the left and right
> side.
> The other tracts look
> fine. I played with threshold, but the size didn't
> increase. So,
> I guess that something
> wrong happened with the tractography of that particular
> bundle.
> I checked the aparc+aseg
> output (attached): it seems right to me, but could you
> please
> double-check?
> Let me also know if you have any suggestions, and if you
> need
> more information or output
> files.
> Best,
> Michele
>
> Inline image 1
>
>
>
> On Thu, Sep 4, 2014 at 11:55 PM, Anastasia Yendiki
>  wrote:
>
>   Hi Ludy - If your gradient table is formatted in 3
> rows
> you need to
>   either:
>
>   1. Convert it to 3 columns so you can use it with
> the 5.3
> version of
>   tracula, which requires the gradient table to be
> formatted
> in columns
>
>   OR
>
>   2. Download the tracula update that can use gradient
> tables formatted in
>   rows
>
>   Hope this helps,
>   a.y
>
>   On Thu, 4 Sep 2014, ls...@bidmc.harvard.edu wr

Re: [Freesurfer] Cortical gray matter surface area

[Douglas N Greve]

You can run something like

cd $SUBJECTS_DIR/subject

  mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f 
stats/lh.aparc.pial.stats -b -a label/lh.aparc.annot -c 
label/aparc.annot.ctab subject lh pial

The "Measure Cortex" fields in the output stats/lh.aparc.pial.stats will 
be measures of the pial surface as will the SurfArea, MeanCurv, 
GausCurv, FoldInd, and CurvInd fields for each ROI (thickness and number 
of vertices will stay the same)

doug

On 09/11/2014 07:29 PM, will brown wrote:
> Sure. We'd like to know how to find the surface area of the cortical 
> grey matter from the pial surface. So specifically, what is the 
> surface area of the pial/grey matter boundary of the cortex for each 
> hemisphere?
>
> We're using Freesurfer v5.3 on Centos 6.
>
> Thanks,
> Will Brown
>
>
> On Fri, Sep 12, 2014 at 9:11 AM, Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
> sorry, this thread has gotten too deep. Can someone summarize the
> question?
>
>
> On Thu, 11 Sep 2014, _andre...@sapo.pt 
> wrote:
>
>
> Ok. Then, I'm not sure if everything is correct with the
> command lines since
> I use 5.0.
>
> Any thought on this Freesurfer team?
>
> Thanks,
> Andreia
>
> Citando will brown  >:
>
>   Thanks again, for the record, I'm using freesurfer
> version 5.3.0
>   on Centos 6.
>
>   On 9/09/2014 11:00 PM, <_andre...@sapo.pt
> > wrote:
>
> Hi Will,
>
> Just to clarify, what version of FS are you using? I
> think it might not be 5.0 and I don't know if
> everything aplies if we are using different
> versions.
>
>
> 1) Yes, it is only based on the pial surface (and
> these command lines are for the aparc, DK altas).
> The second set provides the surface area for each
> hemisphere without including, for example, the pial
> surface that you see in the hippocampus which is not
> accurate and one should not care about. In the end,
> the second set gives you the sum of the areas in
> aparc, thus, you can just make a sum of that
> parcellation if you want. I just realized that.
>
> 2) No. In the new stats file, the value that you
> want is at the bottom:
>
> # ColHeaders StructName NumVert SurfArea GrayVol
> ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd
>
> And when running aparcstats2table that's the value
> you should get in the table. I think that # Measure
> Cortex, WhiteSurfArea, White Surface Total Area may
> be including more stuff since it is bigger.
>
>
> If what you want is only the total hemisphere
> surface area you only need to run the second set of
> commands. If you want the area of each DK altas
> parcellation then run the first set and then simply
> add them to get total hemisphere surface area.
>
>
> Someone from Freesurfer staff will correct me if I'm
> wrong. (Please) I'm Ccing Doug since he was replying
> to your previous emails.
>
> Let's wait for their feedback.
>
> Andreia
>
>
>
>
>
> Citando will brown  >:
>
>   Thanks Andreia, this does appear to have
>   worked. Please forgive my ignorance but
>   I do just want to double check two
>   things;
>
> 1) The first commands you have given provide the stats for
> the two hemispheres of the cerebral cortex only based on
> the pial surface, whereas the second set of commands
> provide the pial boundary stats for the whole brain rather
> than just cortex?
>
> 2) The surface area value that I am looking for (grey
> matter surface area at the grey/pial boundary) is listed
> in the new stats table next to: # Measure Cortex,
> WhiteSurfArea, White Surface Total Area, ?
>
> Thanks again,
> Will
>
> On Tue, Sep 9, 2014 at 5:36 PM, will brown
> mailto:willbrown1...@gmail.com>> wrote:
>   Thanks very much Andreia, yes this does look
>   like what I want. I haven't had a chance to
>   test it yet but it does indeed appear to
>   answer my question. Thanks to those that have
>   of

[Freesurfer] WM segmentation

[Shengwei Zhang]

Hi FreeSurfer list members,

I'm working on a white matter hyper-intensity study, and trying to group
the segmented WM labels in lobes based on the wmparc.mgz file made by
recon.

