Cédric,
Does the first column of your Base_File_FreeSurfer.dat contain the
freesurfer subject id? the first column must contain that. from the
email below, where you show one line of the file, it looks like Subj# is
the first column and SubjID is the second.
Nick
On Thu, 2013-09-19 at 14:07
gt;
>
>
>
> -Original Message-
> From: Nick Schmansky
> Date: Wednesday, September 25, 2013 6:44 PM
> To: Cédric Koolschijn
> Cc: "freesurfer@nmr.mgh.harvard.edu"
> Subject: Re: [Freesurfer] QDEC double trouble: 1. VerifySubjects 2.
> MatrixMul
Valtina,
It should be viewable in freeview. Try:
freeview -f mysurface.gii
tksurfer can load .gii files as well. also, mris_convert will convert
to/from gifti. see its --help output.
Nick
On Mon, 2013-04-08 at 08:05 -0400, Valtina Pouegue wrote:
> Hi,
>
>
> I saw in the documentation th
Daniel,
We're repeating our paired-analysis of thickness measures between 5.1
and 5.2. In the meantime, to check for correctness, open the
brain.finalsurfs.mgz file with the surfaces overlayed, and check the
intensity value of the voxels which appear to be non-cortical 'black
spaces', relative to
Mike,
We dont have a RHEL 5.9 system to replicate the issue. However, I did
find a bug in qdec where the 'Min' value in the Threshold settings would
not update the display when a value was entered. This bug was
introduced when the 'Mid' value was removed (which is why I think the
v5.1 qdec works
Veronica,
Hi, can you copy me on the subject data upload? You can upload data
here:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Nick
On Mon, 2013-04-15 at 12:30 -0400, Bruce Fischl wrote:
> Hi Veronica,
>
> we haven't seen that before. Can you upload your subject including th
Tudor,
In the recon-all.log, it has this line:
ERROR: writing lh.jacobian_white.fwhm15.fsaverage.mgh
but earlier in the log it saved lh.jacobian_white.fwhm10.fsaverage.mgh
correctly, so this indicates to me that it might have run out of disk
space. is that the case?
to answer the others:
2. not
Marcos,
Thanks for looking into this. We dont have a Fedora 18 system to
replicate the problem on, but we're looking at the section of code
described in bugzilla report. We may need your help to test any fixes
we devise.
Nick
On Mon, 2013-04-15 at 17:59 -0300, Marcos Martins da Silva wrote:
>
make
it executable:
chmod a+x tkmedit.bin
it contains a potential fix to the problem (but i dont have a way to
replicate the error to test it).
Nick
On Mon, 2013-04-15 at 18:02 -0400, Nick Schmansky wrote:
> Marcos,
>
> Thanks for looking into this. We dont have a Fedora 18
Veronica,
Can you send me the recon-all.log? The one where it is getting hung
when you run this:
recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial
this should work, by importing the flair and then re-running the surface
creation code, but perhaps there is a dependency bug th
Eduard,
Can you send the whole recon-all.log file? The error show below is a
strange one. It appears as if the string "ERROR: could not determine
file" is the input to mri_convert, and I'm not sure how that can happen.
Also double check (by viewing in freeview) that T2raw.mgz is a valid
file (i
hickness/score slopes (ie,
> an interaction between group factor and continuous factor).
> >
> >
> > E) The average brain with inflated cortex that results are
> > projected on – is this the same average that is normally used in
> > most papers,
>0.0407 0.6128 0.115766.9172
> > > > -0.0232 -0.0912 0.491150.6094
> > > > 0.0000 0.0000 0. 1.
> > > >
> > > > I also attach the "normal" streamline log file
Graham and other wiki users,
The wiki is still accessible if you use 'https' instead of 'http'.
Because wiki pages link to each other, you may run into links where you
need to repeat this change.
We're hoping the spambots that were slowing our wiki system will go away
if accesses continue to fai
Graham,
Hi, to answer each:
Intel vs AMD: no preference. also, CPU speed is not critical. Its
better to have at least 4GB, and budget 4GB per subject you want to
process simultaneously. Try to get a 'Sandy bridge' motherboard
architecture or whatever is newer. This allows better addressing o
ant to say 400MB per subject, not 400GB per subject:)
>
>
>
> On 4/24/13 8:42 PM, Nick Schmansky wrote:
>> Graham,
>>
>> Hi, to answer each:
>>
>> Intel vs AMD: no preference. also, CPU speed is not critical. Its
>> better to have at least
Hi Graham,
Freesurfer works with Ubuntu with one small change that's documented on
the Downloads page (symlinking a library file). I dont know if others
have used Mint, but Debian works with freesurfer w/o mods as far as i
know. Ubuntu seems to be the most common choice of freesurfer users
gauge
Joerg,
Later this evening or tomorrow we'll post a beta that has the fixes for
this problem for you to try on Ubuntu. When its ready, the centos6_x86_64
build will appear in this directory:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/
Nick
> Dear freesurfer administrators,
t; the newest version of glibc.
