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Today's Topics:
1. Re: Surface Viewer Issue. (Gregory Kirk)
2. Re: Mismatched dimensions with T1 and Flair inputs {Disarmed}
(Vilde)
3. Re: v5.1 control point mri_ca_normalize bug (Marx, Gabe)
4. Re: v5.1 control point mri_ca_normalize bug (Bruce Fischl)
5. Re: rawfunc2surf-sess with a limited set of surface files
(Douglas N Greve)
6. functional correlation (Brian Donley)
7. Re: rawfunc2surf-sess with a limited set of surface files
(Reza Rajimehr)
8. mri_thickness & mri_make_surfaces (Seung-Goo KIM)
9. Re: WM & Pial Segmentation Errors (Varjabedian, Ani)
10. "deployed" (compiled) MATLAB scripts path manipulation
(slehar@nmr.mgh.harvard.edu)
11. 8 spots remain in the FreeSurfer course (Allison Stevens)
12. excluding labels (Adam, Ruth)
13. FSGD Format Error (Retzepi, Kallirroi)
----------------------------------------------------------------------
Message: 1
Date: Wed, 08 Oct 2014 14:47:27 -0500
From: Gregory Kirk <gkirk@wisc.edu>
Subject: Re: [Freesurfer] Surface Viewer Issue.
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <76a0cbb215b316.54354e7f@wiscmail.wisc.edu>
Content-Type: text/plain; CHARSET=US-ASCII
i saw this problem on one redhat installation, not on any others, seems something with the X library orientation
information and openGL
greg
On 10/08/14, Jamie Hanson wrote:
> Hi Freesurfer List,
>
>
> I had a (hopefully quick) question about surface viewers and data orientation in tksurfer v. freeview.
>
>
> I processed all my data in freesurfer v5.3.0 (on a linux cluster) and noticed something odd when I viewed surfaces. For tksurfer, the surfaces were upside down when I opened them (see attached pic: tksurfer.png); for freeview, the data looked fine (see attached pic: freeview.png).
>
>
> I believe the orientation of the images is correct (judging by the freeview axes), but wondered if this was something others had run into? I uploaded an example subject to the Martinos Center FileDrop (link: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=9491zcnivqw).
>
>
> Any thoughts are greatly appreciated! Thanks much!
>
>
> Best,
> Jamie.
>
>
>
> --
> Jamie L. Hanson
> Postdoctoral Fellow, Carolina Consortium on Human Development
> Duke University
> 417 Chapel Drive
> Duke West Campus
> Sociology-Psychology Building, Room 07A
> Durham, NC 27710
> Email: jamielarshanson@gmail.com
> Website: http://jamiehanson.org/
------------------------------
Message: 2
Date: Wed, 8 Oct 2014 22:01:06 +0200
From: Vilde <vildeskard@hotmail.com>
Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair
inputs {Disarmed}
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <DUB122-W3321C71B2BEC2FA5D6BE4CD2A30@phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
I will try that.
Have a good day!
Date: Wed, 8 Oct 2014 14:07:38 -0400
From: fischl@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs
you would have to first run recon-all -all on the T1
On Wed, 8 Oct 2014,
Vilde wrote:
> Thank you Bruce!
>
> If I understand you correctly, would the command be
>
> Recon-all -s subj_name -FLAIRpial.nii ?
>
> Or would I first have to do recon-all with only T1 as input and then do
> another command after it has finished running? And in that case, what would
> that command be?
>
> Best,
> Vilde
>
> Date: Wed, 8 Oct 2014 11:56:51 -0400
> From: fischl@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs
>
> Hi Vilde
>
> no, you can't give recon-all a flair directly, it needs a T1 do do the
> recon on. You use the flair at the end to do a post-hoc deformation using
> -flairpial I believe
>
> cheers
> Bruce
>
>
> On Wed, 8 Oct 2014, Vilde wrote:
>
> > Dear mailing list,
> > I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, for
> > pial surface refinement. This results in an error message saying the
> > dimensions are mismatched. (The third dimension of the T1 and Flair are
> > different by one slice. ) I do not, however, have a problem running
> > recon-all with only one T1 input. I am using Freesurfer v 5.1 .