But I found that there's a large part of "unsegmented WM" near ventricles,
and wonder if such labels are consistently assigned among subjects, because
most of the WM hyperintensity voxels are located within these locations. Or
is there other way to segment the 'unsegmented WM' in more details?

I'd appreciate any help related to this topic.

Shengwei
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Re: [Freesurfer] FW: Most recent/complete FreeSurfer + Patches?

[Gurney, Jenny]

Thanks, Zeke.  OK, that makes sense about the static vs. dynamic linking 
information.  Good to know about the usage of UPX in case we need to 
'decompress' at some point and use 'ldd' and get specific library dependency 
information.

The list of binaries/scripts came via the FTP download site here:  
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/

>From the 'Release Notes' page, it looks like the 'official' patches are:

mri_segstats
mni152reg
recon-all

Does that sounds right?  And (going back to the original question) could we 
just overlay these on 5.3.0-HCP with no expected issues?

Thanks,
Matt House, Jenny Gurney and John Flavin @WU in STL

-Original Message-
From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu]
Sent: Thursday, September 11, 2014 9:55 AM
To: freesurfer@nmr.mgh.harvard.edu; Gurney, Jenny
Subject: Re: [Freesurfer] FW: Most recent/complete FreeSurfer + Patches?

Jenny,

May I ask were you got those list of binaries... Was is from the Release Notes 
page? I ask because we link to some "official" patches on the release notes 
page but we also frequently give people "dev" versions of some binaries to help 
solve a particular issue that they may be having.
Those dev version are not official patches.

Also, the release version appear statically linked because they get  run 
through a utility called 'upx' which shrinks them but changes how the 'file' 
and 'ld' command process them. The binaries you mention below have not been run 
through that utility.

-Zeke

On 09/09/2014 01:09 PM, Gurney, Jenny wrote:
> Hi guys!
>
> We would like to install the latest and greatest FreeSurfer on the
> processing cluster used by the CNDA at Washington University.  We're
> thinking about installing the 5.3.0-HCP, and then over that, the
> released 5.3.0 patches.  We're looking for verification that doing the
> install this way makes sense and that these two code sets don't
> conflict in any way.
>
> We know that the 5.3.0-HCP version updates the mris_make_surfaces,
> however, the patches do not include that update, which is why we are
> thinking about starting with 5.3.0-HCP as the base install.  Note that
> this is being done on CentOS 6.x
>
> The currently available patches seem to include:
>
> mni152reg
>
> mri_mcsim
>
> mri_segstats
>
> recon-all
>
> tksurfer-sess
>
> tksurferfv
>
> Is that a complete list or did we miss some binaries/scripts?
>
> Also, it seems that the 'patch' binaries are dynamically linked, while
> the release binaries are statically linked.  Besides dependency
> issues, could this cause an issue with results consistency, etc. if
> other system libraries get updated?
>
> Thanks, guys.  Hope all is well.
>
> Matt House, Jenny Gurney and John Flavin @WU in STL
>
>
> --
> --
>
> The material in this message is private and may contain Protected
> Healthcare Information (PHI). If you are not the intended recipient,
> be advised that any unauthorized use, disclosure, copying or the
> taking of any action in reliance on the contents of this information
> is strictly prohibited. If you have received this email in error,
> please immediately notify the sender via telephone or return mail.
>
>
> ___
> 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 
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The material in this message is private and may contain Protected Healthcare 
Information (PHI). If you are not the intended recipient, be advised that any 
unauthorized use, disclosure, copying or the taking of any action in reliance 
on the contents of this information is strictly prohibited. If you have 
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Re: [Freesurfer] FW: Most recent/complete FreeSurfer + Patches?

[Douglas N Greve]