> Em Qui, 2013-05-02 Ã s 11:46 -0400, Nick Schmansky escreveu:
>
>> Joerg,
>>
>> Later this evening or tomorrow we'll post a beta that has the fixes for
>> this problem for you to try on Ubuntu. When its ready, the
>> centos
gt;longitudinal analysis?
>>
>>Is it because for linear mixed effects models analysis you need a base
>>template for each time point?
>>
>>Thanks,
>>
>>Sarah
>>
>>From: Sarah Whittle
>>Sent: Frida
this link is here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/
the centos6_x86_64 build is there now. the others will appear as they
finish their builds, which can take quite a bit of time... so check back
every day or so
n.
> ok, I think Nick posted a link of where t
s glibc problem?
> Em Sex, 2013-05-03 Ã s 17:46 -0400, Nick Schmansky escreveu:
>
>> this link is here:
>>
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/
>>
>> the centos6_x86_64 build is there now. the others will appear as they
>> fini
Luke,
It is just mris_make_surfaces that has changed (and a bug was found and
fixed in mri_mask, but that bug only affected certain edits, and you would
get a blank volume if you encountered that bug) so you can do the
following to patch 5.2 to match 5.3:
get mris_make_surfaces (and mri_mask) for
Joe,
This error appears when a binary built on CentOS 6 is run on an OS with an
older glibc, like CentOS 4/5. Fsl no longer builds on 4/5 so that is why this
appeared for you recently. Update to CentOS 6 if you are at the nmr center or
use the fsl by doing this
setenv FSL_DIR /usr/pubsw/packag
sion 5.3.0 over 5.2.0 ?...
>
> Sincerely,
>
>
> Gonzalo Rojas Costa
>
>
> On Fri, May 3, 2013 at 5:46 PM, Nick Schmansky
> wrote:
>> this link is here:
>>
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/
>>
>> the centos6_x8
Nicola and Nick,
Can you try the tkmedit.bin found here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
copy it to the freesurfer/tktools directory (the wrapper script
'tkmedit' in the bin dir calls the binary in the tktools dir).
I'm hoping the problem you ar
Martina,
Can you send me the recon-all.log file?
Nick
On Tue, 2013-05-07 at 17:38 +0200, martina.andell...@fastwebnet.it
wrote:
> Hi Freesurfer experts,
> I've got Ubuntu version 13.04 installed on my computer, and after I saw the
> post
> : "http://www.mail-archive.com/freesurfer@nmr.mgh.harv
ement and have people agree to a license prior to
> downloading? Lots of folks probably enter bogus information into the
> registration form anyway.
> Just trying to be constructive.
>
> Thanks very much for your help
>
> Nick
>
> On 05/07/2013 12:14 PM, Nick Schmansky wrot
.3 and 5.3 BETA.
>
> Thanks
>
> Nick
>
> On 05/07/2013 05:06 PM, Nick Schmansky wrote:
> > Nick,
> >
> > Can you request another license file? The info in the .license file
> > that is shown in your email below does not appear to be valid. There is
>
The original also yields
> a license error (no segfault). You are right, my earlier test called
> tkmedit.bin directly.
>
> Thanks
>
> Nick
>
> On 05/08/2013 12:07 PM, Nick Schmansky wrote:
> > Nick,
> >
> > Hi, I found what might the source of the problem
to add to this, the registration it uses is performed on the whole head,
so skull/skin/dura/fat/neck is included, which make the registration
less susceptible to mis-registration due to lesions/atrophy/resection.
n.
On Wed, 2013-05-08 at 15:15 -0400, Douglas N Greve wrote:
> I don't know, I don'
ents crypt differently (working theory anyway).
you can confirm that mri_convert is using this new lib by typing:
cd $FREESURFER_HOME/bin
ldd ./mri_convert
and you should see libcrypt in the list with a path to the freesurfer/lib
dir.