> >
> > I read in the release notes that in version 5.2 you can use the flag -FLAI
> R
> > when you are using a flair image as input. I suppose this will not run in
> an
> > earlier version?
> > Would it be correct to use the following command :
> >
> > recon-all -s [subject] -i T1.nii -i flair.nii -all
> >
> > Kind regards,
> > Vilde
> >
> >
> >
>
> _______________________________________________ Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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
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>
_______________________________________________
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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------------------------------
Message: 3
Date: Wed, 8 Oct 2014 21:02:34 +0000
From: "Marx, Gabe" <Gabe.Marx@ucsf.edu>
Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <EFC972BC4D7D0340A51A7B3A4DD397CCC6845B@ex06.net.ucsf.edu>
Content-Type: text/plain; charset="utf-8"
Hi Bruce,
I appreciate the response!
I am sorry, I am a bit confused. The release notes state:
"An option is to disable the running of mri_ca_normalize when re-running the -autorecon2 or -autorecon2-cp stage after adding control points by adding the flag -nocanorm to the end of recon-all. We will continue to investigate a more automated solution to detection of this problem. The more permanent workaround for v5.1 users is to edit their recon-all script making the following change, which will disable usage of control points with ca_norm:
# find these lines:
set cmd = (mri_ca_normalize)
if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile)
# and comment-out the second line like this:
set cmd = (mri_ca_normalize)
#if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile)
# then re-run your subjects with the flags: -autorecon2 -autorecon3 -clean-aseg"
Are you saying the -nocanorm flag will result in inaccurate data?
Thanks!
Gabe
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Wednesday, October 08, 2014 8:12 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug
Hi Gabe
this wasn't really a bug per-se, just induced some behavior that people didn't like. You can't skip the mri_ca_normalize step or the aseg won't be accurate. The aseg patch I believe just starts autorecon2-cp after the aseg hs been created, but Nick or Zeke can correct me if I'm wrong.
cheers
Bruce
On Mon, 6 Oct 2014, Marx, Gabe wrote:
>
> Hello Freesurfer experts,
>
> ?
>
> I had a question regarding the v5.1 control point mri_ca_normalize
> bug. I read the release notes and know that this bug can be worked
> around by adding the ?nocanorm flag to my recon-all however I have
> become worried about the ramifications of skipping mri_ca_normalize in my pipeline.
> Would someone be able to give me a better description as to what
> mri_ca_normalize is doing and what I am sacrificing by taking it out
> of my pipeline? Furthermore, in regards to the patch for the recon-all
> script to fix this bug, what is the patch doing exactly? ?If I had
> some data in which I used the ?nocanorm flag and other data in which I
> used the patch would I still be able to make valid analysis if I merged them?
> Would there be significant inconsistencies?
>
> ?
>
> Thanks!
>
> ?
>
> Best,
>
> Gabe
>
>
>
------------------------------
Message: 4
Date: Wed, 8 Oct 2014 17:05:41 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Nick Schmansky <nicks@nmr.mgh.harvard.edu>
Message-ID: <alpine.LRH.2.03.1410081705140.27957@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
I don't think you want to run with -nocanorm. Just commenting out the
addition of the -f $ControlPointsFile should be sufficient. Right Nick?
On
Wed, 8 Oct 2014, Marx, Gabe wrote:
> Hi Bruce,
>
> I appreciate the response!
>
> I am sorry, I am a bit confused. The release notes state:
>
> "An option is to disable the running of mri_ca_normalize when re-running the -autorecon2 or -autorecon2-cp stage after adding control points by adding the flag -nocanorm to the end of recon-all. We will continue to investigate a more automated solution to detection of this problem. The more permanent workaround for v5.1 users is to edit their recon-all script making the following change, which will disable usage of control points with ca_norm:
>
> # find these lines:
> set cmd = (mri_ca_normalize)
> if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile)
>
> # and comment-out the second line like this:
> set cmd = (mri_ca_normalize)
> #if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile)
>
> # then re-run your subjects with the flags: -autorecon2 -autorecon3 -clean-aseg"
>
> Are you saying the -nocanorm flag will result in inaccurate data?
