[Freesurfer] curvature

[Jacobs H (NP)]

Dear FreeSurfer,

In the stats files (e.g aparc) there are also statistics for the "integrated 
rectified mean curvature", "integrated rectified gaussian curvature", "folding 
index" and "intrinsic curvature index".
To what kind of properties do these measures refer and which one is advised to 
be used?

Many thanks!
Heidi
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Re: [Freesurfer] Adjusted or unadjusted CT values and interpretation of volume values in ocn.dat from group analysis

[Douglas N Greve]

On 09/20/2017 01:54 PM, Elizabeth Bartlett wrote:
> Hello Freesurfer experts,
>
> I have performed a group level analysis of volume and cortical 
> thickness using mri_glmfit and performed multiple comparisons 
> correction with mri_glmfit-sim. I used the contrast matrix 0 1 0 to 
> analyze 1 group with 2 covariates, along the 1st covariate (education) 
> with the 2nd covariate being age.
>
> I get 2 significant clusters (after mult. comp. corr.) for CT and 2 
> for volume. When I look at the values in ./cache.th30.abs.y.ocn.dat, 
> the average CT values within my sample are 2.57 and 2.50 for the 2 
> regions.
>
> _My first question is: _are the CT values outputted to ocn.dat 
> adjusted for my 2nd covariate (age) or are they unadjusted CT values 
> within the sig. cluster?
>
unadjusted
>
>
> The volume values contained within the ocn.dat files are also in the 
> same range as the CT values, with averages of 2.50 and 1.87 for left 
> superior frontal and right inferior parietal volume, respectively.
>
>
> _My second question is:_ What is the metric for volume reported in 
> ocn.dat? These values seem too low to be total cluster volume for each 
> subject expressed as mm^2. The volumes reported in 
>  ./cache.th30.abs.sig.cluster.summary are more like what we I expect 
> for volume (283.24 mm^2). Could these values be the average volume 
> surrounding each vertex in the inflated mesh (volume contained within 
> the surrounding vertices)?
>
Yes, the average. You can multiply it by the number of vertices in the 
cluster to get total volume
>
>
> Thank you,
>
>
> Elizabeth
>
>
>
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Re: [Freesurfer] lobes volume (WM and GM)

[Douglas N Greve]

No, not for lobe volume. Have you seen the original wmparc paper?


On 09/20/2017 04:53 PM, Gonzalo Rojas Costa wrote:
> Hi Douglas:
>
>I am looking for papers that used the volume of each lobe computed
> using freesurfer, but I couldn't found it...  Do you know any?...
>
>Sincerely,
>
>
> Gonzalo Rojas Costa
> Laboratory for Advanced Medical Image Processing
> Department of Radiology
> Clínica las Condes
> Lo Fontecilla 441, Las Condes, Santiago, Chile.
> Tel: 56-2-2105170
> Cel: 56-9-97771785
> www.clc.cl
> http://www.aribrain.info
> https://scholar.google.com/citations?user=LO7LZ3oJ
> https://www.researchgate.net/profile/Gonzalo_Rojas2
> https://cl.linkedin.com/in/gonzalorojascosta
>
>
> On Wed, Sep 20, 2017 at 5:47 PM, Douglas N Greve
>  wrote:
>> We did not have a strong reason, just that it seemed to give maps that
>> looked reasonable
>>
>>
>>
>> On 09/20/2017 04:42 PM, Gonzalo Rojas Costa wrote:
>>> Hi Douglas:
>>>
>>> Why you specified 5mm as the default value for the --wmparc-dmax
>>> option in mri_aparc2aseg command?
>>>
>>> Sincerely,
>>>
>>>
>>> Gonzalo Rojas Costa
>>> Laboratory for Advanced Medical Image Processing
>>> Department of Radiology
>>> Clínica las Condes
>>> Lo Fontecilla 441, Las Condes, Santiago, Chile.
>>> Tel: 56-2-2105170
>>> Cel: 56-9-97771785
>>> www.clc.cl
>>> http://www.aribrain.info
>>> https://scholar.google.com/citations?user=LO7LZ3oJ
>>> https://www.researchgate.net/profile/Gonzalo_Rojas2
>>> https://cl.linkedin.com/in/gonzalorojascosta
>>>
>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
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>>
>>
>>
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>> dispose of the e-mail.
>

