[Freesurfer] Calculating Gray Matter Density

[Andrew Jahn]

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Hello,

Does FreeSurfer have an option for calculating gray matter density during
recon-all, or does one need to calculate it manually? In that case, what is
the formula?

The reason I would like to compute density is to replicate the effects show
in this paper:
http://www.jneurosci.org/content/early/2017/05/02/JNEUROSCI.3550-16.2017. I
have seen other threads on FreeSurfer indicating that density is gray
matter per unit volume, but it's unclear how to compute this.


Thanks!

-Andy
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[Freesurfer] Talairach Failure

[Andrew Jahn]

Hi,

I got the following error when trying to run recon-all on an MP-RAGE
T1-weighted image:

Fri Apr 10 16:25:01 EDT 2009
talairach_avi done
\n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n
#
#...@# Talairach Failure Detection Fri Apr 10 16:25:02 EDT 2009
/usr/local/freesurfer/subjects/MPRAGE/mri
\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0., pval=0. < threshold=0.0050)
Darwin The-Ohio-State-University-Server.local 9.6.0 Darwin Kernel Version
9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386


And this was the command I typed:

recon-all -subject MPRAGE -i fmprage.nii -all



auto-recon works for other T1's using a FLASH sequence, for example, but
failed on this one.  Any help would be greatly appreciated.

Thank you!

-Andrew
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[Freesurfer] Multiple Processors

[Andrew Jahn]

Hi,

I am running Freesurfer on a Mac OS X 10.5 computer with a 2x2.8 GHz
Quad-Core Intel Xeon processor.  My question is, are there any subcommands
to run recon-all assigning the processors to different jobs?  Or is the
speed of recon-all just dependent on pure processing power, no more?

Thanks!

-Andrew
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[Freesurfer] Unable to Open GUI

[Andrew Jahn]

Hi,

We are operating x86_64 redhat linux on a server, and we recently installed
FreeSurfer on the surfer to help with running multiple recon-all's.
However, whenever I attempt to run tkmedit or tksurfer, I get the following
error:

[and...@scan2 Anatomicals]$ tkmedit Focus_reg_009 brainmask.mgz
GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not surrported by
display:
 :1.0

Is this a problem specific to the VNC Viewer I am using (Chicken of the VNC
on a Mac OS X), or some other compilation problem?

Thanks!

-Andrew
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[Freesurfer] RE: GLUT Error

[Andrew Jahn]

Hi again,

I have been encountering an error when attempting to use either tksurfer or
tkmedit via VNC on a local server.  Here is the output whenever I type
tkmedit or tksurfer:

GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by
display: 1.0

I looked through the threads regarding this problem, but still have been
unable to find a solution.  The output of 'cat /etc/redhat-release' is Red
Hat Enterprise Linux WS release r (Nahant Update 7) and here is the output
from the command ldd `which tkmedit.bin`:

libtix8.1.8.4.so => not found
libtk8.4.so => /usr/lib64/libtk8.4.so (0x003d43d0)
libtcl8.4.so => /usr/lib64/libtcl8.4.so (0x003d43b0)
libGLU.so.1 => /usr/X11R6/lib64/libGLU.so.1 (0x003d4830)
libGL.so.1 => /usr/lib64/libGL.so.1 (0x003d4850)
libXext.so.6 => /usr/X11R6/lib64/libXext.so.6 (0x003d44f0)
libX11.so.6 => /usr/X11R6/lib64/libX11.so.6 (0x003d44d0)
libXmu.so.6 => /usr/X11R6/lib64/libXmu.so.6 (0x003d4790)
libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x003d4710)
libtiff.so.3 => /usr/lib64/libtiff.so.3 (0x003d4c00)
libz.so.1 => /usr/lib64/libz.so.1 (0x003d4510)
libcrypt.so.1 => /lib64/libcrypt.so.1 (0x003d48a0)
libdl.so.2 => /lib64/libdl.so.2 (0x003d44b0)
libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x003d4530)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x003d4750)
libm.so.6 => /lib64/tls/libm.so.6 (0x003d4490)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x003d4730)
libc.so.6 => /lib64/tls/libc.so.6 (0x003d4460)
libGLcore.so.1 => /usr/lib64/libGLcore.so.1 (0x002a95586000)
libnvidia-tls.so.1 => /usr/lib64/tls/libnvidia-tls.so.1
(0x003d4440)
libXt.so.6 => /usr/X11R6/lib64/libXt.so.6 (0x003d4a10)
libSM.so.6 => /usr/X11R6/lib64/libSM.so.6 (0x003d4570)
libICE.so.6 => /usr/X11R6/lib64/libICE.so.6 (0x003d4550)
/lib64/ld-linux-x86-64.so.2 (0x003d4390)

