[Freesurfer] All coordinates of volume of interest

[Aziz Nanthaamornphong]

Hi,

Is there a way to get all coordinates (x,y,z) of the particular volume of
interest (e.g., left-insula, left-thalamus)?

Best,
Aziz.
-- 

Aziz Nanthaamornphong, Ph.D.,
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz
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Re: [Freesurfer] modifying files on older versions of FS

[Bruce Fischl]

wow, 4.4, that's pretty old. Not sure, I guess try it
Bruce
On Thu, 16 Jun 2016, 
Alexopoulos, Dimitrios wrote:




I have successfully processed data with FS v5.3 (linux/CentOS) using
recon-all -all.

 

Is it possible to make modifications to the 5.3-generated brainmask.mgz
(primarily dura removal) and wm.mgz files using a much older 4.4 version of
FS and then re-run recon-all on 5.3 with these modified files. I’d also be
generating control points (control.dat file) on 4.4 as well.

 

In other works are there file formatting differences between these FS
versions for just these 3 files that could pose a problem when re-running
the dataset.

 

Jim



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[Freesurfer] Brodmann annotation on fsaverage

[Reza Rajimehr]

Hi,

Freesurfer has an annotation file for Brodmann areas, which is
?h.PALS_B12_Brodmann.annot. This Brodmann parcellation doesn't seem to be
accurate in certain regions (e.g. in retrosplenial and perirhinal cortex).
Does anyone have an alternative Brodmann atlas that can be visualized in
Freesurfer (i.e. on fsaverage)?

We are particularly interested in medial structures in occipital, parietal,
and temporal lobe.

Best,
Reza
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Re: [Freesurfer] modifying files on older versions of FS

[Alexopoulos, Dimitrios]

We haven't been able to get FS 5.3 (running on a linux server) output to 
display on our Win 7 PC's using Xming or Exceed X11 emulators.
We get errors (below) on all our PCs. Appears to be related to low-end video 
cards not-supporting openGL.

[sge-login1 ~]$ tksurfer
GLUT: Fatal Error in tksurfer.bin: OpenGL GLX extension not supported by 
display: localhost:10.0

[sge-login1 ~]$ tkmedit
GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by 
display: localhost:10.0



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
Sent: Thursday, June 16, 2016 4:58 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] modifying files on older versions of FS

Why would  you want to do that?

Peace,

Matt.

From: 
>
 on behalf of "Alexopoulos, Dimitrios" 
>
Reply-To: Freesurfer support list 
>
Date: Thursday, June 16, 2016 at 4:06 PM
To: Freesurfer support list 
>
Subject: [Freesurfer] modifying files on older versions of FS

I have successfully processed data with FS v5.3 (linux/CentOS) using recon-all 
-all.

Is it possible to make modifications to the 5.3-generated brainmask.mgz 
(primarily dura removal) and wm.mgz files using a much older 4.4 version of FS 
and then re-run recon-all on 5.3 with these modified files. I'd also be 
generating control points (control.dat file) on 4.4 as well.

In other works are there file formatting differences between these FS versions 
for just these 3 files that could pose a problem when re-running the dataset.

Jim

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Information. If you are not the intended recipient, be advised that any 
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Re: [Freesurfer] modifying files on older versions of FS

[Matt Glasser]

Why would  you want to do that?

Peace,

Matt.

From:   on behalf of "Alexopoulos,
Dimitrios" 
Reply-To:  Freesurfer support list 
Date:  Thursday, June 16, 2016 at 4:06 PM
To:  Freesurfer support list 
Subject:  [Freesurfer] modifying files on older versions of FS

I have successfully processed data with FS v5.3 (linux/CentOS) using
recon-all -all.
 
Is it possible to make modifications to the 5.3-generated brainmask.mgz
(primarily dura removal) and wm.mgz files using a much older 4.4 version of
FS and then re-run recon-all on 5.3 with these modified files. I¹d also be
generating control points (control.dat file) on 4.4 as well.
 
In other works are there file formatting differences between these FS
versions for just these 3 files that could pose a problem when re-running
the dataset.
 
Jim


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Information. If you are not the intended recipient, be advised that any
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notify the sender via telephone or return email.
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Re: [Freesurfer] GLM_Fit Question

[Arkadiy Maksimovskiy]

Hi Freesurfers,

I am having a similar problem with the FSGD file as the user indicated at
this thread:

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40599.html

I am trying to access the script that Doug wrote in order to fix it,
however, the link to download the script does not seem to be working. I was
wondering if someone might be able to upload it again.

