[Freesurfer] 'Invalid' license file

[Lee.Reid]

Hi,
Our IT department have recently upgraded our cluster OS and now Freesurfer 
complains that its license is invalid. I have tried rebuilding, and acquiring a 
new license, but these do not fix the problem. The license file I am using 
works in my Ubuntu 12.04 computer - it has been copied across as a file, not 
via a text editor - and used to work on an older version of the same OS.

Do you know of any solution to this issue?

I've tried everything I have seen on the mailing list, including naming it 
.license and license.txt, checking for whitespace, etc.
Our OS is now SUSE Linux Enterprise Server 12 SP1 (x86_64).

Many thanks,
Lee



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[Freesurfer] which CUDA version driver to use

[Karamfil Bahchevanov]

Dear Freesurfers,

I'd like to experiment with faster proceesing, in fact I'd like to try
CUDA. However there are several possible drivers for my quadro K2000. I'm
not sure which one to choose. Should I install the latest 7.5. version, or
use the older version 6, or even older? I'm not sure if the latest will run
with freesurfer smoothly.
Here is my system: Xeon e5-1620, QUADRO K2000
I'm running Freesurfer v5.3 on CentOS 6.8, kernel 2.6.32-642.1.1.el6.x86_64.

Thank you,
KMB
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[Freesurfer] Subject: Re: Zero cortical thickness

[A Nunes]

Hi Douglas,

I meant a surface area extracted from a surface based atlas.

Thanks
Adonay
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Re: [Freesurfer] Zero cortical thickness

[Douglas Greve]

what do you mean by "area"? do you mean one of the cortical ROIs or do 
you mean a general location?


On 8/15/16 4:13 PM, A Nunes wrote:
> Hi,
>
> I have read in the mailing list about zero cortical thickness, but I
> still have some doubts.
>
> I am calculating the average cortical thickness of some areas, and
> there are a few that almost all the subjects' thickness is zero,
> others only some subjects score zero. For the ones that almost all
> subjects is zero, I would guess is not considered cortical, however,
> all my areas are cortical.
>
> - If I compute a ttest against two groups, should I set the zeros as
> NaNs? or are the zero thickness meaningful (a genuine measure or a
> segmentation artifact)?
>
> -Should I use the -l ?h.cortex.label to avoid having zero thickness in
> some areas? If so, at which point? the commands used are:
>
> mri_surf2surf --srcsubject fsaverage --trgsubject subjid --hemi ?h
> --sval-annot fsaverage/label/?h.areas.annot --tval
> $SUBJECTS_DIR/subjid/label/?h.areas.annot
>
> mris_anatomical_stats -a
> $SUBJECTS_DIR/subjid/label/?h.areas.annot$SUBJECTS_DIR/subjid/label/?h.areas.annot
>   -f $SUBJECTS_DIR/subjid/stats/?h.areas.stats -b  subjid ?h
>
>
> Thanks
> Adonay
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>

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[Freesurfer] Zero cortical thickness

[A Nunes]

Hi,

I have read in the mailing list about zero cortical thickness, but I
still have some doubts.

I am calculating the average cortical thickness of some areas, and
there are a few that almost all the subjects' thickness is zero,
others only some subjects score zero. For the ones that almost all
subjects is zero, I would guess is not considered cortical, however,
all my areas are cortical.

- If I compute a ttest against two groups, should I set the zeros as
NaNs? or are the zero thickness meaningful (a genuine measure or a
segmentation artifact)?

-Should I use the -l ?h.cortex.label to avoid having zero thickness in
some areas? If so, at which point? the commands used are:

mri_surf2surf --srcsubject fsaverage --trgsubject subjid --hemi ?h
--sval-annot fsaverage/label/?h.areas.annot --tval
$SUBJECTS_DIR/subjid/label/?h.areas.annot

mris_anatomical_stats -a
$SUBJECTS_DIR/subjid/label/?h.areas.annot$SUBJECTS_DIR/subjid/label/?h.areas.annot
 -f $SUBJECTS_DIR/subjid/stats/?h.areas.stats -b  subjid ?h


Thanks
Adonay
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[Freesurfer] Job postings: Post-doc & Data manager/programmer

[Gregory Book]

The Olin Neuropsychiatry Research Center, located in Hartford CT, USA is
looking to fill 2 open positions.