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Re: [Freesurfer] merge in a sigle label the results obetained in fs-fast

[Douglas N Greve]

Try mri_mergelabels


On 09/21/2017 07:47 AM, std...@virgilio.it wrote:
> Hi list,
>
> I would to merge (separatelly pos and neg) in a sigle .label which 
> contain all the clusters which represent the seed-cortical 
> connectivity after fs-fast analysis.
> I aim to avoid to extraxt manually single label for cluster by tksurfer.
>
> Thanks,
>
>
> Stefano
>
>
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Re: [Freesurfer] Error in Qcache

[Douglas N Greve]

No, sorry, we may be slowly phasing qdec out, so you can try to use the 
"command line" stream (mris_preproc, mris_fwhm, and mri_glmfit with 
visualization in FreeView)


On 09/21/2017 02:57 AM, Emmanuel Nwosu wrote:
> Hi All,
>
> I will want to know if this error on this link
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-April/051464.html
> was resolved. I am having a similar problem while sampling to the 
> fsaverage. Thanks
>
> Kind regards
> Emmanuel

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Re: [Freesurfer] recon-all question

[Douglas N Greve]

You could run it with -label-V1

This is run at the end of recon-all and should only take a few min and 
would change the recon-all.log file.





On 09/21/2017 01:57 PM, STACEY M SCHAEFER wrote:
>
> Hello,
>
>
> I want to run recon-all again on scans that have already been 
> hand-edited, the appropriate recon-all flags ran, and resulting output 
> checked and approved.  The images look good, but when the hippocampal 
> subfield routine was later run on the images, it crashed, leaving an 
> error in the recon-all.log.  We want to be anal, and make sure there 
> is no error again after running recon-all.  In other words, we want 
> the last line in the recon-all.log to reflect that the images all 
> completed successfully.
>
>
> Is there a recommended flag (or flags) at this point?  In other words, 
> there are no additional edits to incorporate in the recon-all job, but 
> we also don't want the earlier edits, control points, etc. ignored in 
> this last rerun of recon-all.
>
>
> Thank you for your help!
>
> Stacey
>
>
>
> *Stacey M. Schaefer, Ph.D.*
> Center for Healthy Minds
>
> University of Wisconsin-Madison
>
> 625 W Washington Ave
>
> Madison WI 53703
>
> 608-263-9321
>
>
>
>
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Re: [Freesurfer] Edits to aparc+aseg

[Douglas N Greve]

we don't have a path for editing aparc+aseg. Are the areas unknown on 
the surface?


On 09/21/2017 02:20 PM, Jake Rieke wrote:
> Hi FreeSurfers,
>
> I have a group of subjects with manual edits to the aparc+aseg volume. 
> These edits were made to re-label unknown regions of cortex. I am 
> wondering what recon-all flags I could use to implement the changes 
> and re-generate cortical stats based on these edits. Thanks in advance.
>
> Best regards,
> Jake
>
>
>
>
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[Freesurfer] Edits to aparc+aseg

[Jake Rieke]

Hi FreeSurfers,

I have a group of subjects with manual edits to the aparc+aseg volume.
These edits were made to re-label unknown regions of cortex. I am wondering
what recon-all flags I could use to implement the changes and re-generate
cortical stats based on these edits. Thanks in advance.

Best regards,
Jake
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[Freesurfer] recon-all question

[STACEY M SCHAEFER]

Hello,


I want to run recon-all again on scans that have already been hand-edited, the 
appropriate recon-all flags ran, and resulting output checked and approved.  
The images look good, but when the hippocampal subfield routine was later run 
on the images, it crashed, leaving an error in the recon-all.log.  We want to 
be anal, and make sure there is no error again after running recon-all.  In 
other words, we want the last line in the recon-all.log to reflect that the 
images all completed successfully.