Also, here is the content of the .xdebug_tkmedit file following an
unsuccessful tkmedit command:

tkmedit started: Thu May 14 14:55:44 2009

tkmedit.bin

$Id: tkmedit.c,v 1.320.2.9 2009/01/27 20:41:02 greve Exp $ $Name: stable4 $


Any help or advice is greatly appreciated in advance.  Thanks!

-Andrew
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[Freesurfer] Finishing WMParc

[Andrew Jahn]

Hello,

I recently ran a batch file on several subjects, but set a time limit which
prevented some of them from finishing all the steps of recon-all.  In the
recon-all-status.log for some of them, the last line is "WMParc".  I was
unable to find which option of recon-all would do only this step; should I
just rerun them with autorecon3?

Thanks,

-Andy
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[Freesurfer] Binary files not executable

[Andrew Jahn]

Hello,

I recently installed FreeSurfer on one of my laptops running Ubuntu and get
the following error when I attempt to run tkmedit:

Exec format error. Binary file not executable.


I thought I remembered something about setting a soft link for one of the
libraries in Ubuntu.  Am I on the right track here?


Thank you,

-Andrew
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[Freesurfer] Rerunning aseg.stats

[Andrew Jahn]

Hello,

I recently ran a batch file which seemed to run fine for nearly all the
participants.  Yet, when I did an asegstats2table command on all the
subjects, I received the following error for three of them:

WARNING: cannot find
/nfs/01/osu5323/freesurfer/freesurfer/subjects/JUL11_2009E/stats/aseg.stats.
proceeding to next file
WARNING: cannot find
/nfs/01/osu5323/freesurfer/freesurfer/subjects/JUL12_2009C/stats/aseg.stats.
proceeding to next file
WARNING: cannot find
/nfs/01/osu5323/freesurfer/freesurfer/subjects/JUL12_2009G/stats/aseg.stats.
proceeding to next file

I checked the status of /scripts/recon-all-status.log, and it said that
recon-all finished without errors.  Would I want to only rerun step 11 of
the recon-all workflow, which is Aseg volumetric labeling and statistics?

Thank you,

-Andrew
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[Freesurfer] asegstats2table command not found

[Andrew Jahn]

Hi,

I am running FreeSurfer version 4.3, and when I type 'asegstats2table' I get
a "command not found" error.  I have my path set correctly (virtually all of
the other commands in the freesurfer/bin directory work), but for some
reason both asegstats2table and aparcstats2table do not.  Any ideas?

Thanks,

-Andrew
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Re: [Freesurfer] asegstats2table command not found

[Andrew Jahn]

Here is the output of my permissions:

[The-Ohio-State-University-Server:Angled/tmp2/AddEdge] scnlab% ls -al
$FREESURFER_HOME/bin/*stats2table
-rwxrwxrwx  1 root  wheel   9013 Jan 21  2009
/usr/local/freesurfer/bin/aparcstats2table
-rwxrwxrwx  1 root  wheel  13351 Jan 21  2009
/usr/local/freesurfer/bin/asegstats2table

And here's what I get just typing in the command:

[The-Ohio-State-University-Server:Angled/tmp2/AddEdge] scnlab%
asegstats2table
asegstats2table: Command not found.