Nick
> Hi Nick (Schmansky),
>
> sorry to jump bac
Gari,
At the NMR Center we use NFS v4 without problems with freesurfer. Is the
SUBJECTS_DIR writable? Note that in the default freesurfer distribution,
the freesurfer/subjects directory is not writable (contains sample and
template subjects).
Nick
> Hi,
> Has anybody got problems using FS wit
Katie,
The next release, v5.3 (hopefully next week), will fix a problem with
running on Ubuntu 13, but freesurfer works on Ubuntu 12 as well (with one
modification described on our download page).
So there are no reasons not to pick Ubuntu other than who will maintain
it. If its just one machine
d the sys admin for the output of the system-config-nfs, I
> don't
> have admin privileges to run it.
>
> thanks again!
> Gari
>
>
>
> On Fri, May 10, 2013 at 11:46 PM, Nick Schmansky
> wrote:
>
>> Gari,
>>
>> At the NMR Center we use NFS v4
Fedora 18, Ubuntu 13 and Gentoo 64 users,
another beta of the upcoming v5.3 is available here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz
this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users
who
to my first contribution:
> > >
> > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> >
Mia,
Hi, in looking at the mri/orig/001.mgz, the image in the sagital and
coronal planes look inverted. also, i noticed this mri_info:
dimensions: 566 x 256 x 992
voxel sizes: 1., 1., 1.
which seems like unusual input. how was this converted from the dicom?
did it necessitate
Freesurfers,
The new version of Freesurfer, v5.3, is available for download!
Recall from our prior posting that this is intended to
replace v5.2, which had a problem with pial and white surface
generation affecting thickness and area measures.
Users should not use v5.2 for any surface-based st
Andreas,
DOSS was removed from qdec because the contrast generation code in qdec
was not appropriate for it (and we didnt have time to add it). You will
have to use the command-line mri_glmfit and create your own contrasts to
use DOSS. There are examples on the wiki i think.
Nick
> Hi surfers
Akio,
You should just run -autorecon2 instead of -subcortseg in order to get the
subcortical segmentation.
Nick
> Hi Freesurfer experts,
>
> After installing v5.3.0 (CentOS 6 64bit), the command "recon-all -s test
> -i sample-001.mgz -i sample-002.mgz -autorecon1" finished without error.
>
> Th
Jamie,
Does running with the -all flag run all the way to complete without error?
We recommend running with -all and then inspect for defects afterwards
instead of running the first run in stages.
Nick
> Hi Freesurfer List-
>
> My group just recently installed 5.3.0 and I kept running into the
Kristina,
We havent created a Windows Virtual Machine freesurfer bundle yet, but
if you already have, or know how to create, an xubuntu vm instance on
windows, then all you have to do is download and install the centos
distribution from within that xubunbtu instance. if your xubuntu is 32,
then y
Mark,
How was the .gca file created? Can you send us this file?
Nick
On Tue, 2013-08-20 at 14:15 -0500, Mark Plantz wrote:
> Thanks for the responses.
>
>
> I think I have determined the cause of the error. I thought it would
> be OK to run recon-all with a .gca atlas that contained some dif
kk,
can you send me your qdec.table.data? qdec automatically assigns a
factor as a fixed fctor if it is not a number (as sscanf determines), so
maybe there is a data point that is wrong.
nick
On Mon, 2012-06-11 at 11:42 -0400, Kushal Kapse wrote:
> hi,
>
> i am trying to do group analysis in
Akio,
the results of our dev tree will be different from the stable branch (as
we are continually incorporating improvements in the dev tree which
eventually make their way into the public stable release). The new
OpenMP code will also change the results, but we have found not
significant differe
s not function correctly?
>
> (2) Is there any special reason why we can use more than one thread only
> in 'mri_ca_register'?
> At this point in time, I would like to speed up 'mri_em_register' as
> well (and some others programs too, in the future).
> Any comment
Cat,
Hi, unfortunately qdec doesnt support loading multiple labels. However,
you can use tksurfer to do that. Another useful thing to know is that
the right most column of a label file can hold a stats value, so with a
bit of text editing/scripting, you can store say a p-value into the rois
labe
Peter,
Thanks for this info. The Mac OS versions compared in the paper were 10.5
and 10.6 (Leopard and Snow Leopard). One of the major changes between
these two versions was the switch from a 32b kernel to a 64b kernel
(whereas Snow Leopard and Lion both use a 64b kernel). I havent been able
to
Mike,
I have run such tests in the past (which showed about 2-3% variability in
hippo volume due to randomness) and Doug has done similar tests, but
admittedly running a large scale analysis and showing the results on a
wiki page would be useful. Something like running our Buckner40 and/or
ADNI60
aiko,
in particular, grep on HAVE_OPENMP in the c files in dev/utils. eg
gcamorph.c., also dev/mri_ca_register/mri_ca_register.c. we havent done
anything with em reg, but welcome any improvements you can make per what
you see with how ca_reg was done.
this is the pattern of speed improvements w
Anne,
It looks like the diagnosis.levels file has 'MApsychosis' as a level but
the error message says 'Psychosis', so they would need to match.