On 09/12/2014 11:32 AM, Gurney, Jenny wrote:
> Thanks, Zeke.  OK, that makes sense about the static vs. dynamic linking 
> information.  Good to know about the usage of UPX in case we need to 
> 'decompress' at some point and use 'ldd' and get specific library dependency 
> information.
>
> The list of binaries/scripts came via the FTP download site here:  
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/
This is something that I put together and others on the team have not 
necessarily been contributing to it (not even me on all occasions), so 
it might not be complete.
>
> >From the 'Release Notes' page, it looks like the 'official' patches are:
>
> mri_segstats
> mni152reg
> recon-all
>
> Does that sounds right?  And (going back to the original question) could we 
> just overlay these on 5.3.0-HCP with no expected issues?
That looks right. Again, I don't know about the HCP release
doug
>
> Thanks,
> Matt House, Jenny Gurney and John Flavin @WU in STL
>
> -Original Message-
> From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu]
> Sent: Thursday, September 11, 2014 9:55 AM
> To: freesurfer@nmr.mgh.harvard.edu; Gurney, Jenny
> Subject: Re: [Freesurfer] FW: Most recent/complete FreeSurfer + Patches?
>
> Jenny,
>
> May I ask were you got those list of binaries... Was is from the Release 
> Notes page? I ask because we link to some "official" patches on the release 
> notes page but we also frequently give people "dev" versions of some binaries 
> to help solve a particular issue that they may be having.
> Those dev version are not official patches.
>
> Also, the release version appear statically linked because they get  run 
> through a utility called 'upx' which shrinks them but changes how the 'file' 
> and 'ld' command process them. The binaries you mention below have not been 
> run through that utility.
>
> -Zeke
>
> On 09/09/2014 01:09 PM, Gurney, Jenny wrote:
>> Hi guys!
>>
>> We would like to install the latest and greatest FreeSurfer on the
>> processing cluster used by the CNDA at Washington University.  We're
>> thinking about installing the 5.3.0-HCP, and then over that, the
>> released 5.3.0 patches.  We're looking for verification that doing the
>> install this way makes sense and that these two code sets don't
>> conflict in any way.
>>
>> We know that the 5.3.0-HCP version updates the mris_make_surfaces,
>> however, the patches do not include that update, which is why we are
>> thinking about starting with 5.3.0-HCP as the base install.  Note that
>> this is being done on CentOS 6.x
>>
>> The currently available patches seem to include:
>>
>> mni152reg
>>
>> mri_mcsim
>>
>> mri_segstats
>>
>> recon-all
>>
>> tksurfer-sess
>>
>> tksurferfv
>>
>> Is that a complete list or did we miss some binaries/scripts?
>>
>> Also, it seems that the 'patch' binaries are dynamically linked, while
>> the release binaries are statically linked.  Besides dependency
>> issues, could this cause an issue with results consistency, etc. if
>> other system libraries get updated?
>>
>> Thanks, guys.  Hope all is well.
>>
>> Matt House, Jenny Gurney and John Flavin @WU in STL
>>
>>
>> --
>> --
>>
>> The material in this message is private and may contain Protected
>> Healthcare Information (PHI). If you are not the intended recipient,
>> be advised that any unauthorized use, disclosure, copying or the
>> taking of any action in reliance on the contents of this information
>> is strictly prohibited. If you have received this email in error,
>> please immediately notify the sender via telephone or return mail.
>>
>>
>> ___
>> 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.
>
>
> 
>
> The material in this message is private and may contain Protected Healthcare 
> Information (PHI). If you are not the intended recipient, be advised that any 
> unauthorized use, disclosure, copying or the taking of any action in reliance 
> on the contents of this information is strictly prohibited. If you have 
> received this email in error, please immediately notify the sender via 
> telephone or return mail.
>
> ___
> 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: 6

Re: [Freesurfer] FW: Most recent/complete FreeSurfer + Patches?

[Z K]

Hello,

Yeah I would ignore the contents of that ftp site and simply go with 
whatever the contents are on the Release Notes page. The 3 files you 
have listed make sense based on my quick glance of that page.

And yes, I would simply overlay those files on top of the originals. 
Although it may be a good idea to back up the originals.

-Zeke


On 09/12/2014 11:32 AM, Gurney, Jenny wrote:
> Thanks, Zeke.  OK, that makes sense about the static vs. dynamic linking 
> information.  Good to know about the usage of UPX in case we need to 
> 'decompress' at some point and use 'ldd' and get specific library dependency 
> information.
>
> The list of binaries/scripts came via the FTP download site here:  
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/
>
>  From the 'Release Notes' page, it looks like the 'official' patches are:
>
> mri_segstats
> mni152reg
> recon-all
>
> Does that sounds right?  And (going back to the original question) could we 
> just overlay these on 5.3.0-HCP with no expected issues?
>
> Thanks,
> Matt House, Jenny Gurney and John Flavin @WU in STL
>
> -Original Message-
> From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu]
> Sent: Thursday, September 11, 2014 9:55 AM
> To: freesurfer@nmr.mgh.harvard.edu; Gurney, Jenny
> Subject: Re: [Freesurfer] FW: Most recent/complete FreeSurfer + Patches?
>
> Jenny,
>
> May I ask were you got those list of binaries... Was is from the Release 
> Notes page? I ask because we link to some "official" patches on the release 
> notes page but we also frequently give people "dev" versions of some binaries 
> to help solve a particular issue that they may be having.
> Those dev version are not official patches.
>
> Also, the release version appear statically linked because they get  run 
> through a utility called 'upx' which shrinks them but changes how the 'file' 
> and 'ld' command process them. The binaries you mention below have not been 
> run through that utility.
>
> -Zeke
>
> On 09/09/2014 01:09 PM, Gurney, Jenny wrote:
>> Hi guys!
>>
>> We would like to install the latest and greatest FreeSurfer on the
>> processing cluster used by the CNDA at Washington University.  We're
>> thinking about installing the 5.3.0-HCP, and then over that, the
>> released 5.3.0 patches.  We're looking for verification that doing the
>> install this way makes sense and that these two code sets don't
>> conflict in any way.
>>
>> We know that the 5.3.0-HCP version updates the mris_make_surfaces,
>> however, the patches do not include that update, which is why we are
>> thinking about starting with 5.3.0-HCP as the base install.  Note that
>> this is being done on CentOS 6.x
>>
>> The currently available patches seem to include:
>>
>> mni152reg
>>
>> mri_mcsim
>>
>> mri_segstats
>>
>> recon-all
>>
>> tksurfer-sess
>>
>> tksurferfv
>>
>> Is that a complete list or did we miss some binaries/scripts?
>>
>> Also, it seems that the 'patch' binaries are dynamically linked, while
>> the release binaries are statically linked.  Besides dependency
>> issues, could this cause an issue with results consistency, etc. if
>> other system libraries get updated?
>>
>> Thanks, guys.  Hope all is well.
>>
>> Matt House, Jenny Gurney and John Flavin @WU in STL
>>
>>
>> --
>> --
>>
>> The material in this message is private and may contain Protected
>> Healthcare Information (PHI). If you are not the intended recipient,
>> be advised that any unauthorized use, disclosure, copying or the
>> taking of any action in reliance on the contents of this information
>> is strictly prohibited. If you have received this email in error,
>> please immediately notify the sender via telephone or return mail.
>>
>>
>> ___
>> 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.
>
>
> 
>
> The material in this message is private and may contain Protected Healthcare 
> Information (PHI). If you are not the intended recipient, be advised that any 
> unauthorized use, disclosure, copying or the taking of any action in reliance 
> on the contents of this information is strictly prohibited. If you have 
> received this email in error, please immediately notify the sender via 
> telephone or return mail.
>
>
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[Freesurfer] tracula -prep fails at mri_convert