I am using Python 2.4.4.  Does FreeSurfer require a different version?

Thanks,

-Andrew


On Mon, Oct 26, 2009 at 12:36 PM, Krish Subramaniam <
kr...@nmr.mgh.harvard.edu> wrote:

>
> - Do they have proper permissions?
> ls -al $FREESURFER_HOME/bin/*stats2table
>
> -if they do.. might something be wrong with the default Python?
>
> can you paste the entire output you get?
>
> Krish
>
>
> On Oct 26, 2009, at 12:29 PM, Andrew Jahn wrote:
>
>  Hi,
>>
>> I am running FreeSurfer version 4.3, and when I type 'asegstats2table' I
>> get a "command not found" error.  I have my path set correctly (virtually
>> all of the other commands in the freesurfer/bin directory work), but for
>> some reason both asegstats2table and aparcstats2table do not.  Any ideas?
>>
>> Thanks,
>>
>> -Andrew
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>>
>
>
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Re: [Freesurfer] asegstats2table command not found

[Andrew Jahn]

That did the trick.  Thank you so much!

-Andrew

On Mon, Oct 26, 2009 at 1:57 PM, Krish Subramaniam <
kr...@nmr.mgh.harvard.edu> wrote:

> I think the Python you have is not in the standard path /usr/bin .. you can
> verify it by typing
>
> which python
>
> It's wrong for the stats2table scripts to assume Python is in that standard
> path. So it's a bug. For a quick fix, you can change the first line of both
> files from
> #!/usr/bin/python
> to
> #!/usr/bin/env python
>
> ( this assumes env to be in your standard path.. and most of the time it
> is.. if you don't have, change that line to the path of the executable --
> like #!/opt/local/bin/python )
>
> The next release will fix this.
>
> Thanks
> Krish
>
>
> On Oct 26, 2009, at 1:46 PM, Andrew Jahn wrote:
>
>  Here is the output of my permissions:
>>
>> [The-Ohio-State-University-Server:Angled/tmp2/AddEdge] scnlab% ls -al
>> $FREESURFER_HOME/bin/*stats2table
>> -rwxrwxrwx  1 root  wheel   9013 Jan 21  2009
>> /usr/local/freesurfer/bin/aparcstats2table
>> -rwxrwxrwx  1 root  wheel  13351 Jan 21  2009
>> /usr/local/freesurfer/bin/asegstats2table
>>
>> And here's what I get just typing in the command:
>>
>> [The-Ohio-State-University-Server:Angled/tmp2/AddEdge] scnlab%
>> asegstats2table
>> asegstats2table: Command not found.
>>
>> I am using Python 2.4.4.  Does FreeSurfer require a different version?
>>
>> Thanks,
>>
>> -Andrew
>>
>>
>> On Mon, Oct 26, 2009 at 12:36 PM, Krish Subramaniam <
>> kr...@nmr.mgh.harvard.edu> wrote:
>>
>> - Do they have proper permissions?
>> ls -al $FREESURFER_HOME/bin/*stats2table
>>
>> -if they do.. might something be wrong with the default Python?
>>
>> can you paste the entire output you get?
>>
>> Krish
>>
>>
>> On Oct 26, 2009, at 12:29 PM, Andrew Jahn wrote:
>>
>> Hi,
>>
>> I am running FreeSurfer version 4.3, and when I type 'asegstats2table' I
>> get a "command not found" error.  I have my path set correctly (virtually
>> all of the other commands in the freesurfer/bin directory work), but for
>> some reason both asegstats2table and aparcstats2table do not.  Any ideas?
>>
>> Thanks,
>>
>> -Andrew
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>>
>>
>>
>
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[Freesurfer] 2nd Level Analyses in FreeSurfer

[Andrew Jahn]

Hi all,

I am interested in using Freesurfer to project volume data onto the inflated
brains run through the FS pipeline.  I am using SPM and have been able to
project 1st level con and spmT images onto the corresponding subject's
inflated anatomical.

