date:20170922

[Freesurfer] Research Engineer position in Neuroimaging (Madrid, Spain)

2017-09-22 Thread Susanna Carmona Cañabate

*Research Engineer position in Neuroimaging at the *“Biomedical Imaging and
Instrumentation Group (BiiG) ”, Madrid.



The BiiG is a research organization located in Madrid (Spain) and
affiliated with the “Instituto de Investigación Sanitaria Gregorio Marañón”
and the “Universidad Carlos III”. The group is markedly multidisciplinary
and has a broad research interest, from the development of new imaging
techniques to processing methodologies and their application in practice.



The candidate will support the *neuroimaging subdivision* of the group and
will be involved in the development, maintenance and optimization of a
*neuroimaging
platform* that manages the storage and processing of multimodal brain MRI
data using *cloud resources*. Most of his/her work will be integrated into
a project that studies the *neural basis of human pregnancy*.



*Qualifications:*

· *Biomedical Engineering,* *Computational Neuroscience* *or related
field* *with
a strong computational background.*

· *Proficiency in* *oral and written English.*

· *Experience with* *Matlab and other* *programming languages (C, C++, bash*
 *and Python, Java)*

· *Interest* *in* *neuroimaging* *research.*

· *Ability to effectively interact with a multi-disciplinary team of
investigators and staff.*

· *Ability to work independently and as part of a team.*



*Preferences:*

*· **Experience with neuroimaging processing softwares* *(*FreeSurfer*,
FSL, SPM, AFNI, ANTs and* *BrainVisa) will be very relevant for the
selection of the applicant.*

· *Familiarity with stimuli presentation softwares such as Eprime,
Presentation or Psychtoolbox is preferred.  *

· *Methods and statistical background is preferred.*



*Salary** based on experience and qualifications. *

*Interested applicants should submit a cover letter and resume to*
*scarm...@hggm.es
. *

*Deadline**: 1st of November 2017*
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[Freesurfer] Fwd: nu_correct failure

2017-09-22 Thread miracle ozzoude

-- Forwarded message --
From: miracle ozzoude 
Date: Thu, Sep 21, 2017 at 11:20 AM
Subject: nu_correct failure
To: Douglas N Greve 

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] lobes volume (WM and GM)

2017-09-22 Thread Gonzalo Rojas Costa

Hi Douglas:

  I am looking for that paper, but I couldn't found it... Which is it ?

  Sincerely,


Gonzalo Rojas Costa
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 Thu, Sep 21, 2017 at 6:21 PM, Douglas N Greve
 wrote:
> 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
>>>
>>> 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/
>>>
>>>
>>>
>>> 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.
>>
>>
>
> --
> 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] curvature

2017-09-22 Thread Bruce Fischl


Hi Heidi

it's hard to say which one should be used - that is really dependent on 
your biological hypothesis. The "index" calculations are from David Van 
Essen paper. Sorry, I don't have the ref handy. The "integrated rectified" 
ones are just taking the absolute value of each, then summing them up over 
the surface.


cheers
Bruce


On Fri, 22 Sep 2017, Jacobs H (NP) wrote:


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] lobes volume (WM and GM)

2017-09-22 Thread Douglas N Greve

https://www.ncbi.nlm.nih.gov/pubmed/19027860


On 09/22/2017 10:11 AM, Gonzalo Rojas Costa wrote:
> Hi Douglas:
>
>I am looking for that paper, but I couldn't found it... Which is it ?
>
>Sincerely,
>
>
> Gonzalo Rojas Costa
> 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 Thu, Sep 21, 2017 at 6:21 PM, Douglas N Greve
>  wrote:
>> 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

 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/



 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.
>>>
>> --
>> 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/
>>
>

-- 
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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[Freesurfer] longtitudinal pipeline

2017-09-22 Thread miracle ozzoude

Hello Freesurfer,

For the longitudinal pipeline, the website/ recon-all -help suggested that
I calculate the different  on the results from the longitudinal command
(e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were
named 0001a.long.0001.longbase and 0001b.long.0001.longbase. is there a
command i can use to preform this?

Second question, i want to extract the output of the longitudinal pipeline
using asegstats2table and aparcstats2table commands. what flag/s should i
include in  the original command to perform this?

Thanks.
Paul
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[Freesurfer] Error in segmentHA_T1

2017-09-22 Thread Tiril Pedersen Gurholt

Dear Experts,

I recently installed Freesurfer development version (dated Sept. 16, 2017) on a
Mac Sierra (10.12.6).