[Peggy Skelly]

Hi,

I'm processing 3T data with 60 direction vectors and 2 images with b-val =
0. Trac-all -prep has been failing at the command:

> mri_convert --frame 0 31
/dmri/dwi.nii.gz /dmri/lowb.nii.gz
> mri_convert: extra argument ("/dmri/lowb.nii.gz")
> type mri_convert -u for usage

Since --frame seems to only want one value, but we have 2 images with low b
values. Has anyone encountered this problem before?

Peggy


trac-all.log
Description: Binary data


bvals
Description: Binary data
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[Freesurfer] Qdec "create stats tables" error

[Markus Gschwind]

Dear all,

I am trying to make work Qdec on my system ubuntu 12.04.

freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

After I have loaded my qdec.table.dat and renamed the analysis folder ,
when I then try to create the "stats tables", I get an error and it blocks
at 20% of the waiting bar.


Data table loading completed successfully.
>
> SUBJECTS_DIR is '~/Documents/ARNAUD/'
>
> mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/
>
> mkdir: cannot create directory `/usr/local/freesurfer/subjects/qdec':
>> Permission denied
>
> ERROR: In
>> /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx,
>> line 230
>
> vtkKWQdecApp (0x289a94e0):
>
> Script:
>
> vtkTemp2 GenerateStatsDataTables
>
> Returned Error on line 1:
>
> Uncaught exception: command failed: mkdir -p
>> /usr/local/freesurfer/subjects/qdec/stats_tables/
>
>
>> Stack trace:
>
> Uncaught exception: command failed: mkdir -p
>> /usr/local/freesurfer/subjects/qdec/stats_tables/
>
>
>> while executing
>
> "vtkTemp2 GenerateStatsDataTables"
>
>
> It seems that it tries to write into the default SUBJECT_DIR, thing that I
do not understand as I put the actual SUBJECT_DIR in the top line of
qdec.table.dat (and it is correctly recognized in the qdec window
SUBJECTS_DIR).

How could I come around that problem?

Thanks in advance!
Markus
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Re: [Freesurfer] Qdec "create stats tables" error

[Martin Reuter]

Hi Markus,

maybe for some weird reason it uses the subjects_dir from the 
environment variable instead of the qdec file (that would probably be a 
bug). If that's the case, try setting the subject dir on the command 
line before starting qdec:

setenv SUBJECTS_DIR ~/Documents/ARNAUD/
(or the full path). If you use a bash shell, use the equivalent export 
command for that.


Best, Martin

On 09/12/2014 03:30 PM, Markus Gschwind wrote:

Dear all,

I am trying to make work Qdec on my system ubuntu 12.04.

freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

After I have loaded my qdec.table.dat and renamed the analysis folder 
, when I then try to create the "stats tables", I get an error and it 
blocks at 20% of the waiting bar.



Data table loading completed successfully.

SUBJECTS_DIR is '~/Documents/ARNAUD/'

mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/

mkdir: cannot create directory
`/usr/local/freesurfer/subjects/qdec': Permission denied

ERROR: In
/usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx,
line 230

vtkKWQdecApp (0x289a94e0): 

  Script: 


vtkTemp2 GenerateStatsDataTables

  Returned Error on line 1: 


Uncaught exception: command failed: mkdir -p
/usr/local/freesurfer/subjects/qdec/stats_tables/


Stack trace: 


Uncaught exception: command failed: mkdir -p
/usr/local/freesurfer/subjects/qdec/stats_tables/


  while executing

"vtkTemp2 GenerateStatsDataTables"


It seems that it tries to write into the default SUBJECT_DIR, thing 
that I do not understand as I put the actual SUBJECT_DIR in the top 
line of qdec.table.dat (and it is correctly recognized in the qdec 
window SUBJECTS_DIR).