Thank you in advance for your help,

Arkadiy
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[Freesurfer] modifying files on older versions of FS

[Alexopoulos, Dimitrios]

I have successfully processed data with FS v5.3 (linux/CentOS) using recon-all 
-all.

Is it possible to make modifications to the 5.3-generated brainmask.mgz 
(primarily dura removal) and wm.mgz files using a much older 4.4 version of FS 
and then re-run recon-all on 5.3 with these modified files. I'd also be 
generating control points (control.dat file) on 4.4 as well.

In other works are there file formatting differences between these FS versions 
for just these 3 files that could pose a problem when re-running the dataset.

Jim


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Information. If you are not the intended recipient, be advised that any 
unauthorized use, disclosure, copying, distribution 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 email.
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[Freesurfer] FSFAST- Cerebellum

[sabin khadka]

Hi all,
I am trying to extract mean time series BOLD data using FSFAST from Cortical 
ROIs + sub cortical ROIs and cerebellum.
preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 
-per-run -stc odd    mri_segstats --annot fsaverage lh aparc --i 
rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000 --excludeid 
1004 --avgwf CorticalTimeSeries_lh.txt     
mri_segstats --annot fsaverage rh aparc --i 
rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 --excludeid 
2004 --avgwf CorticalTimeSeries_rh.txt    
and for cortical time series
mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab 
/opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id 17 
--id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58 --i 
rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf 
subCorticalTimeSeries.txt    
But I am not sure on how exactly to extract time series from cerebellar 
regions. So if I want to extract time series from regions as described in 
Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in 
FreeSurferCololLUT.txt? If not could you please direct me to processes that I 
can use. 

 Cheers,
Sabin Khadka___
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Re: [Freesurfer] Hippocampal subfields error

[Greenberg, Jonathan]

Thanks.
Has anyone else encountered this error message or knows how it can be solved?
Thank you
Jonathan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis 
[mhib...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 12:44 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

No, I just wanted to mention that in case it helps with troubleshooting what 
went wrong with the new dev version build.

Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan 
[jgreenbe...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 11:24 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

Thanks Matt. Did you somehow get it to work or recognize the file without the 
ctf extension?
Thanks
Jonathan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis 
[mhib...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 11:10 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

I've also gotten this error recently, with T1, T2, and combined T1+T2 
hippocampal segmentations.  It looks like the  files exist at 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
 exist, they just don't have the ".ctf" file extension.

Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan 
[jgreenbe...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 10:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Hippocampal subfields error

Hi all
I ran recon-all on data from about 60 participants pre and post an 
intervention, with the hippocampal subfields flag
(e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). 
The recon-all.log file states that the process finished without errors. 
However, the hippocampal-subfieldsT1.log indicated the following:
"Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
 (see below for the full content of hippocampal-subfieldsT1.log).
I tried to run only the hippocampal subfield recon-all again (e.g. "recon-all 
-s recon-all -all -subjid SPS01-1910_pre_lazar hippocampal-subfields-T1") and 
received the same error message.
I tried to look in the indicated folder 
("/autofs/cluster/freesurfer/centos6_x86_64/dev/bin") and found a file named 
segmentSubjectT1_autoEstimateAlveusML (without the ctf extension). I do not 
know if this is the source of the problem.

My FREESURFER_HOME directory is 
/autofs/cluster/freesurfer/centos6_x86_64/stable6/. My SUBJECTS_DIR is 
/autofs/cluster/lazar/Projects/jonathan-miracle/unpacking-dicoms/SUBJECTS_DIR/.

Any suggestions? (full hippocampal-subfieldsT1.log below)
Thank you!
Jonathan

hippocampal-subfieldsT1.log content:

#
#@# Hippocampal Subfields processing (T1 only) left Thu Jun 16 09:58:23 EDT 2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
#
#@# Hippocampal Subfields processing (T1 only) right Thu Jun 16 09:58:26 EDT 
2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf


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Re: [Freesurfer] Apply mris_apply_reg for a label

[Bruce Fischl]

Hi Alexandre

try mri_label2label using the ?h.sphere.left_right

cheers
Bruce
On Thu, 16 Jun 2016, Alexandre Routier wrote:


Hello everyone,
I have a label for the left hemisphere for my subject but I don't understand
the syntax to apply mris_apply_reg on this label to obtain the right
hemisphere version.

mris_left_right_register was performed to get lh.sphere.left_right
and lh.sphere.left_right but I don't know how to use this for
the mris_apply_reg command.

