posted on behalf of Dr. Rahul Desikan:
=
The UCSF Department of Radiology and Biomedical Imaging is looking for a
researcher with strong interests in neuroimaging interested in a Specialist
position at UCSF. We are a neurodevelopment and neuroimaging lab.
Daniel,
The recon-all script sets OMP_NUM_THREADS to 1 at the start of the script, and
is changed only if the -openmp num flag is used. its very strange that you
are seeing em_reg set to 40. in your recon-all.log, search for ‘openmp’, and
it should show ‘1’ by default. you could also add
Mia,
Hi, what sort of error? I looked at the image in freeview, and it looks
like the patient is missing their left frontal lobe. The surfaces look
ok in that region given that.
btw, to make viewing in freeview easy, add this to your .cshrc, all one
line:
alias fv freeview -v mri/T1.mgz
Mia,
Hi, I took a quick look at your BI22_SurferOutput/mri/orig/001.mgz and
the problem appears to be with this input. The orientation is wrong,
and it doesnt quite look like an mprage or equivalent. Unfortunately,
after looking through your dicom series, it doesnt look like any of them
are
Antonin,
This is bug in recon-all that will be fixed for the next release. You
can edit your recon-all, adding the lines with a +, to include this fix
via this diff:
set mdir=$SUBJECTS_DIR/${subjid}/mri
set sdir=$SUBJECTS_DIR/${subjid}/surf
+ set tdir=$SUBJECTS_DIR/${subjid}/touch
if
Josh,
You can get an FS version that is close to v6 here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev
Any testing on top of the hippocampal fields functionality would be greatly
appreciated!
Nick
On May 12, 2015, at 5:42 AM, Eugenio Iglesias e.igles...@bcbl.eu wrote:
Hi
Schmansky,
MGH [ni...@nmr.mgh.harvard.edu]
Sent: 08 May 2015 19:05
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
Erik,
If you wanted to test a 'beta' of v6, which has the new hippocampal
stream, then our current internal 'dev' build, which is very close
Aaron,
The are the *.oasis.chubs.* labels found in the
$FREESURFER_HOME/subjects/fsaverage/labels directory. You will need to
use mris_label2label to map them to your subject. Have a look at the
'ba labels' section of recon-all for an example of this mapping
operation.
N.
On Thu, 2015-05-07
Erik,
If you wanted to test a 'beta' of v6, which has the new hippocampal
stream, then our current internal 'dev' build, which is very close to
being the upcoming v6, can be downloaded from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
This goes for anyone else on the list who
Deirdre,
the -show-edits flag in recon-all will print edits.
N.
On Thu, 2015-05-07 at 12:29 -0400, Deirdre O Shea wrote:
Dear Freesurfer experts,
I wondered how I might be able to track all the edits I make on each
subject e.g., how many control points etc. But most specifically if
Kody,
The ReconAllDevTable wiki page describes the stream that is under
development. For v5.3, you will want this page:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.3
Be aware though that the commands listed may not be *exactly* as that
found in a v5.3 run, as this table is
Francesca,
I looked at the files you sent and replicated the problem. It is due to
creating your lh.EKppa.annot file using FreeSurferColorLUT.txt as the
colortable file. You should create your own colortable file, which is
simple to do, and create a new .annot file using that colortable (ie,
Francesca,
How was lh.EKppa.annot created? Is it a custom list of annotations?
Does it include an embedded colortable appropriate for those
annotations?
Can you send me the files 'lh.EKppa.annot' and 'lh.white'? I can try to
replicate the problem.
Also, can you run this:
mris_info
Ranjan,
after downloading, confirm the integrity of the tarball by running
md5sum on it. you should get the following sum:
6642289df823ebc27de52af57e9b3989
also, make sure you have at least 4.2GB of space prior to download.
some older partitions have a 4GB max size (probably not the case, but
Katherine,
if these files were created on a Mac in TextEdit, the carriage returns might be
the problem. I’ve attached corrected files. On the Mac, to correct it, i did
this:
pico qdec.table.dat
then press Ctrl-O to save, and Esc-D to change to DOS format before pressing
enter to save.
, processing all these
images is the bottleneck now.
Pradeep
On Tue, Dec 16, 2014 at 6:31 AM, Nick Schmansky, MGH
ni...@nmr.mgh.harvard.edu wrote:
Pradeep,
Our lab will be getting a Haswell-based system soon and will
evaluate
any speed gains
Pradeep,
Our lab will be getting a Haswell-based system soon and will evaluate
any speed gains. The system is a Dell PowerEdge R730 with an Intel®
Xeon® E5‐2643 v3 3.4GHz processor.
N.
On Mon, 2014-12-15 at 13:43 +0530, pradeep mahato wrote:
Hello everyone,
Have anyone used Broadwell
To add to this thread, you could also use the parcellations from the DKT
atlas that we provide, produced by the -cortparc3 flag of recon-all
(which is run by default), which is based on 40 healthy subjects from
the Mindboggle-101 project, described here:
http://mindboggle.info/data.html
N.
On
you can try downloading our nightly 'dev' build of freeview, from here:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
or here's a quicker way (this is a one-line command... wget file):
wget
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/freeview.bin
and
Ezra,
The labeling of gm and wm that you see in the aseg.mgz file is not used
to produce the cortical statistics found in the .stats files. The
aseg.mgz grey matter appears this way because the aseg.mgz file is
produced prior to running our 'surface stream', which produces the
accurate gm/wm
correct (the thing to do is comment-out the addition of the control
points).
n.