How could I come around that problem?

Thanks in advance!
Markus


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--
Dr. Martin Reuter

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu

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Re: [Freesurfer] Qdec "create stats tables" error

[Markus Gschwind]

Hi Martin!

Thanks!
Yes, indeed typing in the command
export SUBJECTS_DIR= before starting qdec solved the first
problem... there are others to follow...

When now writing the table stats file:

Data table loading completed successfully.

SUBJECTS_DIR is '~/Documents/ARNAUD/'

mkdir -p /home/user/Documents/ARNAUD/qdec/stats_tables/


> --

asegstats2table --common-segs --meas volume --tablefile
> /home/user/Documents/ARNAUD/qdec/stats_tables/aseg.volume.stats.dat
> --statsfile=aseg.stats --subjects s01 s02 s03 s04 s05 s06 s07 s08 s09 s10
> s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27

SUBJECTS_DIR : ~/Documents/ARNAUD/

Parsing the .stats files
> ERROR: The stats file ~/Documents/ARNAUD/s01/stats/aseg.stats is not found
> or is too small to be a valid statsfile
> Use --skip flag to automatically skip bad stats files
> ERROR: In
> /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx,
> line 230
> vtkKWQdecApp (0x28594510):
> Script:
> vtkTemp2 GenerateStatsDataTables
> Returned Error on line 1:
> Uncaught exception: command failed: asegstats2table --common-segs --meas
> volume --tablefile
> /home/user/Documents/ARNAUD/qdec/stats_tables/aseg.volume.stats.dat
> --statsfile=aseg.stats --subjects s01 s02 s03 s04 s05 s06 s07 s08 s09 s10
> s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27
> Stack trace:
> Uncaught exception: command failed: asegstats2table --common-segs --meas
> volume --tablefile
> /home/user/Documents/ARNAUD/qdec/stats_tables/aseg.volume.stats.dat
> --statsfile=aseg.stats --subjects s01 s02 s03 s04 s05 s06 s07 s08 s09 s10
> s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27
> while executing
> "vtkTemp2 GenerateStatsDataTables"


The file ~/Documents/ARNAUD/s01/stats/aseg.stats is very well there and
seems very normal, with plenty of numbers in it.

The /home/user/Documents/ARNAUD/qdec/stats_tables/ folders are created, but
empty.

Any further ideas?
Thanks !

Markus

2014-09-12 21:47 GMT+02:00 Martin Reuter :

>  Hi Markus,
>
> maybe for some weird reason it uses the subjects_dir from the environment
> variable instead of the qdec file (that would probably be a bug). If that's
> the case, try setting the subject dir on the command line before starting
> qdec:
> setenv SUBJECTS_DIR ~/Documents/ARNAUD/
> (or the full path). If you use a bash shell, use the equivalent export
> command for that.
>
> Best, Martin
>
>
> On 09/12/2014 03:30 PM, Markus Gschwind wrote:
>
> Dear all,
>
>  I am trying to make work Qdec on my system ubuntu 12.04.
>
>  freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
>
>  After I have loaded my qdec.table.dat and renamed the analysis folder ,
> when I then try to create the "stats tables", I get an error and it blocks
> at 20% of the waiting bar.
>
>
>   Data table loading completed successfully.
>>
>> SUBJECTS_DIR is '~/Documents/ARNAUD/'
>>
>> mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/
>>
>> mkdir: cannot create directory `/usr/local/freesurfer/subjects/qdec':
>>> Permission denied
>>
>> ERROR: In
>>> /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx,
>>> line 230
>>
>> vtkKWQdecApp (0x289a94e0):
>>
>> Script:
>>
>> vtkTemp2 GenerateStatsDataTables
>>
>> Returned Error on line 1:
>>
>> Uncaught exception: command failed: mkdir -p
>>> /usr/local/freesurfer/subjects/qdec/stats_tables/
>>
>>
>>>  Stack trace:
>>
>> Uncaught exception: command failed: mkdir -p
>>> /usr/local/freesurfer/subjects/qdec/stats_tables/
>>
>>
>>>  while executing
>>
>> "vtkTemp2 GenerateStatsDataTables"
>>
>>
>>  It seems that it tries to write into the default SUBJECT_DIR, thing
> that I do not understand as I put the actual SUBJECT_DIR in the top line of
> qdec.table.dat (and it is correctly recognized in the qdec window
> SUBJECTS_DIR).
>
> How could I come around that problem?
>
> Thanks in advance!
> Markus
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
> Dr. Martin Reuter
>
> Instructor in Neurology
>   Harvard Medical School
> Assistant in Neuroscience
>   Dept. of Radiology, Massachusetts General Hospital
>   Dept. of Neurology, Massachusetts General Hospital
> Research Affiliate
>   Computer Science and Artificial Intelligence Lab,
>   Dept. of Electrical Engineering and Computer Science,
>   Massachusetts Institute of Technology
>
> A.A.Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, MA 02129
>
> Phone: +1-617-724-5652
> Email:
>mreu...@nmr.mgh.harvard.edu
>reu...@mit.edu
> Web  : http://reuter.mit.edu
>
>
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>
>
> The information in this e-mail is 

Re: [Freesurfer] FsFast Functional Connectivity Analysis

[Jiahe Zhang]

Hi Doug,

My issue is I am not intending to use a labeled segmented ROI. My main goal
is to calculate the connectivity strength between two binarized ROIs that
are functionally defined. Can fcseed-config accept non Freesurfer segmented
ROIs?