>
> Thanks!
> Gabe
>
> -----Original Message-----
> From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Wednesday, October 08, 2014 8:12 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug
>
> Hi Gabe
>
> this wasn't really a bug per-se, just induced some behavior that people didn't like. You can't skip the mri_ca_normalize step or the aseg won't be accurate. The aseg patch I believe just starts autorecon2-cp after the aseg hs been created, but Nick or Zeke can correct me if I'm wrong.
>
> cheers
> Bruce
>
>
>
> On Mon, 6 Oct 2014, Marx, Gabe wrote:
>
>>
>> Hello Freesurfer experts,
>>
>> ?
>>
>> I had a question regarding the v5.1 control point mri_ca_normalize
>> bug. I read the release notes and know that this bug can be worked
>> around by adding the ?nocanorm flag to my recon-all however I have
>> become worried about the ramifications of skipping mri_ca_normalize in my pipeline.
>> Would someone be able to give me a better description as to what
>> mri_ca_normalize is doing and what I am sacrificing by taking it out
>> of my pipeline? Furthermore, in regards to the patch for the recon-all
>> script to fix this bug, what is the patch doing exactly? ?If I had
>> some data in which I used the ?nocanorm flag and other data in which I
>> used the patch would I still be able to make valid analysis if I merged them?
>> Would there be significant inconsistencies?
>>
>> ?
>>
>> Thanks!
>>
>> ?
>>
>> Best,
>>
>> Gabe
>>
>>
>>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
------------------------------
Message: 5
Date: Wed, 08 Oct 2014 17:38:16 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] rawfunc2surf-sess with a limited set of
surface files
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5435AEC8.3020009@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Try it without -i fmc
On 10/08/2014 04:38 AM, Reza Rajimehr wrote:
> One more question:
>
> I tried to run:
>
> rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg
> iter05.sphere.reg -fwhm 2 -per-session
>
> And I got this:
>
> ERROR: experts key needed (-expkey)
>
> Not sure what this flag is.
>
> Reza
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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/
------------------------------
Message: 6
Date: Wed, 8 Oct 2014 16:48:11 -0500
From: Brian Donley <brian.donley@gmail.com>
Subject: [Freesurfer] functional correlation
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAJO=T5tRjhKMPMJh_PuHKDBv=F0LagPV69so58KYENmCium+QQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hello Freesurfers
A bit new to the program, so I hope the following makes sense. We would
like to do a bottom-up vertex-by-vertex analysis to see where functional
activation correlates with thickness. We've done our functional analyses
through SPM and can get those maps into tksurfer. Most of the tutorials and
information I see has to do with, for example, defining a ROI based on
functional data and extracting the thickness measures "under" that ROI. But
this would be a little different
Does this make sense, and is this doable in freesurfer? If so, could
someone point me to the relevant tutorial or commands?
I appreciate your help
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Message: 7
Date: Thu, 9 Oct 2014 00:12:04 -0400 (EDT)
From: "Reza Rajimehr" <reza@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] rawfunc2surf-sess with a limited set of
surface files
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<42178.18.93.15.69.1412827924.squirrel@mail.nmr.mgh.harvard.edu>
Content-Type: text/plain;charset=iso-8859-1
Hi Doug,
Removing -i fmc did not help, and I still get the same error.
By looking at the rawfunc2surf-sess script, it looks like specifying an
argument for -surfreg makes ExpKeyNeeded = 1. Can I just specify something
for -expkey? Is this something that is used only in the name of log file?
Thanks,
Reza
Try it without -i fmc
On 10/08/2014 04:38 AM, Reza Rajimehr wrote:
> One more question:
>
> I tried to run:
>
> rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg
> iter05.sphere.reg -fwhm 2 -per-session
>
> And I got this:
>
> ERROR: experts key needed (-expkey)
>
> Not sure what this flag is.