My question is, if I wanted to look at 2nd level SPM results on an inflated
brain, would it make the most sense to project them onto fsaverage?  For
example,

spmregister --s fsaverage --mov spmT_0001.hdr --reg register.dat

Or, is there a way to average the surfaces of the subjects in the study and
then project their second levels onto that averaged surface?


Thanks!

-Andrew
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[Freesurfer] Parametrics in FreeSurfer

[Andrew Jahn]

Hi FreeSurfer experts,

I was wondering whether you are able to use parametric modulators during
FS-FAST.  All I can see from the mkanalysis-sess gui is setting up
contrasts, but I would also like to see how other parameters affect the size
and shape of the bold response.  Is there any way to do this in Freesurfer?
If not, is there a way to visualize parametric analyses done in another
software package (e.g., SPM) on a brain processed in freesurfer?

Thanks!

-Andrew
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Re: [Freesurfer] Parametrics in FreeSurfer

[Andrew Jahn]

What I had in mind was entering additional information about each regressor.
 For example, in addition to the onset telling you what class of stimulus
was presented at that time, you could encode the emotional valence of the
stimulus as a continuous variable.  From there, you could examine whether
the magnitude of the valence had an effect on the HRF.  The concept is
identical to the "Parametric Modulator" option in SPM and the "AM_2" option
in AFNI.

Thanks,

-Andrew

On Thu, Jun 17, 2010 at 4:54 PM, Douglas N Greve
wrote:

> What kind of parameters do you want to change? Eg, delay or dispersion of
> the HRF?
>
> doug
>
> Andrew Jahn wrote:
>
>> Hi FreeSurfer experts,
>>
>> I was wondering whether you are able to use parametric modulators during
>> FS-FAST.  All I can see from the mkanalysis-sess gui is setting up
>> contrasts, but I would also like to see how other parameters affect the size
>> and shape of the bold response.  Is there any way to do this in Freesurfer?
>>  If not, is there a way to visualize parametric analyses done in another
>> software package (e.g., SPM) on a brain processed in freesurfer?
>>
>> Thanks!
>>
>> -Andrew
>> 
>>
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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
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
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Re: [Freesurfer] Path Setup of FREESURFER_HOME

[Andrew Jahn]

Hello,

I just downloaded and installed Freesurfer onto a new computer, and after
going through all the steps outlined on the download and installation page,
I get the following error when trying to run recon-all:

sudo recon-all -s bert -all
FREESURFER_HOME: Undefined variable.


However, I have set an absolute path to FREESURFER_HOME:

 freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni

Any ideas on what is going on?  I would appreciate any feedback.


Thanks!

-Andrew
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[Freesurfer] Visualizing SPM Results on Template FreeSurfer Brain

[Andrew Jahn]

Hello,

I have second-level results in .img/.hdr format that I have just run through
SPM.  I was wondering whether there is a way to visualize these results onto
a template FreeSurfer surface model in MNI space.  Is this possible, or can
you only visualize second-levels which have been processed through
FreeSurfer?


Thanks,

-Andrew
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[Freesurfer] Registering Two Anatomical Images

[Andrew Jahn]

External Email - Use Caution

Hello,

I have a raw anatomical image called raw.mgz, which I have manually
annotated using Freeview; the resulting annotations are saved in a file
called seg.mgz. I want to compare this to the annotations automatically
generated by recon-all, so I ran the image through the recon-all processing
stream. However, the original dimensions of the raw.mgz image are
256x209x256, and recon-all resamples the image to 256x256x256 resolution.

If I want to compare the amount of overlap between my annotations and those
generated by FreeSurfer - specifically, the aparc+aseg.mgz file created by
recon-all - what is the best way to register the seg.mgz file to
aparc+aseg.mgz? I looked through the documentation of mri_vol2vol, but I
wasn't sure which registration file to use. Is it one of the transformation
files contained in the "transforms" folder from the image that has been
processed through recon-all?


Thank you!

-Andy
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