Thanks,
JIahe

On Fri, Sep 12, 2014 at 11:08 AM, Douglas N Greve  wrote:

>
> You need to have your ROI as a segmentation in the anatomical
> (conformed) space. If it is a label on the surface, you can use
> mri_label2vol to turn it into a volume (make sure to use --proj frac 0 1
> .1  to fill the ribbon). When you run funcroi-config specify -seg
> yourseg.mgz 1 where yourseg.mgz is the output of mri_label2vol and "1"
> refers to the fact that the output volume is a binary mask where your
> ROI is 1 and everything else is 0
>
> doug
>
>
> On 09/12/2014 09:05 AM, Jiahe Zhang wrote:
> > Hi Doug,
> >
> > I was able to get the surface connectivity analysis to run
> > successfully for the L.Cingulate example that you posted online
> > (
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
> ).
> > For my own analysis, I'm hoping to use my own functionally defined
> > ROIs instead of freesurfer segmented regions. For that, do I pass a
> > vol2surf command on my spherical ROIs and then run the same analysis?
> > I saw that to prepare a ROI for this kind of analysis, I need to
> > create a configuration file using funcroi-config, but this command
> > seems to use anatomical ROIs based on freesurfer segmentation again.
> >
> > Could you advise how to proceed?
> >
> > Thanks,
> > Jiahe
> >
> >
> > On Mon, Aug 11, 2014 at 5:18 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > How did you look at fmcpr.up.sm6.fsaverage.lh.nii.gz? If you did
> > not do
> > this, try it
> >
> > tksurfer fsaverage lh inflated -ov fmcpr.up.sm6.fsaverage.lh.nii.gz
> -t
> > fmcpr.up.sm6.fsaverage.lh.nii.gz
> >
> > This will bring up an overlay as well as a time course
> >
> >
> > On 08/11/2014 05:05 PM, Jiahe Zhang wrote:
> > > Both looked fine. First value in .mincost is .45
> > >
> > >
> > > On Mon, Aug 11, 2014 at 4:51 PM, Douglas N Greve
> > > mailto:gr...@nmr.mgh.harvard.edu>
> >  > >> wrote:
> > >
> > > two ways:
> > >
> > > 1. run tkregister-sess to visually check them
> > > 2. look at the first value in register.dof6.dat.mincost. It
> > is hard to
> > > say what a threshold is for a good registration, but typical
> > > values are
> > > about .5 or so. If it is .8 or more, it is probably a
> > problem (and
> > > probably the initialization is not good)
> > >
> > >
> > > On 08/11/2014 04:35 PM, Jiahe Zhang wrote:
> > > > I'm not sure how to check the registration. I see a
> > > register.dof6.dat
> > > > being produced for each run but I can't tell if it
> > contains the
> > > > correct parameters. How can I tell if the registration was
> > accurate?
> > > >
> > > >
> > > > On Mon, Aug 11, 2014 at 4:01 PM, Douglas N Greve
> > > >  > 
> >  >>
> > >  > 
> > >  >  > > >
> > > > did you check the registration?
> > > >
> > > > On 08/11/2014 03:53 PM, Jiahe Zhang wrote:
> > > > > There's nothing even when the threshold is set to 0.
> > > > >
> > > > > I just checked the preprocessing outputs. I can see
> > > normal-looking
> > > > > volumes
> > > > > fmcpr.nii.gz
> > > > > fmcpr.up.nii.gz
> > > > > fmcpr.up.sm6.mni305.2mm.nii.gz
> > > > >
> > > > > But there is nothing when I open
> > > fmcpr.up.sm6.fsaverage.lh.nii.gz or
> > > > > fmcpr.up.sm6.fsaverage.rh.nii.gz
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Wed, Aug 6, 2014 at 6:40 PM, Douglas N Greve
> > > > >  > 
> > >  > >
> > >  > 
> >  >>>
> > > >  > 
> > >  > >
> > > >  > 

Re: [Freesurfer] Qdec "create stats tables" error

[Markus Gschwind]

Dear Martin,

Actually, I found that it doesn't like the ~/ for /home/username

When replacing the first line in the qdec.table.dat
SUBJECTS_DIR=/home/username/...

and also export the SUBJECTS_DIR in the terminal with the foll path, it
works nicley!