>
> Reza
------------------------------
Message: 8
Date: Thu, 9 Oct 2014 12:42:07 +0200
From: Seung-Goo KIM <solleo@gmail.com>
Subject: [Freesurfer] mri_thickness & mri_make_surfaces
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <4E85C9BD-03CD-4781-A989-432D9EAF7389@gmail.com>
Content-Type: text/plain; charset="windows-1252"
Hi all,
I?m trying to compute cortical thickness using mris_thickness (stable 5), but getting slightly different results from the recon-all 5.1.0-amd64-2.13 (mri_make_surfaces, stable 5).
Hinted from an old thread: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05994.html, I set the switch ?-N 20", but it returns different values: 50% of vertices have identical values with the cross-correlation of about 0.98 and RMS of 0.08 mm, which is of course very high, but a bit odd while I was expecting nearly identical results. When I checked the scatter plots, the mris_thickness returns a bit smaller values for many vertices than the standard result. Is this somewhat expected difference between mri_make_surfaces and mris_thickness?
Also I found that mri_thickness reads ??h.gray?, not ??h.pial?. As I assumed that it reads ??h.pial? and ??h.white? to compute thickness, so I just linked ??h.pial? to ??h.gray?. Is this assumed input for mris_thickness?
Best regards,
--
Seung-Goo KIM
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------------------------------
Message: 9
Date: Thu, 9 Oct 2014 14:01:55 +0000
From: "Varjabedian, Ani" <AVARJABEDIAN@mgh.harvard.edu>
Subject: Re: [Freesurfer] WM & Pial Segmentation Errors
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <1412863314.22885.45.camel@sangwoo.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Michael,
I took a look at your data and it seems that you paired a T2 image with
a T1 image when you submitted to recon all. Recon-all will try to
average these together, and since they have such different contrasts,
you will end up with a poor template for surfaces later on.
Try running recon-all again without the T2 and see if that helps.
-Ani
On Wed, 2014-10-08 at 17:21 +0000, Smith, Michael wrote:
> Ah, sorry for some reason it just wasn?t clicking before. I was able to
> upload a dataset. Thanks!
>
> On 10/8/14, 10:59 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote:
>
> >Hi Michael
> >
> >you need to follow the directions on this page:
> >
> >http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
> >
> >in particular, make sure you change directories before trying to put
> >
> >cheers
> >Bruce
> >
> >On Wed,
> >8 Oct 2014,
> >Smith,
> >Michael wrote:
> >
> >> See attached
> >>
> >> On 10/8/14, 10:46 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote:
> >>
> >>> can you send us the details of your ftp command?
> >>> On Wed, 8 Oct 2014, Smith,
> >>> Michael wrote:
> >>>
> >>>> Hi Bruce,
> >>>>
> >>>> Do I not have permission to transfer files to the remote machine? I
> >>>>can
> >>>> login fine as an anonymous user but when I attempt to use the put
> >>>> command
> >>>> it says it could not create the file.
> >>>>
> >>>> On 10/7/14, 7:33 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu>
> >>>>wrote:
> >>>>
> >>>>> Hi Michael
> >>>>>
> >>>>> sure, the T2 can help if you have it (although you'll need to
> >>>>>download
> >>>>> some
> >>>>> updated binaries), but it is impossible to tell from these images
> >>>>>what
> >>>>> is
> >>>>> going on. Looks either the intensity normalization, mri_segment or
> >>>>> mris_make_surfaces failed. You can try the expert options for each
> >>>>>one
> >>>>> to
> >>>>> prespecify the range of allowable intensities for gray and white
> >>>>> matter.
> >>>>> If
> >>>>> you upload the subject to our ftp site (the whole subject directory
> >>>>> tarred
> >>>>> and gzipped) we will take a look
> >>>>>
> >>>>> cheers
> >>>>> Bruce
> >>>>>
> >>>>> On Mon, 6 Oct 2014, Smith, Michael wrote:
> >>>>>
> >>>>>> Hi,
> >>>>>>
> >>>>>> I?ve been having trouble on a few of our subjects with getting the
> >>>>>> white
> >>>>>> matter and pial surface files to ?line up? correctly with the volume
> >>>>>> files.