Nick
On Tue, 2012-07-03 at 15:51 +0200, Anne Uhlmann wrote:
> Hello FreeSurfers,
>
> I have a similar problem as described in an old thread
> (http:/
Carolina,
It means its smoothing on the surface with a kernel of 10mm full-width
half-max. Smoothing on the surface can generally be larger than in a
volume. See these slides for a description of the difference:
http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.surface-based-analysis.ppt
you can u
Chris,
This is an unusual error. I dont know why nu_correct would be found for
some subjects but not others, if its being run on the same platform. I
can only think this is a network issue. Is it replicable? nu_correct can
be run from the command line.
The intensity normalization issues in v5
>
> Attached is the table and the levels files. Do you know what is wrong?
>
> Best regards,
>
> Viola
>
>
>
> Von: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von &qu
Fidel,
I don't know why those files are missing from the Tiger ppc distribution,
but i confirmed that indeed they are. Here is a tarball of the
distribution which contains everything:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz
The problem with the ICV calc in v5.1 is explained in the v5.1 Known
Issues section of the ReleaseNotes page, which i've also just updated
with notes on a workaround:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
the workaround is to type these commands:
cd subjid/mri
talairach_avi --i
Hi,
Yes, they do, just overwrite the ones in freesurfer/bin.
Nick
On Mon, 2012-08-27 at 09:45 -0700, Cat Chong wrote:
> Hello Experts,
>
>
> Just a quick question: Do the Tracula updates(dmri_mergepaths, etc)
> for snow_leopard replace the 'old' ones in freesurfer's "bin"
> directory?
> che
try running:
recon-all -s -skullstrip -no-wsgcaatlas
if that works, continue the rest with:
recon-all -s -autorecon2 -autorecon3
n.
On Wed, 2012-08-29 at 17:01 +, Darren R Gitelman wrote:
> Hi
>
> I am having a problem getting recon-all to finish on 1 subject.
>
> The first time I r
does freeview otherwise appear to be working? that is, does it crash?
the 'invalid drawable' messages can be ignored on the mac.
n.
On Wed, 2012-08-29 at 14:29 -0700, Cat Chong wrote:
>
> Dear Experts:
> I have worked my way through Tracula and things seem to work fine, but
> when I try to
i think there should be an error log that outputs the errors that
mri_ca_train found. or you can run mri_ca_train with the -check flag.
it performs checks looking for voxels that are in the wrong hemisphere,
based on the talairach registration.
for mri_convert, be sure to include the flag
-rt n
Darren,
I forgot to mention that you'll need to add
-clean-bm
after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be
retained and the new one will be saved as brainmask.auto.mgz.
Nick
On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
> Nick, List:
>
>
>
> Still
Deirdre,
this is the infamous 'sliver' problem. consult this page for solutions:
https://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems
Nick
On Wed, 2012-09-05 at 13:39 -0400, Deirdre O Shea wrote:
> Hello,
>
> I am just getting to get grips with using FreeSurfer to reconstruct
>
ice will be appreciate it.
>
> Thanks,
>
> Fidel
>
>
> On 20-Aug-12, at 8:48 AM, Nick Schmansky wrote:
>
> Fidel,
>
> I don't know why those files are missing from the Tiger ppc
> distribution,
> but i confirmed that indeed they are. Here is a tarball of the
&
400, Anthony Dick wrote:
> Hello--was just thinking about upgrading to Mountain Lion. Am I to
> assume freesurfer will not work if I do this?
>
> Anthony
>
> On 9/10/12 11:58 AM, Nick Schmansky wrote:
> > Fidel,
> >
> > Sorry, but the GEMS tools are not built for
Liz,
a 64bit build is in the works. in the meantime, you can get a version
of mri_robust_register built for lion (64b) here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-lion/
Nick
On Tue, 2012-10-02 at 12:12 -0400, Martin Reuter wrote:
> Hi Liz,
>
> I have no idea about
Wil,
I've just uploaded the latest-greatest dev build of freeview.bin for
centos6 here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
hopefully that will work. there could be library dependency issues
though.