When trying to run segmentHA_T1.sh I encounter a java problem: "JavaVM: Failed
to load JVM:
/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib».

See full error message below. The java.opts file in MCRv80/bin/maci64 is dated
Nov. 5, 2014. There also appears to be a problem with a Matlab app (?),
although matlab runtime has been installed.

Any ideas as to how to fix these problems?

Best regards,

Tiril

Error message:

#
#@# Hippocampal Subfields processing (T1) left Fri Sep 22 20:17:14 CEST 2017
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is
.:/Applications/freesurfer/MCRv80//runtime/maci64:/Applications/freesurfer/MCRv80//bin/maci64:/Applications/freesurfer/MCRv80//sys/os/maci64:
Warning: application is running on a locale different from the original
platform locale.
JavaVM: Failed to load JVM:
/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib
JavaVM FATAL: Failed to load the jvm library.
2017-09-22 20:17:16.597 segmentSubjectT1_autoEstimateAlveusML[10313:171678]
This process is attempting to exclude an item from Time Machine by path without
administrator privileges. This is not supported.
2017-09-22 20:17:16.599 segmentSubjectT1_autoEstimateAlveusML[10313:171678]
This process is attempting to exclude an item from Time Machine by path without
administrator privileges. This is not supported.
2017-09-22 20:17:16.599 segmentSubjectT1_autoEstimateAlveusML[10313:171678]
This process is attempting to exclude an item from Time Machine by path without
administrator privileges. This is not supported.
2017-09-22 20:17:16.600 segmentSubjectT1_autoEstimateAlveusML[10313:171678]
This process is attempting to exclude an item from Time Machine by path without
administrator privileges. This is not supported.
2017-09-22 20:17:16.600 segmentSubjectT1_autoEstimateAlveusML[10313:171678]
This process is attempting to exclude an item from Time Machine by path without
administrator privileges. This is not supported.
2017-09-22 20:17:16.601 segmentSubjectT1_autoEstimateAlveusML[10313:171678]
This process is attempting to exclude an item from Time Machine by path without
administrator privileges. This is not supported.
2017-09-22 20:17:16.601 segmentSubjectT1_autoEstimateAlveusML[10313:171678]
This process is attempting to exclude an item from Time Machine by path without
administrator privileges. This is not supported.
2017-09-22 20:17:16.602 segmentSubjectT1_autoEstimateAlveusML[10313:171678]
This process is attempting to exclude an item from Time Machine by path without
administrator privileges. This is not supported.
2017-09-22 20:17:16.602 segmentSubjectT1_autoEstimateAlveusML[10313:171678]
This process is attempting to exclude an item from Time Machine by path without
administrator privileges. This is not supported.
JavaVM: Failed to load JVM:
/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib
JavaVM FATAL: Failed to load the jvm library.
Fatal Error on startup: Unable to start the JVM because of a bad Java option or
unknown error.
Please check your java.opts file.

#
#@# Hippocampal Subfields processing (T1) right Fri Sep 22 20:17:16 CEST 2017
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is
.:/Applications/freesurfer/MCRv80//runtime/maci64:/Applications/freesurfer/MCRv80//bin/maci64:/Applications/freesurfer/MCRv80//sys/os/maci64:
Warning: application is running on a locale different from the original
platform locale.
JavaVM: Failed to load JVM:
/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib
JavaVM FATAL: Failed to load the jvm library.
2017-09-22 20:17:18.151 segmentSubjectT1_autoEstimateAlveusML[10355:171872]
This process is attempting to exclude an item from Time Machine by path without
administrator privileges. This is not supported.
2017-09-22 20:17:18.151 segmentSubjectT1_autoEstimateAlveusML[10355:171872]
This process is attempting to exclude an item from Time Machine by path without
administrator privileges. This is not supported.
2017-09-22 20:17:18.152 segmentSubjectT1_autoEstimateAlveusML[10355:171872]
This process is attempting to exclude an item from Time Machine by path without
administrator privileges. This is not supported.
2017-09-22 20:17:18.152 segmentSubjectT1_autoEstimateAlveusML[10355:171872]
This process is attempting to exclude an item from Time Machine by path without
administrator privileges. This is not supported.
2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872]
This process is attempting to exclude an item from Time Machine by pat