The Olin Neuropsychiatry Research Center has an opening for a post-doc
specializing in neuroinformatics, big-data analysis, and machine learning.
The Olin Center is the psychiatric research center within Hartford
Hospital’s Institute of Living campus, in Hartford, CT. We house a Siemens
Skyra 3T whole-body MRI, multiple EEG, TMS, and eye tracking systems, an
internal historical database of nearly 13,000 MRI sessions, and a 400-core
Linux compute cluster. The candidate will pursue their own research with a
focus on neuroinformatics and big-data analysis and assist multiple
principle investigators with large scale analyses. The candidate will
contribute to the development of the open-source Neuroinformatics Database (
http://github.com/gbook/nidb) and publish journal articles on their own
research and software development. MS degree in engineering, science,
neuroscience, or psychology is required, PhD preferred. Candidate is
expected to have experience in SQL programming and at least one other
programming language. Proficiency in multiple programming languages such as
Perl, C, C++, JavaScript, PHP, Matlab, and Python is highly desirable.
Contact Greg Book at gregory.b...@hhchealth.org

The Olin Neuropsychiatry Research Center is seeking a data
manager/programmer to help maintain neuroimaging databases in support of
multiple NIH funded projects. The Olin Center is a neuropsychiatric
research center within Hartford Hospital’s Institute of Living campus. We
house a 3T MRI, multiple EEG, TMS, and eye tracking systems, an internal
database of nearly 13,000 MRI sessions, and a 400-core compute cluster. The
primary responsibilities of the data manager will be to maintain internal
and public imaging databases by performing the following tasks: remove
personally identifiable information, perform uploads to NIH repositories,
identify missing data, organize identifiers, support remote sites with data
importing/uploading, and ensure data redundancy and backups. Additionally,
the data manager may contribute to the development of the Neuroinformatics
Database (http://github.com/gbook/nidb) using SQL, PHP, Perl, C++ and other
programming languages for the purpose of making data management more
efficient and robust. The data manager also will have the opportunity to
participate in research projects and contribute to manuscripts. Bachelor’s
degree in engineering, science, neuroscience, or psychology is required,
Masters or higher is preferred. Candidate is expected to have experience in
SQL programming. Proficiency in multiple programming languages is highly
desirable. Contact Greg Book at gregory.b...@hhchealth.org
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Re: [Freesurfer] dividing Freesufer subfields into one anterior, middle and posterior region

[Iglesias, Eugenio]

Hi Erik,

there’s no FreeSurfer program to do this in a straightforward manner. But you 
can:

1. read in the hippocampal subfield segmentation  into matlab with the MRIread 
function in the $FREESURFER_HOME/matlab directory.
2. extract the major axis with the hippocampus using PCA.
3. Subdivide the subfields along that axis

You can find code to do 2 and 3 here: https://github.com/garikoitz/hippovol

Cheers,

/Eugenio

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


On 15 Aug 2016, at 17:26, Erik Lindberg 
> wrote:

Dear FS experts. I want to divid the FS subfield segementation into a anterior 
part, one middle part and posterior segment - or potentially divide the rang 
into 10% of the whole rang - and then move backword until I extracted 10 
subparts.

Is there some way I can do that?

Thanks
Erik
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[Freesurfer] dividing Freesufer subfields into one anterior, middle and posterior region

[Erik Lindberg]

Dear FS experts. I want to divid the FS subfield segementation into a
anterior part, one middle part and posterior segment - or potentially
divide the rang into 10% of the whole rang - and then move backword until I
extracted 10 subparts.

Is there some way I can do that?

Thanks
Erik
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Re: [Freesurfer] How to run part of TRACULA

[Athanasia Metoki]

Dear Anastasia,

Now I understand and it makes perfect sense! Thank you very much for your
answers.

Best,
Nasia Metoki

*Athanasia Metoki*
Psychology Doctoral Student - Brain and Cognitive Sciences Program
Cognitive Neuroscience Laboratory
Temple University
Department of Psychology
1701 N 13th St.
Philadelphia, PA 19122
Email: athanasia.met...@temple.edu

