Hi,Doug
When I runpreproc-sess -fsd bold -fwhm 0 -surface self lhrh -sf sessid
-per-run,I met the following problems.Can you tell me why?
preproc-sess
sess01
$Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $
Linux localhost.localdomain 2.6.18-308.el5PAE #1 SMP Tue Feb 21
Hi Bruce,
is there any recommended protocol for T2 acquisition to be used in the 5.2
recon-all stream?
Should we used the same voxel size as the T1? (we are using 1 mm3 right
now).
If it is going to improve the skull striping and pial surface creation, we
might acquire specific T2 images just
Dear Freesurfer community,
I have processed a subject (name:P061_pre, 3D MPRAGE T1) with Freesurfer
5.1. A resection area has been defiened on this volume and exists as a
binary volume (1:voxels of interest, 0:others) lesionMask.mgz. I now
would like to project this volume on the surface of
Dear All
I have a question about upcoming Freesurfer course registration (April 29 _
May 1). The registration link was supposed to be open and sent by today,
but I still have not received it.
I was wondering if you have any information and can help me.
Thanks a lot
Nooshin
Hi Chikku-- What is your discrete variable? does it have more than one
level? is it entered in the fsgd file? It looks like your discrete
variable(s) is not defined properly. It must have at least two levels
(e.g. Male/Female, RightHanded/LeftHanded, etc.). Check your fsgd file to
so it is
Hi Gari
we use a bandwidth and readout matched (to our multi-echo mprage) T2-SPACE
with a FLAIR inversion pulse. Andre (ccd) can give you the details
cheers
Bruce
On Thu, 7 Mar 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Bruce,is there any recommended protocol for T2 acquisition to be used
see:
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFiledo=gettarget=FreeSurfer_Suggested_Morphometry_Protocols.pdf
Hi Gari
we use a bandwidth and readout matched (to our multi-echo mprage) T2-SPACE
with a FLAIR inversion pulse. Andre (ccd) can give you the details
and 1mm isotropic
On Thu, 7 Mar 2013, Nick Schmansky wrote:
see:
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFiledo=gettarget=FreeSurfer_Suggested_Morphometry_Protocols.pdf
Hi Gari
we use a bandwidth and readout matched (to our multi-echo mprage) T2-SPACE
with a
Many thanks for your answers!
I have another question:
Usually we work with 1 mm3 T1-s, but we have a 0.7 mm3 sequence as well.
Lüsebrink et al (2013) say that: FreeSurfer is not designed to process
data with a spatial resolution other than 1 mm and was modified to avoid
this limitation.
When
The output of mri_vol2surf is not a surface but an overlay on a surface.
You will need to run something like:
freeview -f
$SUBJECTS_DIR/$subject/surf/lh.inflated:overlay=lesionMask_surf.mgh
You'll need to set the threshold to 0.5 in order to see the mask.
doug
On 03/07/2013 05:53 AM,
Dear list,
I was wondering whether you have any suggestions on how to optimize
accuracy of the Freesurfer output (both cortical and subcortical) in images
aquired on lower scanning resolutions than 3 T (for examle 1 T)?
Kind Regards, Linn
___
FYI
-- Forwarded message --
Date: Thu, 7 Mar 2013 11:27:02 -0500
From: Dara Manoach d...@nmr.mgh.harvard.edu
To: a...@nmr.mgh.harvard.edu
Subject: [All] post-doc position available
Postdoctoral Fellowship at the Martinos Center for Biomedical
Imaging and the Psychiatric
Hi Gari
the post-hoc surface deformation will use whatever resolution you have,
and works quite nicely with .7mm scans.
cheers
Bruce
On Thu, 7 Mar 2013, Garikoitz
Lerma-Usabiaga wrote:
Many thanks for your answers!
I have another question:
Usually we work with 1 mm3 T1-s, but we have a
Hi, I have 8 folders of 26 slice odf dicom. Yesterday, I launched the
conversion to .mgz with the command recon-all -i
path-to-first-structural [-i path-to-second-structural] -s
subjid . All my folders are created but in the Orig folder I don't fige files
.mgz.
I think that the processing time
Hi Tim, I don't think you can use tkmedit for this. tkmedit is a bit
rigid and expects things to be a certain way (ie, not in native space).
Try using freeview instead.
doug
On 03/07/2013 03:19 PM, Timothy Brown wrote:
Dear FreeSurfer users,
I wish to view volumes and surfaces in native
Canyou send the recon-all.log file? Is should be in the scripts folder.