Nick
On Tue, 2012-10-09 at 18:32 +, Irwin, Wil
Daniel,
See this page which i just created which describes a workaround to a
problem some people are having with the Talairach stage in the v5.1
release:
https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1
Nick
On Wed, 2012-10-17 at 08:24 +0200, Daniel Ferreira wrote:
> Dear experts,
>
> Pl
ain and standars are slided down to the
> bottom of the window.
> See a new output attached.
>
> What can be happening here? Any idea to fix it?
>
> thanks
>
>
Mark,
I've posted the recon-all that will be used in the upcoming v5.2, which
contains the fix whereby control points are no longer used in the aseg,
here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/
you can copy it to your v5.1 distro, but note i've named it
recon-al
Tony,
the powerpc is a big-endian processor, so make sure the BYTEORDER gets
defined as 4321 by configure (see a Makefile). see dcm.c for code that
depends on endianness and make sure the big-endian code gets compiled.
i dont think the configure.in script is smart enough to setup the endian
order
the new mris_topo_fixer is here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/
On Wed, 2012-10-24 at 09:22 -0400, Bruce Fischl wrote:
> yes, that should be fine.
>
> On Wed, 24 Oct 2012, Anne Uhlmann wrote:
>
> > OK, thank you. That would be great.
> > Can I ju
Hannah,
Hi! I think on the Mac, the command is:
cp -LR
that is, a capital R instead of lowercase (which is the case on linux).
I'll update the wiki page.
Nick
On Mon, 2012-11-05 at 16:30 +0100, Bruehl, Hannah wrote:
> Hi,
>
>
> I have a problem with the command for creating a frozen versi
Luke,
A quick answer (w/o looking into it too much): does:
mris_info rh.pial
give you the info you need? what i'm not sure of is whether everything
you see in that output is available in the structure that the matlab
surface reader loads.
Nick
On Wed, 2012-11-07 at 09:17 -0500, Luke Bloy wr
http://wideman-one.com/gw/brain/fs/surfacefileformats.htm doesn't
> mention any of this info being in the file. is there an updated spec
> file on the file formats?
>
>
> Thanks.
> -Luke
>
>
>
>
>
> On Wed, Nov 7, 2012 at 3:26 PM, Nick Schmansky
>
Rito,
Hi, tkregister2 works for me on lion. do tkmedit and tksurfer work? did
you install XQuartz via these instructions?
https://surfer.nmr.mgh.harvard.edu/fswiki/MacTksurfer
Actually i dont know if it necessary for lion to install XQuartz, but that
is what i am running on my lion system (bec
Hugh,
That fix is described in the Known Issues section of 5.1 on the Release
Notes page:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
look for the section where you need to edit your recon-all script to
comment-out the line where the control point is used by ca_norm.
Nick
On Tue, 2
Negar,
This appears to be a strange problem. From the recon-all.log file, the
important error is this one:
GCAread(/usr/local/freesurfer/average/RB_all_2008-03-26.gca): couldn't
expand gcs to 1114693712
which means it failed to alloc the 1.2GB needed to load the atlas. but
given that earlier i
attached snapshots indicate that possibly you are already
running the centos vm.
Nick
On Tue, 2012-12-04 at 17:41 -0500, Nick Schmansky wrote:
> Negar,
>
> This appears to be a strange problem. From the recon-all.log file, the
> important error is this one:
>
> GCAread(/usr/local/
Greg,
one of the -qcache outputs is named 'fwhm0', which will be unsmoothed.
you can also specify creation of just that file by adding '-fwhm 0' after
the -qcache flag.
Nick
> Hi ,
>
> I have winkler variety surface area data that is already smoothed and
> converted to vertex wise data on my a
PPJ,
Hi, if you want, you can send me the input files (the two aseg's and the
lta) and i can try to replicate the segfault in a debugger.
also, if you want, there is a beta of the upcoming v5.2 which is posted
here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
which you could
Fred,
You can try an updated mris_calc for the mac found here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/
Nick
On Mon, 2012-12-31 at 13:21 +0200, Rudolph Pienaar wrote:
> Hi Fred --
>
> I'm currently traveling and have limited internet connectivity. I'll be
Hi,
A beta of the upcoming v5.2 is available here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
the hold-up has been getting the 64b mac lion build working, which has
been a challenge, but we're close. I dont anticipate these posted linux
builds to change, so barring bugs th
Maria,
In qdec there is not a built-in mechanism to restrict analysis to a
particular region. By design it runs a whole-cortex analysis, masking
just the medial (non-cortical) region, and then i suppose if your lucky
(if your ROI is significant compared to everything else) your region will
appear
Carl,
I see that is one of our Mac OS X builds (the toughest to get working),
we'll try to replicate. Thanks for passing along the info.