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On Mon, Aug 15, 2016 at 8:49 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Nasia - They both have preprocessing steps because recon-all runs on
> the T1 and trac-all runs on the DWIs, so they preprocess different images.
>
> You cannot skip any of the steps in recon-all and still get a
> segmentation. The point of the autorecon schemes is mostly to repeat only
> one part of the processing if you change something in between, not to skip
> part of the processing entirely.
>
> Best,
>
> a.y
>
>
> On Sun, 14 Aug 2016, Athanasia Metoki wrote:
>
> Dear Anastasia,
>>
>> Thank you so much for responding so fast!
>> I see what you're saying and thank you for your input.
>>
>> I have one more question if you don't mind taking a moment to respond. I
>> noticed that both trac-all and recon-all include some preprocessing steps
>> (eg. motion correction, eddy current correction, skull stripping). How
>> come
>> and they both have these steps if one is supposed to run both commands? My
>> understandind is, if someone wants to run TRACULA from scratch, they would
>> need to run both recon-all (first) and trac-all (second). One would have
>> to
>> run recon-all in order to get the cortical parcellation and subcortical
>> segmentation (mri/aparc+aseg.mgz) file  which will be used from trac-all
>> in
>> the mask creation step.
>>
>> In my case where I have some preprocessed data, is there a particular
>> -autorecon# command which only does some of the recon steps that would
>> help
>> me get the cortical parcellation and subcortical segmentation
>> (mri/aparc+aseg.mgz) file that I am missing?
>>
>> I understand I may be asking a lot! Once more thank you very much for your
>> initial response and your time!
>>
>> Best,
>> Nasia Metoki
>>
>>
>> On Sat, Aug 13, 2016 at 8:03 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Athanasia - TRACULA expects certains files named a certain
>>   way to be
>>   there at the end of each preprocessing step. These are described
>>   here:
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdir
>> ectoriesandfile
>>   s
>>
>>   If you are using pre-existing files, you have to make sure that
>>   they
>>   follow the same file/directory naming convention.
>>
>>   You just run recon-all with the default settings. The aparc+aseg
>>   is
>>   created in one of the last steps of recon-all, so all the
>>   previous steps
>>   have to run as well.
>>
>>   Hope this helps!
>>
>>   a.y
>>
>>   On Sat, 13 Aug 2016, Athanasia Metoki wrote:
>>
>>   > Dear Freesurfer Developers,
>>   >
>>   > I am fairly new to image analysis and this is the first time I
>>   use
>>   > Freesurfer.
>>   >
>>   > I have some DTI data and I have already preprocessed them and
>>   ran bedpostX
>>   > using FSL. I ran probabilistic tractography on FSL as well to
>>   get the
>>   > connectivity between two distinct brain areas.
>>   >
>>   > I am also interested in getting the probability distribution
>>   for the
>>   > uncinate fasciculi so I am trying to use TRACULA.
>>   > My question is: Can I use TRCULA without doing preprocessing
>>   and dedpostX
>>   > again? If so, will I need to do the cortical parcelation and
>>   subcortical
>>   > segmentation with recon-all and get the aparc+aseg.mgz file in
>>   order to use
>>   > TRACULA? Which argument would I need to use when I run
>>   recon-all?
>>   >
>>   > Thank you!
>>   >
>>   > Athanasia Metoki
>>   > Psychology Doctoral Student - Brain and Cognitive Sciences
>>   Program
>>   > Cognitive Neuroscience Laboratory
>>   > Temple University
>>   > Department of Psychology
>>   > 1701 N 13th St.
>>   > Philadelphia, PA 19122
>>   > Email: athanasia.met...@temple.edu
>>   >
>>   

Re: [Freesurfer] TRACULA extracting diffusion measures using ASEG or WM parc

[Anastasia Yendiki]

Hi Yoon - Please see "FA ROI analysis" in the diffusion tutorial on the 
freesurfer wiki:


https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion_DtiIntegration#FAROIAnalysis

Best,

a.y

On Mon, 15 Aug 2016, Chung, Yoonho wrote:



Hi Anastasia,


Is it possible to extract diffusion measures FA, ADC etc. within
the subcortical (ASEG) or WM parc ROI regions using the Freesurfer tools? If
possible, can you show how it can be done? Thank you in advance.


Best,

Yoon


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[Freesurfer] TRACULA extracting diffusion measures using ASEG or WM parc

[Chung, Yoonho]

Hi Anastasia,


Is it possible to extract diffusion measures FA, ADC etc. within the 
subcortical (ASEG) or WM parc ROI regions using the Freesurfer tools? If 
possible, can you show how it can be done? Thank you in advance.


Best,

Yoon
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Re: [Freesurfer] FSFAST ROI atlas

[Douglas Greve]

I have not used them myself.


On 8/15/16 10:23 AM, Sabin Khadka wrote:

HI all-

I am using FSFAST to extract ROI time series values for further 
connectivity analysis. I've used Desikan, Destriuex and DKT atlas.


However, I was wondering if anyone has used Power et.al  
2011 rois and/or HCP's newly defined 180/per hemi rois to extract time 
series data. If so could you please advise me on how do it (if they 
are at all possible).


Cheers,
Sabin Khadka


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Re: [Freesurfer] mri_preproc error

[Ruopeng Wang]

Hi Younghoon,

You can adjust those settings from the GUI after you load the surface and 
overlays. Just click “Configure Overlay” button on the left panel after you 
load the overlay. 