Thanks again!
Markus

2014-09-12 22:06 GMT+02:00 Markus Gschwind :

> Hi Martin!
>
> Thanks!
> Yes, indeed typing in the command
> export SUBJECTS_DIR= before starting qdec solved the first
> problem... there are others to follow...
>
> When now writing the table stats file:
>
> Data table loading completed successfully.
>
> SUBJECTS_DIR is '~/Documents/ARNAUD/'
>
> mkdir -p /home/user/Documents/ARNAUD/qdec/stats_tables/
>
>
>> --
>
> asegstats2table --common-segs --meas volume --tablefile
>> /home/user/Documents/ARNAUD/qdec/stats_tables/aseg.volume.stats.dat
>> --statsfile=aseg.stats --subjects s01 s02 s03 s04 s05 s06 s07 s08 s09 s10
>> s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27
>
> SUBJECTS_DIR : ~/Documents/ARNAUD/
>
> Parsing the .stats files
>> ERROR: The stats file ~/Documents/ARNAUD/s01/stats/aseg.stats is not
>> found or is too small to be a valid statsfile
>> Use --skip flag to automatically skip bad stats files
>> ERROR: In
>> /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx,
>> line 230
>> vtkKWQdecApp (0x28594510):
>> Script:
>> vtkTemp2 GenerateStatsDataTables
>> Returned Error on line 1:
>> Uncaught exception: command failed: asegstats2table --common-segs --meas
>> volume --tablefile
>> /home/user/Documents/ARNAUD/qdec/stats_tables/aseg.volume.stats.dat
>> --statsfile=aseg.stats --subjects s01 s02 s03 s04 s05 s06 s07 s08 s09 s10
>> s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27
>> Stack trace:
>> Uncaught exception: command failed: asegstats2table --common-segs --meas
>> volume --tablefile
>> /home/user/Documents/ARNAUD/qdec/stats_tables/aseg.volume.stats.dat
>> --statsfile=aseg.stats --subjects s01 s02 s03 s04 s05 s06 s07 s08 s09 s10
>> s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27
>> while executing
>> "vtkTemp2 GenerateStatsDataTables"
>
>
> The file ~/Documents/ARNAUD/s01/stats/aseg.stats is very well there and
> seems very normal, with plenty of numbers in it.
>
> The /home/user/Documents/ARNAUD/qdec/stats_tables/ folders are created,
> but empty.
>
> Any further ideas?
> Thanks !
>
> Markus
>
> 2014-09-12 21:47 GMT+02:00 Martin Reuter :
>
>>  Hi Markus,
>>
>> maybe for some weird reason it uses the subjects_dir from the environment
>> variable instead of the qdec file (that would probably be a bug). If that's
>> the case, try setting the subject dir on the command line before starting
>> qdec:
>> setenv SUBJECTS_DIR ~/Documents/ARNAUD/
>> (or the full path). If you use a bash shell, use the equivalent export
>> command for that.
>>
>> Best, Martin
>>
>>
>> On 09/12/2014 03:30 PM, Markus Gschwind wrote:
>>
>> Dear all,
>>
>>  I am trying to make work Qdec on my system ubuntu 12.04.
>>
>>  freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
>>
>>  After I have loaded my qdec.table.dat and renamed the analysis folder ,
>> when I then try to create the "stats tables", I get an error and it blocks
>> at 20% of the waiting bar.
>>
>>
>>   Data table loading completed successfully.
>>>
>>> SUBJECTS_DIR is '~/Documents/ARNAUD/'
>>>
>>> mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/
>>>
>>> mkdir: cannot create directory `/usr/local/freesurfer/subjects/qdec':
 Permission denied
>>>
>>> ERROR: In
 /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx,
 line 230
>>>
>>> vtkKWQdecApp (0x289a94e0):
>>>
>>> Script:
>>>
>>> vtkTemp2 GenerateStatsDataTables
>>>
>>> Returned Error on line 1:
>>>
>>> Uncaught exception: command failed: mkdir -p
 /usr/local/freesurfer/subjects/qdec/stats_tables/
>>>
>>>
  Stack trace:
>>>
>>> Uncaught exception: command failed: mkdir -p
 /usr/local/freesurfer/subjects/qdec/stats_tables/
>>>
>>>
  while executing
>>>
>>> "vtkTemp2 GenerateStatsDataTables"
>>>
>>>
>>>  It seems that it tries to write into the default SUBJECT_DIR, thing
>> that I do not understand as I put the actual SUBJECT_DIR in the top line of
>> qdec.table.dat (and it is correctly recognized in the qdec window
>> SUBJECTS_DIR).
>>
>> How could I come around that problem?
>>
>> Thanks in advance!
>> Markus
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> --
>> Dr. Martin Reuter
>>
>> Instructor in Neurology
>>   Harvard Medical School
>> Assistant in Neuroscience
>>   Dept. of Radiology, Massachusetts General Hospital
>>   Dept. of Neurology, Massachusetts General Hospital
>> Research Affiliate
>>   Computer Science and Artificial Intelligence Lab,
>>   Dept. of Electrical Engineering and Computer S

[Freesurfer] trac-all exited with errors

[BigBen2293]

Hey everyone,

 

i have tried to run the trac-all command (Tracula), but it returned an error (bvecs and bvals don't have the same number of entries).