If that does not exist, send the terminal output.
doug
On 03/07/2013 03:37 PM, Valtina Pouegue wrote:
Hi,
I have 8 folders of 26 slice odf dicom. Yesterday, I launched the
conversion to .mgz with the command recon-all -i
You cannot give recon-all a folder as input. It must be an image file.
If you have multiple files, you need multiple -i flags.
doug
On 03/07/2013 03:48 PM, Valtina Pouegue wrote:
Hi,
Here it is
[esther@IP132-207-67-224 ~]$ recon-all -i
/home/esther/Freesurfer/freesurfer/subjects/Patient13B
Hi Nicole,
It looks like recon-all -autorecon2 had trouble segmenting the gray/white
matter. you can try using 3duniformize to make the gray,white matter more
uniform, before doing the freesurfes recon-all. you can also try
skullstrippong in afni with 3dskullstrip first, before freesurfer
Hello Nooshin,
The email containing the registration page went out today at 11am EST. It
can be found here:
https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/register.7678.cgi
Unfortunately, the course was filled within the first two hours of opening
registration, but there is a waitlist and
Hi all,
Did you encounter the error message talairach.m3z does not start as 'MNI
Transform File' when making average of subjects?
I checked all the recon-all.log file and did not find error, but when
running make_average_subject after recon-all, then this error shoot.
To repeat the error
This error may come from regio_read_mincxfm function in registerio.c.
Does this mean something wrong in recon-all?
I forgot to mention that FreeSurfer version is
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song dawnwei.s...@gmail.com wrote:
Hi
sorry, I don't understand. What was the error? I don't see one in this
email. Can you send us the actual screen output?
cheers
Bruce
On Thu, 7 Mar 2013, Xiaowei Song wrote:
This error may come from regio_read_mincxfm function in registerio.c.Does
this mean something wrong in recon-all?
I
Sorry, I did not make it clear.
In make_average_volume.log, the error message is:
1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013
mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ
/usr/local/freesurfer/average/mni305.cor.mgz --xfm
/data/lis9/fs/x/1173622/mri/transforms/talairach.m3z
what was your command line?
On Thu, 7 Mar 2013, Xiaowei Song wrote:
Sorry, I did not make it clear.
In make_average_volume.log, the error message is:
1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013
mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ
Thanks for your help.
My command line is
make_average_subject --out avgGrp139 --subjects `cat
script/subjects.id` --xform
talairach.m3z
On Thu, Mar 7, 2013 at 6:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
what was your command line?
On Thu, 7 Mar 2013, Xiaowei Song wrote:
The xform has to be linear in the xfm format. The m3z cannot be used.
doug
On 03/07/2013 06:44 PM, Xiaowei Song wrote:
Thanks for your help.
My command line is
make_average_subject --out avgGrp139 --subjects `cat
script/subjects.id http://subjects.id` --xform talairach.m3z
On Thu, Mar 7,
Thank you, doug, I will try xfm!
On Thu, Mar 7, 2013 at 7:03 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
The xform has to be linear in the xfm format. The m3z cannot be used.
doug
On 03/07/2013 06:44 PM, Xiaowei Song wrote:
Thanks for your help.
My command line is
Hi Freesurfers,
I have created a label on left hemi.
Is there a command could mirror this label to the right hemi?
I have tried mris_reserve, it doesn't work.
Thanks
Chao Suo
School of Psychiatry, UNSW
RNG, BMRI, Usyd.
___
Freesurfer mailing list
Oh yes. It's my mistake. But should I give the adress of the first file of my
set for having the result in .mgz. Thanks.
Date: Thu, 7 Mar 2013 16:00:53 -0500
From: gr...@nmr.mgh.harvard.edu
To: pval...@hotmail.com; Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Time
You cannot
Hi Salil - I'm cc-ing Doug who may be able to help. The error happens when
bbregister invokes fslregister, in this particular line of fslregister:
set refvol = `stem2fname $SUBJECTS_DIR/$subjid/mri/$fsvol`
When run on brainmask.mgz, it returns ERROR: could not determine file.
a.y
On Wed, 6
yes, if you give it the filename of the first .dcm in the series, the software
will find the other slices and create the .mgz.
On Mar 7, 2013, at 9:02 PM, Valtina Pouegue pval...@hotmail.com wrote:
Oh yes. It's my mistake. But should I give the adress of the first file of my
set for
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