> >>>>>> I?ve attached a screenshot of what is happening: the pial surface
> >>>>>>is
> >>>>>> in red
> >>>>>> and the white matter surface file is in yellow. I have also attached
> >>>>>> an
> >>>>>> example of a ?good? subject for comparison.
> >>>>>>
> >>>>>> I?ve tried looking through the tutorials online but didn?t see
> >>>>>> anything
> >>>>>> that
> >>>>>> was really related to my issue and I was wondering what the best way
> >>>>>> to
> >>>>>> correct this. We have T2 weighted images for several subjects is
> >>>>>>well
> >>>>>> if
> >>>>>> that helps. Not sure if Freesurfer can use T2 images instead of T1
> >>>>>>in
> >>>>>> the
> >>>>>> ?reconall script but I thought I would mention it. Thank you very
> >>>>>> much
> >>>>>> in
> >>>>>> advance!
> >>>>>>
> >>>>>> Best,
> >>>>>>
> >>>>>> Michael S.
> >>>>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Freesurfer mailing list
> >>>> Freesurfer@nmr.mgh.harvard.edu
> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>>
> >>>>
> >>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 10
Date: Thu, 9 Oct 2014 11:08:10 -0400 (EDT)
From: slehar@nmr.mgh.harvard.edu
Subject: [Freesurfer] "deployed" (compiled) MATLAB scripts path
manipulation
To: freesurfer@nmr.mgh.harvard.edu
Cc: martinos-tech@yahoogroups.com
Message-ID:
<57088.172.21.16.53.1412867290.squirrel@mail.nmr.mgh.harvard.edu>
Content-Type: text/plain;charset=iso-8859-1
I have been following the directions on this site to "deploy" (compile) my
MATLAB script so as to be able to run it on launchpad without worrying
about MATLAB licenses.
https://nmr.mgh.harvard.edu/martinos/itgroup/deploytool.html
They say that the deployed script cannot do path manipulations such as
addpath() or path(path,xxx), so the script should use isdeployed to make
sure that such path commands are only executed if isdeployed == 0.
% Only add path if not deployed
if isdeployed==0;
addpath ~nummenma/matlab/work/connectome/HCP_preproc_tools;
end
but then I need to add the path back in again so it can access the
functions on that path. In the deploytool GUI I click Settings (the little
gear icon), and in the upper window "Additional Parameters passed to MCC:"
I inserted
======[ Additional Parameters passed to MCC: ]======
-I ~nummenma/matlab/work/connectome/HCP_preproc_tools
mris_gradient_nonlin__unwarp_volume__batchmode_HCPS.m
====================================================
(A web site I found said you need a path to the m-file itself, not just to
the directory that contains it, and you separate the path and file)
Then I found I had to circumvent more path(path,xxx) commands in my
startup.m file too
======[ startup.m ]======
% If script is not deployed add paths
if isdeployed==0;
%------------ FreeSurfer -----------------------------%
fshome = getenv('FREESURFER_HOME');
fsmatlab = sprintf('%s/matlab',fshome);
if (exist(fsmatlab) == 7)
path(path,fsmatlab);
end
clear fshome fsmatlab;
%-----------------------------------------------------%
%------------ FreeSurfer FAST ------------------------%
fsfasthome = getenv('FSFAST_HOME');
fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
if (exist(fsfasttoolbox) == 7)
path(path,fsfasttoolbox);
end
clear fsfasthome fsfasttoolbox;
%-----------------------------------------------------%
end
=========================
Now at least it compiles without error. But when I run it I get this:
Set up FreeSurfer environment
-------- freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer/stable5_3_0
FSFAST_HOME /usr/local/freesurfer/stable5_3_0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /space/ficus/4/users/SNEF_subjects
MNI_DIR /usr/local/freesurfer/stable5_3_0/mni
FSL_DIR /usr/pubsw/packages/fsl/current
./run_unwarpone.sh
/cluster/matlab/8.2
/space/ficus/4/users/SLOTS_sessions_Step/SLOTS010/aahscout/001/001.mgz
/space/ficus/4/users/SLOTS_sessions_unwarp/SLOTS010/aahscout/001/001.mgz
/space/ficus/4/users/SLOTS_sessions_Step/SLOTS010/unwarpscout001.log
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is
.:/cluster/matlab/8.2/runtime/glnxa64:/cluster/matlab/8.2/bin/glnxa64:/cluster/matlab/8.2/sys/os/glnxa64
The file
'/usr/local/freesurfer/stable5_3_0/matlab/load_nifti.m'
is not in the application's expanded CTF archive at
'/homes/6/slehar/.mcrCache8.2/unwarp2'.