Thanks in advance for your answer.

Alexandre

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[Freesurfer] Apply mris_apply_reg for a label

[Alexandre Routier]

Hello everyone,

I have a label for the left hemisphere for my subject but I don't
understand the syntax to apply mris_apply_reg on this label to obtain the
right hemisphere version.

mris_left_right_register was performed to get lh.sphere.left_right and
lh.sphere.left_right
but I don't know how to use this for the mris_apply_reg command.

Thanks in advance for your answer.

Alexandre
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Re: [Freesurfer] Hippocampal subfields error

[Hibert, Matthew Louis]

No, I just wanted to mention that in case it helps with troubleshooting what 
went wrong with the new dev version build.

Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan 
[jgreenbe...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 11:24 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

Thanks Matt. Did you somehow get it to work or recognize the file without the 
ctf extension?
Thanks
Jonathan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis 
[mhib...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 11:10 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

I've also gotten this error recently, with T1, T2, and combined T1+T2 
hippocampal segmentations.  It looks like the  files exist at 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
 exist, they just don't have the ".ctf" file extension.

Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan 
[jgreenbe...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 10:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Hippocampal subfields error

Hi all
I ran recon-all on data from about 60 participants pre and post an 
intervention, with the hippocampal subfields flag
(e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). 
The recon-all.log file states that the process finished without errors. 
However, the hippocampal-subfieldsT1.log indicated the following:
"Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
 (see below for the full content of hippocampal-subfieldsT1.log).
I tried to run only the hippocampal subfield recon-all again (e.g. "recon-all 
-s recon-all -all -subjid SPS01-1910_pre_lazar hippocampal-subfields-T1") and 
received the same error message.
I tried to look in the indicated folder 
("/autofs/cluster/freesurfer/centos6_x86_64/dev/bin") and found a file named 
segmentSubjectT1_autoEstimateAlveusML (without the ctf extension). I do not 
know if this is the source of the problem.

My FREESURFER_HOME directory is 
/autofs/cluster/freesurfer/centos6_x86_64/stable6/. My SUBJECTS_DIR is 
/autofs/cluster/lazar/Projects/jonathan-miracle/unpacking-dicoms/SUBJECTS_DIR/.

Any suggestions? (full hippocampal-subfieldsT1.log below)
Thank you!
Jonathan

hippocampal-subfieldsT1.log content:

#
#@# Hippocampal Subfields processing (T1 only) left Thu Jun 16 09:58:23 EDT 2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
#
#@# Hippocampal Subfields processing (T1 only) right Thu Jun 16 09:58:26 EDT 
2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf


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[Freesurfer] Job opening: Computational Neuroscience Faculty

[Kendrick Kay]

Computational Neuroscience Faculty
University of Minnesota, Minneapolis, MN, USA

The University of Minnesota seeks 2 scientists with documented backgrounds and 
interests in using brain imaging and computational  neuroscience to understand 
brain function in health and disease.

The University of Minnesota seeks to fill two newly-created positions at the 
level of Assistant Professor, Associate Professor and/or Professor. For each 
position, rank and tenure status will be commensurate with experience. The 
research emphasis can be basic, translational or disease-focused neuroscience 
using innovative modeling and data analysis techniques.  Appropriate tenure 
home departments would depend on the expertise, background and interest and 
could include: Neuroscience, Radiology, Psychiatry, Neurology, Psychology, 
Computer Science and Engineering, Biomedical Engineering, or Electrical and 
Computer Engineering.  Irrespective of tenure home department, the successful 
candidate will be housed at the CMRR, which is an interdepartmental and 
interdisciplinary research laboratory that provides state-of-the-art 
instrumentation, expertise, and infrastructure for high field MRI research. 
CMRR plays a key role in the NIH’s Human Connectome Project and is equipped 
with magnets ranging in field strength from 3 to 10.5 Tesla for human imaging  
and up to 16.4 T for small animal model studies.   

To apply, please see http://neurojobs.sfn.org/jobs/8170600

The University of Minnesota is an Affirmative Action/Equal Opportunity Employer

Candidates will have a Ph.D., M.D./Ph.D. or similar degree in neuroscience, 
biophysics, psychology, biomedical engineering or a related discipline.  
Background and training should include research experience in a combination of 
the following domains: cognitive neurosciences, computational neuroscience, and 
brain imaging technology, in particular Magnetic Resonance Imaging (MRI).  The 
demonstrated ability to work in a collaborative, transdisciplinary and 
interactive environment is a requirement.  The successful candidate will be 
expected to complement and exploit the unique capabilities that exist in the 
Center for Magnetic Resonance Research (CMRR, www.cmrr.umn.edu) in high field 
MRI.