Nick
On Mon, 2013-01-07 at 15:50 -0500, Carl Anderson wrote:
> Hi Everyone,
> I did the full install for 5.2 but got the following crash during
> Talairach:
This line hidden in the output I think is the reason:
mri_make_uchar: Command not found.
That command was introduced in 5.1, and is used by the talairach stage.
As Martin suggests, a separate v5.2 install is necessary.
Nick
On Mon, 2013-01-07 at 15:40 -0500, Martin Reuter wrote:
> Hi Jonathan,
Susan,
there appear to be two problems here. the first and main problem is the
one:
nu_correct: Command not found.
nu_correct is a script which has as its first line:
#!/usr/bin/perl -w
so can you check that you have perl installed at /usr/bin/perl?
better yet, run this script:
fixup_mni_pa
Carissa,
Unfortunately I dont think we can help with this problem, as we
currently do not have the resources to support the Windows VM instance.
However, an alternative that has worked for others is to do the
following: install the FSL Windows VM, described here:
http://fsl.fmrib.ox.ac.uk/fsl/fsl
/usr/bin/perl exists, so that's ok. I've been
> crawling the forums, but I can't find a good answer for what appears
> to be a simple problem. Can I fix this manually?
>
>
> Thanks!
> Susie
>
> On Wed, Jan 9, 2013 at 4:29 PM, Nick Schmansky
> wrote:
&g
Crystal,
I can replicate the failure you are seeing, and the problem is one that
is fixed for the upcoming v5.2. It is described here:
https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1
the first solution described should fix your problem.
Nick
On Mon, 2013-01-14 at 18:49 +, Franklin,
Jon,
the log indicates that mri_em_register was running. does 'top' show if
mri_em_register is running? it can take quite a while (upwards of 40
minutes), and the log can sit unchanged for several minutes during the
section shown in your log.
Nick
On Mon, 2013-01-14 at 15:25 -0500, Jonathan H
Mia,
Generally for me its easier to visualize problems in tkmedit (or
freeview) by loading the volume with the surfaces overlaid, which makes
it easier to see where surfaces failed to follow. For a lobectomy
though, freesurfer might have problems. If you want to send me a link
(offline) to the l
For those willing and brave enough, another beta of v5.2.0 has been posted
here for you to download and test:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
The Mac builds should work (note: the lion build is 64b, snow-leopard is
32b).
The final release still awaits some critic
gt;>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Freesurfer digest..."
>>
>> Today's Topics:
>>
>>1. v5.2.0 beta, round two (Nick Schmansky)
>>2. Re: pial not computing (Borzello, Mia
also there is an issue in v5.1 where the second run of recon-all on a
given platform will produce different results from the first (but
subsequent runs should produce identical results). this issue has been
fixed in the upcoming v5.2 release.
nick
On Tue, 2013-01-22 at 10:18 -0500, Douglas N Gr
Mia,
also i noticed this at the top of the log:
total used free
Mem: 37010736 19490372 17520364
-/+ buffers/cache: 10784236 26226500
Swap: 8393952 1505288243424
it shows that just 1.7GB is available for the recon to run, which is
belo
e solution running the recon in a
> whole new place with more space?
>
> Thanks so much,
> m
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky
> [ni...@nmr.mgh.harv
the best option is to download the beta of v5.2 which linked from here:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes (look for 'Get a
BETA here'). i've confirmed that that atlas is contained in that release.
Nick
> Hi FS experts,
> I read that the current dev version for recon-all i
randomness enabled.
Nick
> Hi Nick,
>
> Could you clarify this? So if we re-run a subject in 5.1 (say after doing
> some edits), we would then need to run it again a third time in order to
> maintain consistency? Thanks.
>
> -Derin
>
>
> On Jan 22, 2013, at 2:17 PM, Nick
Tudor, Greg, and Petr,
I'm currently attempting to replicate this problem. In the meantime,
can you tell me which Windows and which VirtualBox version you are
running this on? I'm at a loss as to why this build no longer works.
Nick
On Mon, 2013-01-28 at 18:19 +, Tudor Popescu wrote:
> De
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