Best,
Ruopeng

> On Aug 14, 2016, at 9:41 PM, YoungHoon Kwon  wrote:
> 
> Hello Freesurfer Developers,
> 
> I'm working on group analysis, and I have done GLM analysis(mris_glmfit) on 
> Linux. Next step is to visualize it, so I followed the instruction from the 
> FsTutorial website. 
> 
> freeview -f 
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5
>  -viewport 3d
> 
> Basically, I ran the commend above, and I got the effor "Unrecognized 
> sub-option flag 'annot_outline'" or "unrecognized sub-opton flag 
> 'overlay_threshold'." I think it's because I'm using old FS version which is 
> 5.1, and the tutorial is based on FS 6.1 version. I tried to use tksurfer, 
> but for some reason, it didn't work. I decided to use a freeview anyway.
> 
> On 5.1 version, what do I need to do to visualize them? How should I deal 
> with overlay threshold and annot_outline? Please let me know.
> 
> Best regards,
> Younghoon Kwon
> 
> 
> 2016-07-14 14:01 GMT-04:00 YoungHoon Kwon  >:
> 
> -- Forwarded message --
> From: YoungHoon Kwon >
> Date: 2016-07-13 21:10 GMT-04:00
> Subject: mri_preproc error
> To: freesurfer@nmr.mgh.harvard.edu 
> 
> 
> Hello FreeSurfer Developers,
> 
> I tried to assemble the data by using mri_preproc, then it shows segmentation 
> fault (core dumped) after running. I searched for the solution, but I 
> couldn't find it.
> 
> Here's information
> 
> Error : Segmentation fault (core dumped)
> 
> Input : FS.txt (FSGD file)
> GroupDescriptorFile 1
> Title All
> Class Male
> Class Female
> Input002_S_4213_AMale
> Input002_S_4225_AMale
> Input002_S_4262_AFemale
> 
> command:
> [knho@in-rady-neuro11 test]$ mris_preproc --fsgd FS.txt \ --target fsaverage 
> --hemi lh \ --meas thickness \ --out practice_result.mgh
> nsubjects = 3
> tmpdir is ./tmp.mris_preproc.2677
> /localscratch3/test
> Log file is practice_result.mris_preproc.log
> Wed Jul 13 19:31:44 EDT 2016
> setenv SUBJECTS_DIR /localscratch3/test
> cd /localscratch3/test
> /net/age3/DATA_from_AGE0/FREESURFER/freesurfer51/bin/mris_preproc --fsgd 
> FS.txt --target fsaverage --hemi lh --meas thickness --out practice_result.mgh
> 
> Linux in-rady-neuro11.indyrad.iupui.edu 
>  3.16.2-201.fc20.x86_64 #1 SMP Mon 
> Sep 15 19:57:50 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
> $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $
> freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
> tmpdir is ./tmp.mris_preproc.2677
> Src lh sphere.reg
> Trg lh sphere.reg
> 
> ---
> #@# 1/3 002_S_4213_A Wed Jul 13 19:31:44 EDT 2016 --
> ---
> mri_surf2surf --srcsubject 002_S_4213_A --srchemi lh --srcsurfreg sphere.reg 
> --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval 
> ./tmp.mris_preproc.2677/002_S_4213_A.1.mgh --sval 
> /localscratch3/test/002_S_4213_A/surf/lh.thickness --sfmt curv --noreshape 
> --no-cortex
> Segmentation fault (core dumped)
> 
> I found some advice from online, and it suggested to run recon-all; however 
> it didn't work. I really don't know what is wrong. Can anyone figure out this 
> error?
> 
> 1) Versioin : FreeSurfer 5.1
> 2) Platform : Linux
> 3) uname -a : Linux in-rady-neuro11.indyrad.iupui.edu 
>  3.16.2-201.fc20.x86_64 #1 SMP Mon 
> Sep 15 19:57:50 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
> 
> 
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[Freesurfer] FSFAST ROI atlas

[Sabin Khadka]

HI all-

I am using FSFAST to extract ROI time series values for further
connectivity analysis. I've used Desikan, Destriuex and DKT atlas.

However, I was wondering if anyone has used Power et.al 2011 rois and/or
HCP's newly defined 180/per hemi rois to extract time series data. If so
could you please advise me on how do it (if they are at all possible).

Cheers,
Sabin Khadka
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Re: [Freesurfer] FreeSurfer TrackVis Transforms

[Anastasia Yendiki]

Hi - Check out the dmri_trk2trk command. In your case, you'd need to pass 
it a transformation file from the registration between your diffusion and 
structural data, which you can compute with bbregister.