--
Kendrick Kay, PhD
Assistant Professor
Center for Magnetic Resonance Research, Room 2-116
University of Minnesota, Twin Cities
   Web: http://cvnlab.net
E-mail: k...@umn.edu


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Re: [Freesurfer] Hippocampal subfields error

[Greenberg, Jonathan]

Thanks Matt. Did you somehow get it to work or recognize the file without the 
ctf extension? 
Thanks
Jonathan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis 
[mhib...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 11:10 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

I've also gotten this error recently, with T1, T2, and combined T1+T2 
hippocampal segmentations.  It looks like the  files exist at 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
 exist, they just don't have the ".ctf" file extension.

Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan 
[jgreenbe...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 10:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Hippocampal subfields error

Hi all
I ran recon-all on data from about 60 participants pre and post an 
intervention, with the hippocampal subfields flag
(e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). 
The recon-all.log file states that the process finished without errors. 
However, the hippocampal-subfieldsT1.log indicated the following:
"Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
 (see below for the full content of hippocampal-subfieldsT1.log).
I tried to run only the hippocampal subfield recon-all again (e.g. "recon-all 
-s recon-all -all -subjid SPS01-1910_pre_lazar hippocampal-subfields-T1") and 
received the same error message.
I tried to look in the indicated folder 
("/autofs/cluster/freesurfer/centos6_x86_64/dev/bin") and found a file named 
segmentSubjectT1_autoEstimateAlveusML (without the ctf extension). I do not 
know if this is the source of the problem.

My FREESURFER_HOME directory is 
/autofs/cluster/freesurfer/centos6_x86_64/stable6/. My SUBJECTS_DIR is 
/autofs/cluster/lazar/Projects/jonathan-miracle/unpacking-dicoms/SUBJECTS_DIR/.

Any suggestions? (full hippocampal-subfieldsT1.log below)
Thank you!
Jonathan

hippocampal-subfieldsT1.log content:

#
#@# Hippocampal Subfields processing (T1 only) left Thu Jun 16 09:58:23 EDT 2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
#
#@# Hippocampal Subfields processing (T1 only) right Thu Jun 16 09:58:26 EDT 
2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf


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Re: [Freesurfer] Hippocampal subfields error

[Hibert, Matthew Louis]

I've also gotten this error recently, with T1, T2, and combined T1+T2 
hippocampal segmentations.  It looks like the  files exist at 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
 exist, they just don't have the ".ctf" file extension.

Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan 
[jgreenbe...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 10:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Hippocampal subfields error

Hi all
I ran recon-all on data from about 60 participants pre and post an 
intervention, with the hippocampal subfields flag
(e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). 
The recon-all.log file states that the process finished without errors. 
However, the hippocampal-subfieldsT1.log indicated the following:
"Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
 (see below for the full content of hippocampal-subfieldsT1.log).
I tried to run only the hippocampal subfield recon-all again (e.g. "recon-all 
-s recon-all -all -subjid SPS01-1910_pre_lazar hippocampal-subfields-T1") and 
received the same error message.
I tried to look in the indicated folder 
("/autofs/cluster/freesurfer/centos6_x86_64/dev/bin") and found a file named 
segmentSubjectT1_autoEstimateAlveusML (without the ctf extension). I do not 
know if this is the source of the problem.

My FREESURFER_HOME directory is 
/autofs/cluster/freesurfer/centos6_x86_64/stable6/. My SUBJECTS_DIR is 
/autofs/cluster/lazar/Projects/jonathan-miracle/unpacking-dicoms/SUBJECTS_DIR/.

Any suggestions? (full hippocampal-subfieldsT1.log below)
Thank you!
Jonathan

hippocampal-subfieldsT1.log content:

#
#@# Hippocampal Subfields processing (T1 only) left Thu Jun 16 09:58:23 EDT 2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
#
#@# Hippocampal Subfields processing (T1 only) right Thu Jun 16 09:58:26 EDT 
2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf


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Re: [Freesurfer] convert from MNI152 to native space

[Leila Reddy]

Hi FS Experts,
I'm trying to use the mni152reg command but I get an error that --lta is not 
recognized.
It appears that fslregister doesn't have this option. There was a previous post 
about this 
problemhttp://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41953.html
but I can't figure out if the problem had been solved. The version of mni152reg 
I am using is$Id: mni152reg,v 1.9 2014/07/07 18:59:08 greve Exp $ on Mac OS 
10.8.