[Freesurfer] Problem with New Hippocampus/Amygdala Segmentation

2017-09-22 Thread Max Owens

Hi Freesurfer Experts,

I'm trying to run the new version 6.0 hippocampus/amygdala segmentation
procedure (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields)
on data from subjects with whom I have already completed recon-all. I have
downloaded the newest development version (and license), as well as the
required matlab runtime. However, I am getting the following error:

“LD_LIBRARY_PATH is
.:freesurfer/MCRv80//runtime/glnxa64:freesurfer/MCRv80//bin/glnxa64:freesurfer/MCRv80//sys/os/glnxa64:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/server:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/client:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64:


Registering imageDump.mgz to hippocampal mask from ASEG

cp: cannot stat ‘freesurfer/average/HippoSF/atlas/AtlasDump.mgz’: No such
file or directory

Error using myMRIread (line 16)

Error in myMRIread: temporary directory does not exist

Error in segmentSubjectT1_autoEstimateAlveusML (line 134)

Command exited with non-zero status 255

@#@FSTIME 2017:09:22:15:55:53 run_segmentSubjectT1_autoEstimateAlveusML.sh
N 13 e 2.85 S 0.11 U 2.85 P 103% M 205292 F 1 R 22759 W 0 c 2477 w 641 I 0
O 63584 L 0.41 0.56 0.64

@#@FSLOADPOST 2017:09:22:15:55:56
run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.41 0.56 0.64

All done! ”

Have you ever seen this error before? If not, can you provide any
suggestions for ways that I might troubleshoot it? I have attached the
command I used and the error log if this is of help.

Thanks very much for your time,

Max


-- 
Max Owens, M.S.
Graduate Student in Psychology
Clinical Neuroscience Lab
University of Georgia
--
USER cns
HOST nic
PROCESSID 3392 
PROCESSOR x86_64
OS Linux
Linux nic 4.4.0-79-generic #100~14.04.1-Ubuntu SMP Fri May 19 18:36:51 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
--
 
#
#@# Hippocampal Subfields processing (T1) left Fri Sep 22 15:55:49 EDT 2017
--
Setting up environment variables
---
LD_LIBRARY_PATH is .:freesurfer/MCRv80//runtime/glnxa64:freesurfer/MCRv80//bin/glnxa64:freesurfer/MCRv80//sys/os/glnxa64:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/server:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/client:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64:
Registering imageDump.mgz to hippocampal mask from ASEG
cp: cannot stat ‘freesurfer/average/HippoSF/atlas/AtlasDump.mgz’: No such file or directory
Error using myMRIread (line 16)
Error in myMRIread: temporary directory does not exist

Error in segmentSubjectT1_autoEstimateAlveusML (line 145)




Command exited with non-zero status 255
@#@FSTIME  2017:09:22:15:55:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 3.68 S 0.19 U 2.99 P 86% M 203156 F 12 R 23139 W 0 c 3076 w 722 I 384 O 63584 L 0.36 0.55 0.63
@#@FSLOADPOST 2017:09:22:15:55:53 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.41 0.56 0.64
#
#@# Hippocampal Subfields processing (T1) right Fri Sep 22 15:55:53 EDT 2017
--
Setting up environment variables
---
LD_LIBRARY_PATH is .:freesurfer/MCRv80//runtime/glnxa64:freesurfer/MCRv80//bin/glnxa64:freesurfer/MCRv80//sys/os/glnxa64:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/server:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/client:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64:
Registering imageDump.mgz to hippocampal mask from ASEG
cp: cannot stat ‘freesurfer/average/HippoSF/atlas/AtlasDump.mgz’: No such file or directory
Error using myMRIread (line 16)
Error in myMRIread: temporary directory does not exist

Error in segmentSubjectT1_autoEstimateAlveusML (line 134)




Command exited with non-zero status 255
@#@FSTIME  2017:09:22:15:55:53 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 2.85 S 0.11 U 2.85 P 103% M 205292 F 1 R 22759 W 0 c 2477 w 641 I 0 O 63584 L 0.41 0.56 0.64
@#@FSLOADPOST 2017:09:22:15:55:56 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.41 0.56 0.64


script
Description: Binary data
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] sim-sign abs/ cluster summary results confirmation

2017-09-22 Thread miracle ozzoude

I forgot to send the cluster summary sheet. Here is it.