Best,

a.y

On Mon, 15 Aug 2016, "김재명" wrote:



Dear expert.


Hi. I'm a newbie using Freesurfer software, and I want to transform the data
of .trk file which is from Trackvis tool.
(https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms)


As there is an information for transforming trk file into the space of
Freesurfer surface, I read it several times but I couldn't implement it on
Linux console. 


The problem is that I cannot understand how to 'load the trk data from a
file' to use the header data such as voxel_size.


I also read TrackVis file format
(at http://trackvis.org/docs/?subsect=fileformat), and read other mails sent
from others, but couldn't solve the problem.


Could you give me a specific steps to solve this?



Many thanks

Jack.


[IMAGE]
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Re: [Freesurfer] How to run part of TRACULA

[Anastasia Yendiki]

Hi Nasia - They both have preprocessing steps because recon-all runs on 
the T1 and trac-all runs on the DWIs, so they preprocess different images.


You cannot skip any of the steps in recon-all and still get a 
segmentation. The point of the autorecon schemes is mostly to repeat only 
one part of the processing if you change something in between, not to skip 
part of the processing entirely.


Best,

a.y

On Sun, 14 Aug 2016, Athanasia Metoki wrote:


Dear Anastasia,

Thank you so much for responding so fast!
I see what you're saying and thank you for your input.

I have one more question if you don't mind taking a moment to respond. I
noticed that both trac-all and recon-all include some preprocessing steps
(eg. motion correction, eddy current correction, skull stripping). How come
and they both have these steps if one is supposed to run both commands? My
understandind is, if someone wants to run TRACULA from scratch, they would
need to run both recon-all (first) and trac-all (second). One would have to
run recon-all in order to get the cortical parcellation and subcortical
segmentation (mri/aparc+aseg.mgz) file  which will be used from trac-all in
the mask creation step.

In my case where I have some preprocessed data, is there a particular
-autorecon# command which only does some of the recon steps that would help
me get the cortical parcellation and subcortical segmentation
(mri/aparc+aseg.mgz) file that I am missing?

I understand I may be asking a lot! Once more thank you very much for your
initial response and your time!

Best,
Nasia Metoki


On Sat, Aug 13, 2016 at 8:03 PM, Anastasia Yendiki
 wrote:

  Hi Athanasia - TRACULA expects certains files named a certain
  way to be
  there at the end of each preprocessing step. These are described
  here:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfile
  s

  If you are using pre-existing files, you have to make sure that
  they
  follow the same file/directory naming convention.

  You just run recon-all with the default settings. The aparc+aseg
  is
  created in one of the last steps of recon-all, so all the
  previous steps
  have to run as well.

  Hope this helps!

  a.y

  On Sat, 13 Aug 2016, Athanasia Metoki wrote:

  > Dear Freesurfer Developers,
  >
  > I am fairly new to image analysis and this is the first time I
  use
  > Freesurfer.
  >
  > I have some DTI data and I have already preprocessed them and
  ran bedpostX
  > using FSL. I ran probabilistic tractography on FSL as well to
  get the
  > connectivity between two distinct brain areas.
  >
  > I am also interested in getting the probability distribution
  for the
  > uncinate fasciculi so I am trying to use TRACULA.
  > My question is: Can I use TRCULA without doing preprocessing
  and dedpostX
  > again? If so, will I need to do the cortical parcelation and
  subcortical
  > segmentation with recon-all and get the aparc+aseg.mgz file in
  order to use
  > TRACULA? Which argument would I need to use when I run
  recon-all?
  >
  > Thank you!
  >
  > Athanasia Metoki
  > Psychology Doctoral Student - Brain and Cognitive Sciences
  Program
  > Cognitive Neuroscience Laboratory
  > Temple University
  > Department of Psychology
  > 1701 N 13th St.
  > Philadelphia, PA 19122
  > Email: athanasia.met...@temple.edu
  >
  
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[Freesurfer] FreeSurfer TrackVis Transforms

[김재명]

Dear expert.Hi. I'm a newbie using Freesurfer software, and I want to transform the data of .trk file which is from Trackvis tool. (https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms)As there is an information for transforming trk file into the space of Freesurfer surface, I read it several times but I couldn't implement it on Linux console. The problem is that I cannot understand how to 'load the trk data from a file' to use the header data such as voxel_size.I also read TrackVis file format (at http://trackvis.org/docs/?subsect=fileformat), and read other mails sent from others, but couldn't solve the problem.Could you give me a specific steps to solve this?Many thanksJack.
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