Is there a recommended flag (or flags) at this point?  In other words, there 
are no additional edits to incorporate in the recon-all job, but we also don't 
want the earlier edits, control points, etc. ignored in this last rerun of 
recon-all.


Thank you for your help!

Stacey



Stacey M. Schaefer, Ph.D.
Center for Healthy Minds

University of Wisconsin-Madison

625 W Washington Ave

Madison WI 53703

608-263-9321


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Re: [Freesurfer] Longitudinal increase in thickness/volume

[Martin Reuter]

Hi Caleb,


is this in a single subject or a group result? In a single subject 
almost anything is expected. E.g. small motion can cause thickness 
changes , so can hydration levels.


Best, Martin



Am 21.09.2017 um 16:53 schrieb Huang, Caleb (NIH/NINDS) [F]:


Hello,


I'm tracking atrophy in the precentral region. I've run the subjects 
through the longitudinal stream. Because of time constraints, I've 
mostly focused on editing the precentral regions as well as any 
significant errors outside of the region. I've observed increases in 
thickness of up to 0.1mm in the precentral region. In some cases 
there's an increase in volume as well. Upon inspection though, the 
precentral wm/pial surfaces look fine. Is this a normal range of error?



Thank you,

-Caleb



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[Freesurfer] nu_correct failure

[miracle ozzoude]

Hello expert,

I ran several subjects on FS v6  and they failed on the same stage
(mri_nu_correct.mni and nu_correct). How can I solve this problem? I have
attache the recon-all.log file for 2 subjects.

Best,
Paul


recon-all.log
Description: Binary data


recon-all.log
Description: Binary data
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Re: [Freesurfer] Mris_volume

[Boyd, Emma]

Hi Fereshte,

Could you please clarify what you mean by "obtain the surface label"?


Thanks,

Emma


-

Emma Boyd

Research Technician II

Laboratory for Computational Neuroimaging

Martinos Center for Biomedical Imaging


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fereshte 

Sent: Thursday, September 21, 2017 10:26 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Mris_volume

Hi Emma
Are there any ways to obtain the surface label then?
Thank you!
On Wed, Sep 20, 2017 at 5:15 PM Boyd, Emma 
> wrote:

Hi Fereshte,


mris_volume does not create any output files, that number you see in the 
terminal is the total volume of a given closed surface.

Try running mris_volume -v  instead and you will see something 
like this in your terminal:


reading ...
surface file read in.
Volume computation took 0 minutes and 1 seconds.
total volume surrounded by the surface is 381271

Emma



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
>
 on behalf of Fereshte 
>
Sent: Wednesday, September 20, 2017 1:45:17 AM
To: Freesurfer support list
Subject: [Freesurfer] Mris_volume

Dear FreeSurfer Developers
Using "mris_volume surface_file_name " now i can't see any output files and 
381271.851642 is shown in the command terminal, i have no idea what the problem 
is. Could you please help?
Thank you!

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Re: [Freesurfer] longitudinal freesurfer- different scanners

[Martin Reuter]

Yes,

see also my answers from 08 and 11 of September on the list.

Best, Martin




Am 17.09.2017 um 19:42 schrieb Martijn Steenwijk:


The longitudinal pipeline will not overcome (contrast) differences due 
to scanner differences. If you register the scans to eachother you 
will see that there are slight differences in WM/GM contrast. Probably 
better to use the scans from the same scanner and not use the third.


*Van:*freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *Namens *Michelle 
VanTieghem

*Verzonden:* zondag 17 september 2017 19:18
*Aan:* Freesurfer support list
*Onderwerp:* Re: [Freesurfer] longitudinal freesurfer- different scanners

Hi all,

I just wanted to follow up on my question:

Would it be ok to use the longitudinal pipeline for scans that were 
acquired on different scanners (e.g time 1 and time 2 on the same 
scanner, time 3 on different scanner)? Would the longitudinal pipeline 
help to account for different scanners, since it creates the average 
base image for all 3 time points? or is this not recommended to use 
different scanners in longitudinal pipeline?