# Input  lh.stroke.fsgd.glmdir/contrast/sig.mgh

# Frame Number  0

# srcsubj fsaverage

# hemi lh

# surface white

# annot aparc

# SUBJECTS_DIR /Users/CT/Documents/stroke

# SearchSpace_mm2 65416.6

# SearchSpace_vtx 149953

# Bonferroni 0

# Minimum Threshold 2

# Maximum Threshold infinity

# Threshold Signabs

# AdjustThreshWhenOneTail 1

# Area Threshold0 mm^2

# CSD thresh  2.00

# CSD nreps5000

# CSD simtype  mc-z

# CSD contrast contrast

# CSD confint  90.00

# Overall max 2.26504 at vertex 146861

# Overall min -2.73325 at vertex 144073

# NClusters  13

# Total Cortical Surface Area 65416.6 (mm^2)

# FixMNI = 0

#

# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
  CWPHi   NVtxs   Annot

   1   -2.733  144073 70.23-31.5  -61.0  -15.8  0.99400  0.99260
0.99540   101  fusiform

   2   -2.537  153213 28.08-14.2   40.2   12.1  1.0
-0.00020  1.057  superiorfrontal

   3   -2.348   57351 30.35-63.3  -39.68.0  1.0
-0.00020  1.077  bankssts

   42.265  146861 20.30-38.8  -57.9   25.4  1.0
-0.00020  1.045  inferiorparietal

   5   -2.261  116880 21.63-33.3  -48.7   60.5  1.0
-0.00020  1.045  superiorparietal

   62.248   83406 24.49 -5.2   28.6   18.6  1.0
-0.00020  1.047  caudalanteriorcingulate

   7   -2.182   90669 20.62-50.9  -56.2  -12.6  1.0
-0.00020  1.028  inferiortemporal

   82.143   32579  5.79 -7.9  -10.3   40.1  1.0
-0.00020  1.014  posteriorcingulate

   9   -2.052  159218  3.21 -5.0  -33.8   32.9  1.0
-0.00020  1.0 7  isthmuscingulate

  10   -2.050  127337  7.16-17.76.2  -15.5  1.0
-0.00020  1.016  lateralorbitofrontal

  11   -2.013   93626  1.61-37.4  -13.7   54.8  1.0
-0.00020  1.0 3  precentral

  12   -2.0069896  0.87-27.3   -0.6  -35.9  1.0
-0.00020  1.0 2  entorhinal

  13   -2.001   75892  0.47-22.0  -33.4  -11.8  1.0
-0.00020  1.0 1  parahippocampal

On Fri, Sep 22, 2017 at 9:37 PM, miracle ozzoude 
wrote:

> Hello,
>
> I ran cortical thickness analyses using the following contrast and fsgd.
> After that, I corrected for multiple comparison using monte carlo 5000 with
> cluster forming threshold of 2 and unsigned/2-tailed t-test (abs). I wanted
> to confirm my interpretation of the results.
>
> 1) Since my contrast is (-1 1 0 0 representing control>stroke), it should
> be red/yellow and if blue, it should be control clusters with colors different from the aformentioned (see attached
> screenshot). How should I interpret them?
>
> 2) I want to view the uncorrected p-values, which of the columns in the
> summary text file should I concentrate, and should the p < or > 0.05?
>
> 3) Looking at the CWP column in the summary text file, can I conclude that
> the obtained regions/clusters are significant? This is because non of the
> cluster-wise p-values are below 0.05 (--cwp 0.05).
>
> 4) Which of the columns represent the sign of my contrast i.e. where
> Control>Stroke and Control
> FSGD file
> GroupDescriptorFile
> Title StrokevsControl
> Class1 Stroke
> Class2 Control
> Variable bmi
> Input 6001 Stroke 20
> Input 8001 Control 30
>
> Contrast:
> -1 1 0 0 (Control>Stroke removing the effects of bmi)
>
> Thank you,
> Paul
>
>
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[Freesurfer] bad midline cut

2017-09-22 Thread Gabor Perlaki

Dear all,
Here is my question again. Somehow, it didn't appear on the Freesurfer
forum. I'm resending it without the attachments.



> I've a subject, where the midline cut is bad (see the attached pictures),
> therefore the segmented left lateral ventricle also includes considerable
> number of voxels from the right one.
> Is it possible to correct it somehow?
>
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[Freesurfer] Research Engineer position in Neuroimaging (Madrid, Spain)

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Re: [Freesurfer] sim-sign abs/ cluster summary results confirmation

[Freesurfer] bad midline cut

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