This is typically caused by calls to ADDPATH in your startup.m or
matlabrc.m files. Please see the compiler documentation and use the
ISDEPLOYED function to ensure ADDPATH commands are not executed by
deployed applications.
An error occurred while trying to determine whether "load_nifti" is a
function name.
MATLAB:err_while_looking_up_function
Error:An error occurred while trying to determine whether "load_nifti" is
a function name.
Error:Error in mclFreeStackTrace.
Any idea what the problem is now? load_nifti is presumably a FreeSurfer
function -- do I now have a problem with my paths to FreeSurfer? I
searched my script code and found no explicit call to "load_nifti", I
presume that is called deep inside some other function. Should I add the
FreeSurfer paths also through the deploytool GUI and not call "nmrenv"?
(from my .cshrc file...
alias nmrenv 'source /usr/local/freesurfer/nmr-stable53-env'
)
------------------------------
Message: 11
Date: Thu, 9 Oct 2014 11:27:07 -0400 (EDT)
From: Allison Stevens <astevens@nmr.mgh.harvard.edu>
Subject: [Freesurfer] 8 spots remain in the FreeSurfer course
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <alpine.LRH.2.03.1410091122430.43717@nmr.mgh.harvard.edu>
Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
Hello everyone,
We have 8 spots remaining in our upcoming FreeSurfer course happening on
October 27-29. We will accept late registrations up to the course date;
however, since the payment deadline has passed, payment is due immediately
upon registration.
Details on the course and a link to the registration page can be found
here:
https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription
Note: This course is the only one where we are currently able to accept
credit card. This likely won't be an option for future courses.
Allison
------------------------------
Message: 12
Date: Thu, 9 Oct 2014 17:35:52 +0200
From: "Adam, Ruth" <Ruth.Adam@med.uni-muenchen.de>
Subject: [Freesurfer] excluding labels
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <4E8BFF03-4A73-4634-A54F-C3759CDF54C7@med.uni-muenchen.de>
Content-Type: text/plain; charset="us-ascii"
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------------------------------
Message: 13
Date: Thu, 9 Oct 2014 15:55:35 +0000
From: "Retzepi, Kallirroi" <KRETZEPI@mgh.harvard.edu>
Subject: [Freesurfer] FSGD Format Error
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <63E2C9A6-FD10-4EE9-A13B-C1D731C6C281@mgh.harvard.edu>
Content-Type: text/plain; charset="us-ascii"
Hi all,
I have been struggling with my .fsgd file. Its header is the following (a total of 119 subjects):
GroupDescriptorFile 1
Title Patients_vs_Controls
MeasurementName thickness
Class PxMale
Class PxFemale
Class ConMale
Class ConFemale
Class PxMPRAGE
Class PxSPGR
Class ConMPRAGE
Class ConSPGR
Class MaleMPRAGE
Class MaleSPGR
Class FemaleMPRAGE
Class FemaleSPGR
Variables Age
Input FS_1 PxFemale PxMPRAGE FemaleMPRAGE 51
..............(rest of subjects)
I think something is up with my Class declaration, since the error message I get is the following:
ERROR: gdfReadV1: Input line 1, subjid = FS_1
Found 3 variables, expected. 1
FSGDF Format Error: file = /group_stats/Px_vs_Con_A.fsgd, tag=Input
Any help would be greatly appreciated!!
Thank you!
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------------------------------
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