Thanks,Leila
 

On Wednesday, June 15, 2016 11:55 AM, Leila Reddy  wrote:
 

 Hi,
I have a binary mask from the WFU_Pickatlas. I think this mask in in the MNI152 
space (when I load_nifti in Matlab I get dimensions of [91 109 91]. I would 
like to convert this mask into the native space of each subject. I tried the 
following command but the results do not look right in Freeview:
 mri_vol2vol --mov mask_MNI152.nii --targ bold/005/f.nii.gz --o 
mask_in_Native.nii --mni152reg
The overlay of the mask on f.nii in Freeview is mostly outside the brain.

How can I go about this step?

Thanks for your help,Leila


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Re: [Freesurfer] Error loading a constructed annotation file

[Bruce Fischl]

Hi Nora

you need to send us the complete command line you ran and also the error 
message and the complete terminal outpu


cheers
Bruce
On Thu, 16 Jun 2016, Bittner, Nora wrote:



Dear freesurfer experts,

 

I constructed an annotation file using mris_label2annot. I did this several
times and every time it worked very well. I was able to use a ctab to define
several colors, load my annotation file into freeview, and look at it.

Now I tried to construct another annotation file in the same manner, but  if
I try to load it into freeview, freeview just crashes. When I constructed
the annotation file I received no error from the terminal output.

 

I can´t understand the error message the terminal gives in the moment
freeview crashes. Since I was always successful in constructing my
annotation files, I wonder why this happens now.

 

I hope you can tell me, what the attached error message means.

Thanking you in advance,

 

Nora Bittner

 

 

 

Arbeitsgruppe Konnektivität

   Institut für Neurowissenschaften und Medizin (INM-1)

   Forschungszentrum Jülich GmbH

   52425 Jülich

   Tel.: 02461-612412

   Email: n.bitt...@fz-juelich.de

 

und

 

Arbeitsgruppe Konnektivität im menschlichen Gehirn

   C. und O. Vogt Institut für Hirnforschung

   Heinrich-Heine-Universität Düsseldorf

   Universitätsklinikum Düsseldorf

   40225 Düsseldorf

   Tel.: 0211-8106109

   Email: n.bitt...@fz-juelich.de

 



---
-
---
-
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
---
-
---
-


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[Freesurfer] Error loading a constructed annotation file

[Bittner, Nora]

Dear freesurfer experts,

I constructed an annotation file using mris_label2annot. I did this several 
times and every time it worked very well. I was able to use a ctab to define 
several colors, load my annotation file into freeview, and look at it.
Now I tried to construct another annotation file in the same manner, but  if I 
try to load it into freeview, freeview just crashes. When I constructed the 
annotation file I received no error from the terminal output.

I can´t understand the error message the terminal gives in the moment freeview 
crashes. Since I was always successful in constructing my annotation files, I 
wonder why this happens now.

I hope you can tell me, what the attached error message means.
Thanking you in advance,

Nora Bittner



Arbeitsgruppe Konnektivität
   Institut für Neurowissenschaften und Medizin (INM-1)
   Forschungszentrum Jülich GmbH
   52425 Jülich
   Tel.: 02461-612412
   Email: n.bitt...@fz-juelich.de

und

Arbeitsgruppe Konnektivität im menschlichen Gehirn
   C. und O. Vogt Institut für Hirnforschung
   Heinrich-Heine-Universität Düsseldorf
   Universitätsklinikum Düsseldorf
   40225 Düsseldorf
   Tel.: 0211-8106109
   Email: n.bitt...@fz-juelich.de





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt





Freeview_Error
Description: Freeview_Error
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[Freesurfer] Hippocampal subfields error

[Greenberg, Jonathan]

Hi all
I ran recon-all on data from about 60 participants pre and post an 
intervention, with the hippocampal subfields flag
(e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). 
The recon-all.log file states that the process finished without errors. 
However, the hippocampal-subfieldsT1.log indicated the following:
"Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
 (see below for the full content of hippocampal-subfieldsT1.log).
I tried to run only the hippocampal subfield recon-all again (e.g. "recon-all 
-s recon-all -all -subjid SPS01-1910_pre_lazar hippocampal-subfields-T1") and 
received the same error message. 
I tried to look in the indicated folder 
("/autofs/cluster/freesurfer/centos6_x86_64/dev/bin") and found a file named 
segmentSubjectT1_autoEstimateAlveusML (without the ctf extension). I do not 
know if this is the source of the problem. 