Thanks!

- M

On Mon, Sep 4, 2017 at 5:27 PM, Michelle VanTieghem 
> 
wrote:


Hello,

Would it be ok to use the longitudinal pipeline for scans that were 
acquired on different scanners (e.g time 1 and time 2 on the same 
scanner, time 3 on different scanner)? Would the longitudinal pipeline 
help to account for different scanners, since it creates the average 
base image for all 3 time points? or is this not recommended?


Thank you,

Michelle

--

Michelle VanTieghem

PhD student in Psychology

Developmental Affective Neuroscience Lab

Columbia University

mrv2...@columbia.edu 



--

Michelle VanTieghem

PhD student in Psychology

Developmental Affective Neuroscience Lab

Columbia University

mrv2...@columbia.edu 



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Re: [Freesurfer] Longitudinal processing -qcache ERROR

[Martin Reuter]

Hi Lisa,

not sure where the problem comes from. But generally one would not do 
the qcache on the base. Qcache maps results to fsaverage and nobody 
should ever look at the base results except for debugging purposes. The 
base is the within-subject template and it is used to initialize the 
longitudinal processing. It is not the baseline (=first time point).


Best, Martin



Am 15.09.2017 um 16:00 schrieb Lisa Delalande:

Hi everyone,

During my PhD, I'm using some longitudinal data and at the setp called 
"BASE" but when i want to make a qcache processing with the last 
version of FreeSurfer (i.e. 6.0)(command used : "*recon-all -base 
template_1-02 -qcache*") it doesn't work. I have a error message :

"Error : cannot find /.../template_1-02/surf/_*lh.w-g.pct.mgh*_"_*
*_
I would like to kown if you know where the problem comes ? And what 
can I do to fix it ?


Thank you,
Best regards,

Lisa


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[Freesurfer] Longitudinal increase in thickness/volume

[Huang, Caleb (NIH/NINDS) [F]]

Hello,


I'm tracking atrophy in the precentral region. I've run the subjects through 
the longitudinal stream. Because of time constraints, I've mostly focused on 
editing the precentral regions as well as any significant errors outside of the 
region. I've observed increases in thickness of up to 0.1mm in the precentral 
region. In some cases there's an increase in volume as well. Upon inspection 
though, the precentral wm/pial surfaces look fine. Is this a normal range of 
error?


Thank you,

-Caleb
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Re: [Freesurfer] Newborn MRI segmentation

[Lilla Zollei]

The neonatal pipeline and its atlasesis not yet released. I am working on 
it, so hopefully you do not need to wait long.
Lilla


On Thu, 21 Sep 2017, Paula Diniz wrote:

> Hi experts!
> 
> I want to perform recon-all pipeline on newborn MRI data.
> 
> How I can do this? Which atlas you recommend?
> 
> Any news about infant pipeline?
> 
> Thanks!!
> 
> Paula Diniz
> 
>
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Re: [Freesurfer] Mris_volume

[Fereshte]

Hi Emma
Are there any ways to obtain the surface label then?
Thank you!
On Wed, Sep 20, 2017 at 5:15 PM Boyd, Emma  wrote:

> Hi Fereshte,
>
>
> mris_volume does not create any output files, that number you see in the
> terminal is the total volume of a given closed surface.
>
> Try running *mris_volume -v * instead and you will see
> something like this in your terminal:
>
>
> reading ...
> surface file read in.
> Volume computation took 0 minutes and 1 seconds.
> total volume surrounded by the surface is 381271
>
> Emma
>
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fereshte <
> fereshte.ramez...@gmail.com>
> *Sent:* Wednesday, September 20, 2017 1:45:17 AM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] Mris_volume
>
> Dear FreeSurfer Developers
> Using "mris_volume surface_file_name " now i can't see any output files
> and 381271.851642 is shown in the command terminal, i have no idea what the
> problem is. Could you please help?
> Thank you!
>
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[Freesurfer] TRACULA trac-all prep error

[Fred Sampedro]

Dear TRACULA users,

I'm trying to preprocess a DTI subject in TRACULA which has an already
reconed-all error-free T1. I followed the tutorial, but trac-all -prep
exited with errors very fast.