On Wed, 2014-10-08 at 17:05 -0400, Bruce Fischl wrote:
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
Joel,
The 'recon-all.log' file in the 'scripts' directory of the subject
should have the version of freesurfer used. Also, the file
'build-stamp.txt' in that same directory will show the version used.
N,
On Tue, 2014-08-26 at 18:31 +, Joel R Pieper wrote:
Hello,
I have 80 subjects'
Katie,
Hi, is the SUBJECTS_DIR set to the proper directory? I see from the
output that it is set to:
SUBJECTS_DIR is
'/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3'
which seems to imply that it might be set to the location of your
freesurfer installation, and not
Hugh,
it looks like the new XQuartz v2.7.6 is breaking tkmedit, and we don't
know why. You will have to revert to using v2.7.5:
http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.5.dmg
Nick
On Mon, 2014-07-14 at 15:25 +0100, Hugh Pemberton wrote:
i've tried reinstalling xquartz (this is
Wang,
what command-line flags were included? can you send me the recon-all.log file
for these runs? The results should be the same with repeated runs if the
default flags were used.
Nick
On Jun 21, 2014, at 10:20 PM, wangkangcheng_gmail kangchengwang0...@gmail.com
wrote:
Dear Bruce
the sequences specified by adni are a good resource:
http://www.adni-info.org/scientists/MRIProtocols.aspx
they’re known to work with freesurfer.
N.
On Jun 20, 2014, at 10:13 AM, Sherwood, Matt matt.sherw...@wright.edu wrote:
Freesurfer,
We recently gained access to a new GE
Jace,
If your system auto-updated to XQuartz v2.7.6, which might have happened
within the past couple weeks, then you should install v2.7.5 instead, as
it seems that another Freesurfer user was able to get tkmedit working
again on OSX 10.7.5 after reverting to v2.7.5.
N.
On Wed, 2014-06-18 at
Linden,
The fastest runtime that I have seen is just under 3.5 hours using a new
and very fast system such as yours, using the -openmp 8 flag.
Processing four participants in separate tcsh sessions is the
recommended way of 'parallel' processing. There are flags in recon-all
to allow splitting
Venkat,
Your system appears to be 32bit distribution, as indicated by 'i686' in
your output string, but the freesurfer you installed is 64b, indicated
by 'x86_64' in our filename. So you will need the 32b dist:
freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz
Also, v5.0.0 is pretty old, I'd
Elijah,
Qdec doesnt support three groups, so you'll need to use the commandline.
Typing 'mri_glmfit --help' will display some output text. y.mgh is an
input file. See also for examples:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
Nick
On Tue, 2014-06-10 at 13:37 +0100, Elijah Mak
Gillian,
This tkmedit crash problem is a strange one. Something must have changed, and
I’ll try to suggest some things to try.
Was your .cshrc file changed? Anything added to it that might change
LD_LIBRARY_PATH s?
What is the output if you run:
otool -L `which tkmedit.bin`
it should be
).
Bastian
On 2 June 2014 20:50, Nick Schmansky, MGH ni...@nmr.mgh.harvard.edu wrote:
Bastian,
Are you using freeview to display the surface? If so, you will need to
get the newest freeview.bin, which is here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview
efforts so far!
Bastian.
On 29 May 2014 02:05, Nick Schmansky, MGH ni...@nmr.mgh.harvard.edu
wrote:
Bastian,
Hi, I've posted a new mris_convert which should solve the problem for
you. It's built for Centos 6, so if you need it for another platform,
let me know. It's here
Mike,
Hi, a new mris_convert I’ve posted to the ftp site corrects this problem. It
will now store the volume geometry info into two giiCoordSys structs, which an
updated freeview will be able to read. mris_convert is here:
Saloni,
are you certain that you ran recon-qcache on subject 54987500? the
error message says that the file lh.thickness.fwhm10.fsaverage.mgh is
missing, and this file is created by -qcache. i'd suggest running:
recon-all -s 54987500 -qcache
then confirm that this file exists.
Nick
Samuel,
Unfortunately the program that's failing is 'mritotal', which is an MNI
tool that is distributed with freesurfer, so it's unlikely that we'll
track this down anytime soon.
However, this program is only run after our primary talairach alignment
utility fails, and it appears from your
Bastian,
Hi, I've posted a new mris_convert which should solve the problem for
you. It's built for Centos 6, so if you need it for another platform,
let me know. It's here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
Nick
On Wed, 2014-05-28 at 11:42
somewhere?
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky,
MGH
Sent: Monday, April 28, 2014 1:35 PM
To: Freesurfer support list
Cc: Zeke Kaufman
Subject: Re: [Freesurfer] Segmentatoin
John,
Have you tried the Centos6_x86_64 build of freesurfer on Fedora 19? The
Centos4_x86_64 build is built against a rather old kernel, and likely to
go away soon anyway.
Generally a debug build is not of much use for tkmedit seg-faults. If
you still have trouble after trying the centos6
This GLIBCXX error appears when running our Centos 6 build on an older
OS. Try using our Centos 4 build.
Nick
On Mon, 2014-02-17 at 09:32 -0500, Bruce Fischl wrote:
yes, it certainly looks like a library problem. You should talk to your
sysadmin, or perhaps Zeke or Nick can comment
cheers
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