My FREESURFER_HOME directory is 
/autofs/cluster/freesurfer/centos6_x86_64/stable6/. My SUBJECTS_DIR is 
/autofs/cluster/lazar/Projects/jonathan-miracle/unpacking-dicoms/SUBJECTS_DIR/.

Any suggestions? (full hippocampal-subfieldsT1.log below)
Thank you!
Jonathan

hippocampal-subfieldsT1.log content:

#
#@# Hippocampal Subfields processing (T1 only) left Thu Jun 16 09:58:23 EDT 2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
#
#@# Hippocampal Subfields processing (T1 only) right Thu Jun 16 09:58:26 EDT 
2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf


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Re: [Freesurfer] Maps/seed on surafce

[Martin Juneja]

Hi Dr. Greve,

I used following command for this:

mkanalysis-sess -analysis LH_XY.surf.lh
-surface fsaverage lh -fwhm 5 -notask -taskreg LH_XYZ.dat 1 -nuisreg
vcsf.dat 5 -nuisreg wm.dat 5  -mcextreg -polyfit 5 -nskip 4 -fsd bold
-TR
 3.

Thanks.

On Wed, Jun 15, 2016 at 3:07 PM, Douglas N Greve 
wrote:

> what was your mkanalysis-sess command?
>
> On 06/08/2016 02:10 PM, Martin Juneja wrote:
> > Dear FreeSurfer and SPM experts,
> >
> > I am trying to calculate functional connectivity maps using FreeSurfer
> > pipeline:
> >
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
> .
> >
> > After defining a seed region on raw anatomical image, I co-registered
> > functional data with anatomical data (as reference) and made sure that
> > the seed is at correct place on both anatomical (top left in attached
> > image) and functional (top right) data. Using SPM, I confirmed
> > co-registration was fine.
> >
> > But after running all the steps of FC, looks like the FC maps are not
> > correct: sig.nii.gz at -fthresh 2 3 (shown at bottom left) because I
> > am not getting significant FC at seed location. Here, bottom right
> > shows the seed location on surface after I convert the seed to
> > fsaverage space (for visualization purpose).
> >
> > Any thoughts, ideas or tips on what went wrong here, would be really
> > appreciated.
> >
> > Thanks.
> >
> >
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>
> --
> 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
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>
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Re: [Freesurfer] unit for hippocampus segmentation results

[Iglesias, Eugenio]

If you mean the new subfield module, then the answer is: cubic mm.


Juan Eugenio Iglesias

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/



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

Sent: Wednesday, June 15, 2016 8:34:09 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] unit for hippocampus segmentation results

Hi freesurfer experts,

We used the development version of freesurfer 6.0 to segment hippocampus. We 
are wondering what the unit is for the segmentation results.

Thanks,

--
Fengji Geng
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[Freesurfer] Z-stat - z.mgh

[Robby De Pauw]

Dear FreeSurfer users

I am not able to extract the Z-values as they are not present in my output:

z.mgh -- z-stat that corresponds to the significance

Are these Z-values always produced (or only in case of two group comparison)? 
Is there a way to produce this map myself?

This is my output after fitting the model (mri_glmfit) and after clusterwise 
correction for MC:

C.dat   cache.th13.abs.sig.voxel.mgh
F.asc   cache.th13.abs.y.ocn.dat
F.csv   cnr.mgh
F.mgh   gamma.mgh
cache.th13.abs.pdf.dat   gammavar.mgh
cache.th13.abs.sig.cluster.mgh   maxvox.dat
cache.th13.abs.sig.cluster.summary   sig.asc
cache.th13.abs.sig.masked.mghsig.csv
cache.th13.abs.sig.ocn.annot sig.mgh
cache.th13.abs.sig.ocn.mgh

I am currently working on the latest version of FreeSurfer:

freesurfer-Darwin-lion-stable-pub-v5.3.0

Thank you for your response,

Greetings

Robby

Robby De Pauw, PT, MT, drs.
T +32 09 332 12 19 | Email robby.dep...@ugent.be

Ghent University | Rehabilitation Sciences and Physiotherapy
Campus Heymans 3B3 (022)
De Pintelaan 185 BE-9000 Ghent
Route to my office

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