Please find attached the log and error files, and the dmrirc. Also bvals
and bvecs (were obtained from dcm2nii). The raw dti.nii.gz has 16 volumes,
the first being b0 and then 15 directions.

Any ideas on what could be happening would be much appreciated,

Thanks a lot in advance,

Fred-


dmrirc.tutorial
Description: Binary data


dtipd1467690.bval
Description: Binary data


dtipd1467690.bvec
Description: Binary data


trac-all.error
Description: Binary data
jue sep 21 11:49:35 CEST 2017
/media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial
/usr/local/freesurfer/bin/trac-all
-prep -c dmrirc.tutorial
Subject t1pd1467690
SUBJECTS_DIR /media/freds/LinuxData/TRACULA_HSP/diffusion_recons
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
freds
utm
Linux utm 4.4.0-96-generic #119-Ubuntu SMP Tue Sep 12 14:59:54 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  127247 
maxlocks unlimited
maxsignal127247 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   32622380 881758812764464   140681104032823313740
Swap:   3998716   0 3998716


Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/09/21-09:49:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: freds  Machine: utm  Platform: Linux  PlatformVersion: 4.4.0-96-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/09/21-09:49:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: freds  Machine: utm  Platform: Linux  PlatformVersion: 4.4.0-96-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/09/21-09:49:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: freds  Machine: utm  Platform: Linux  PlatformVersion: 4.4.0-96-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/09/21-09:49:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: freds  Machine: utm  Platform: Linux  PlatformVersion: 4.4.0-96-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/09/21-09:49:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: freds  Machine: utm  Platform: Linux  PlatformVersion: 4.4.0-96-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/09/21-09:49:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: freds  Machine: utm  Platform: Linux  PlatformVersion: 4.4.0-96-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/09/21-09:49:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: freds  Machine: utm  Platform: Linux  PlatformVersion: 4.4.0-96-generic  CompilerName: GCC  CompilerVersion: 40400 


New invocation of trac-preproc


freds
utm
Linux utm 4.4.0-96-generic #119-Ubuntu SMP Tue Sep 12 14:59:54 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  127247 
maxlocks unlimited
maxsignal127247 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   32622380 882148812760508   140681104038423309868
Swap:   3998716   0 3998716

#-
/usr/local/freesurfer/bin/trac-preproc 
#-
#@# Image corrections jue sep 21 11:49:35 CEST 2017
mri_convert --bvec-voxel 

Re: [Freesurfer] Freeview aborts under centos6

[Markus Gschwind]

Dear Andrew,

So the sys admin has changed the libraries.

however, it did not change anything. Freeview aborts without comment.

Below the command you asked for the result.

Any other ideas? What other info would you like to get?

Sorry for that persisting problem!