I'm using the latest freesurfer and Tracula update.

 

I have attached the corresponding bvecs and bvals files. If the log file is necessary i could sent it in the next mail (it is very big 1,3 MB).

 

Ben




bvals
Description: Binary data


bvecs
Description: Binary data
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Re: [Freesurfer] how to shrink wm surface

[Harms, Michael]

Hi Bruce,
I was wondering if there is info somewhere about what each of those 7 MIN_
and MAX_ variables control regarding the positioning of the white and pial
surfaces?

thanks,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 9/9/14 7:35 AM, "Bruce Fischl"  wrote:

>Hi Andrea
>
>what is the background image? This is usually either a failure of the
>intensity normalization or of the surface deformation/segmentation to
>adaptively estimate the underlying intensity distributions of the
>gray/white matter. If you look in recon-all.log for that subject you will
>find a set of lines like:
>
>setting MIN_GRAY_AT_WHITE_BORDER to 71.1 (was 70)
>setting MAX_BORDER_WHITE to 112.0 (was 105)
>setting MIN_BORDER_WHITE to 83.0 (was 85)
>setting MAX_CSF to 59.1 (was 40)
>setting MAX_GRAY to 100.0 (was 95)
>setting MAX_GRAY_AT_CSF_BORDER to 77.0 (was 75)
>setting MIN_GRAY_AT_CSF_BORDER to 47.2 (was 40)
>
>
>
>in your case for example you will probably find that the min_border_white
>is too high or tha the max_gray is too low. You can set these using the
>expert opts for both mri_segment and mris_make_surfaces.
>
>cheers
>Bruce
>
>
>On Tue, 9 Sep 2014, Andrea
>Horváth wrote:
>
>> Dear Freesurfers,
>>
>>
>> After running recon-all, the wm surfaces are too close to the pial
>>surface,
>> some gray matter is segmented as white matter as seen in the attached
>> picture (red cross: a bigger cortical part is included in the white
>>matter).
>>
>> How can I shrink the wm surface?
>>
>> Thank you for your help!
>>
>> Andrea
>>
>>
>>
>>
>>
>>
>>



The materials in this message are private and may contain Protected Healthcare 
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intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
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Re: [Freesurfer] how to shrink wm surface

[Matt Glasser]

Have a look at mris_make_surfaces.c, this is how I learned about most of
this stuff as the code is pretty well commented (and Bruce telling me
things).

Peace,

Matt.

On 9/12/14, 11:01 PM, "Harms, Michael"  wrote:

>
>Hi Bruce,
>I was wondering if there is info somewhere about what each of those 7 MIN_
>and MAX_ variables control regarding the positioning of the white and pial
>surfaces?
>
>thanks,
>-MH
>
>--
>Michael Harms, Ph.D.
>
>---
>Conte Center for the Neuroscience of Mental Disorders
>Washington University School of Medicine
>Department of Psychiatry, Box 8134
>660 South Euclid Ave.   Tel: 314-747-6173
>St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
>On 9/9/14 7:35 AM, "Bruce Fischl"  wrote:
>
>>Hi Andrea
>>
>>what is the background image? This is usually either a failure of the
>>intensity normalization or of the surface deformation/segmentation to
>>adaptively estimate the underlying intensity distributions of the
>>gray/white matter. If you look in recon-all.log for that subject you will
>>find a set of lines like:
>>
>>setting MIN_GRAY_AT_WHITE_BORDER to 71.1 (was 70)
>>setting MAX_BORDER_WHITE to 112.0 (was 105)
>>setting MIN_BORDER_WHITE to 83.0 (was 85)
>>setting MAX_CSF to 59.1 (was 40)
>>setting MAX_GRAY to 100.0 (was 95)
>>setting MAX_GRAY_AT_CSF_BORDER to 77.0 (was 75)
>>setting MIN_GRAY_AT_CSF_BORDER to 47.2 (was 40)
>>
>>
>>
>>in your case for example you will probably find that the min_border_white
>>is too high or tha the max_gray is too low. You can set these using the
>>expert opts for both mri_segment and mris_make_surfaces.
>>
>>cheers
>>Bruce
>>
>>
>>On Tue, 9 Sep 2014, Andrea
>>Horváth wrote:
>>
>>> Dear Freesurfers,
>>>
>>>
>>> After running recon-all, the wm surfaces are too close to the pial
>>>surface,
>>> some gray matter is segmented as white matter as seen in the attached
>>> picture (red cross: a bigger cortical part is included in the white
>>>matter).
>>>
>>> How can I shrink the wm surface?
>>>
>>> Thank you for your help!
>>>
>>> Andrea
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>
>
>
>The materials in this message are private and may contain Protected
>Healthcare Information or other information of a sensitive nature. If you
>are not the intended recipient, be advised that any unauthorized use,
>disclosure, copying or the taking of any action in reliance on the
>contents of this information is strictly prohibited. If you have received
>this email in error, please immediately notify the sender via telephone
>or return mail.
>
>___
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>
>
>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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