And thanks for your help!
Markus


ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/libvtk*
lrwxrwxrwx 1 sagon unige  21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so ->
libvtkalglib.so.5.6.0
lrwxrwxrwx 1 sagon unige  21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6 ->
libvtkalglib.so.5.6.0
-rwxr-xr-x 1 sagon unige  146394 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6.0
lrwxrwxrwx 1 sagon unige  21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so ->
libvtkCommon.so.5.6.0
lrwxrwxrwx 1 sagon unige  21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6 ->
libvtkCommon.so.5.6.0
-rwxr-xr-x 1 sagon unige 3703594 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6.0
lrwxrwxrwx 1 sagon unige  24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so ->
libvtkCommonTCL.so.5.6.0
lrwxrwxrwx 1 sagon unige  24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6 ->
libvtkCommonTCL.so.5.6.0
-rwxr-xr-x 1 sagon unige 1499456 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6.0
lrwxrwxrwx 1 sagon unige  26 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so ->
libvtkDICOMParser.so.5.6.0
lrwxrwxrwx 1 sagon unige  26 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6 ->
libvtkDICOMParser.so.5.6.0
-rwxr-xr-x 1 sagon unige  145360 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6.0
lrwxrwxrwx 1 sagon unige  21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so ->
libvtkexoIIc.so.5.6.0
lrwxrwxrwx 1 sagon unige  21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6 ->
libvtkexoIIc.so.5.6.0
-rwxr-xr-x 1 sagon unige  312372 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6.0
lrwxrwxrwx 1 sagon unige  24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFiltering.so ->
libvtkFiltering.so.5.6.0
lrwxrwxrwx 1 sagon unige  24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6 ->
libvtkFiltering.so.5.6.0
-rwxr-xr-x 1 sagon unige 4502701 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6.0
lrwxrwxrwx 1 sagon unige  27 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so ->
libvtkFilteringTCL.so.5.6.0
lrwxrwxrwx 1 sagon unige  27 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6 ->
libvtkFilteringTCL.so.5.6.0
-rwxr-xr-x 1 sagon unige 2185191 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6.0
lrwxrwxrwx 1 sagon unige  19 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so ->
libvtkftgl.so.5.6.0
lrwxrwxrwx 1 sagon unige  19 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 ->
libvtkftgl.so.5.6.0
-rwxr-xr-x 1 sagon unige   60005 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6.0
lrwxrwxrwx 1 sagon unige  31 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so ->
libvtkGenericFiltering.so.5.6.0
lrwxrwxrwx 1 sagon unige  31 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6 ->
libvtkGenericFiltering.so.5.6.0
-rwxr-xr-x 1 sagon unige  294583 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6.0
lrwxrwxrwx 1 sagon unige  34 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so ->
libvtkGenericFilteringTCL.so.5.6.0
lrwxrwxrwx 1 sagon unige  34 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so.5.6
-> libvtkGenericFilteringTCL.so.5.6.0
-rwxr-xr-x 1 

Re: [Freesurfer] Fs 6

[Peer Herholz]

Hey John,

as you can see on the FreeSurfer download page, you need
either a linux or macOS system to run FreeSurfer natively
(https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall).

There are several ways to tackle your problem:

1. get a linux or macOS machine
2. run FreeSurfer within a virtual machine on your windows host, e.g.
using the great NeuroDebian (http://neuro.debian.net/vm.html)
3. run FreeSurfer within a docker on your windows host, e.g.
using the mindboggle docker (https://hub.docker.com/r/nipy/mindboggle/), 
which also comes with amazing additional software such as ANTS and 
mindboggle
4. apparently it’s also possible to run FreeSurfer on windows 10 these days, 
pls check 
here: 
http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/

However, I assume most peeps would recommend running FreeSurfer within a system 
which 
was also used for development and testing.

HTH, best, Peer


> On Sep 21, 2017, at 8:29 AM, John Papatriantafyllou  
> wrote:
> 
> dear FS experts,
> is there any tutorial to install FS 6 under windows 10?
> John 
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> at
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> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.

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[Freesurfer] merge in a sigle label the results obetained in fs-fast

[stdp82]

Hi list,
I would to merge (separatelly pos and neg) in a sigle .label which contain all 
the clusters which represent the seed-cortical connectivity after fs-fast 
analysis.I aim to avoid to extraxt manually single label for cluster by 
tksurfer.
Thanks,

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[Freesurfer] Newborn MRI segmentation

[Paula Diniz]

Hi experts!

I want to perform recon-all pipeline on newborn MRI data.

How I can do this? Which atlas you recommend?

Any news about infant pipeline?


Thanks!!


Paula Diniz
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[Freesurfer] Error in Qcache

[Emmanuel Nwosu]

Hi All,

I will want to know if this error on this link
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-April/051464.html
was resolved. I am having a similar problem while sampling to the
fsaverage. Thanks

Kind regards
Emmanuel
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[Freesurfer] Fs 6

[John Papatriantafyllou]

dear FS experts,

is there any tutorial to install FS 6 under windows 10?
John
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