Dear FreeSurfer users,
we started to analyze structural MRI data from two large cohorts (one
with over 2100 and the other with over 1100 subjects).
Preprocessing is completely done for all datasets and I've worked myself
through this Qdec tutorial
Still looking for an answer why my analysis gives me an ill conditioned
error. I have run this analysis fine before, with a timewindow of 22, but
when I tried to change the time window to 34, selxavg3-sess gives me an ill
conditioned error on some of the runs (each run is being analyzed
Hello,
Is there a lookup table I can use to convert free surfer labels to lobes?
Either label nos (1006, 2006 etc) or label names (ctx-rh-superiorfrontal)? I
have 86 labels and want an easy way to differentiate them into the
corresponding lobes.
Thanks,
S
Hi all,
I have been trying to run freesurfer on a case for awhile now. After
receiving multiple errors when using the skull stripped nifti (nii.gz)
file, I tried to use the original dicoms as the input. While I haven't run
into any errors, the process seems to have frozen at CORRECTING DEFECT
Hi Eli
I think that defect is simply too big (it would take forever to fix). It's
more than half of the size of a typical cortical hemisphere model. Did you
check the skull stripping? And send us images (medial and lateral) of the
?h.inflated.nofix in tksurfer
cheers
Bruce
On Thu, 28 Feb
Dear experts,
I would like to study cortical thickness asymmetries. According to old
messages it seems impossible so I would like to know if it is always the
case or not ? Maybe, there is a command to subtract the values for each
vertex in the left hemisphere minus the values for each vertex
I think you are right, the auto skull stripping probably didn't quite do
the job. We are working on trying to skull strip the dicoms manually before
starting over again. In the meantime, I uploaded the lh-inflated (that
seems to be the only one in the subjects/[SUBJECT]/surf/ folder).
Thanks
Also, is there a way to associate these labels with motor/auditory/visual
cortices? Or do I have to use the specific parcellations?
On Feb 28, 2013, at 9:25 AM, Sudhin A. Shah sut2...@med.cornell.edu wrote:
Hello,
Is there a lookup table I can use to convert free surfer labels to lobes?
After a conventional FS run you can do the following:
$mri_annotation2label --subject subj --hemi hemi --lobesStrict
hemi.lobesStrict.annot
Which will create an annotation file hemi.lobesStrict.annot
containing the lobar labels. To extract these into their own individual
label files, do
The process is still running but nothing new written in the last 24 hrs.
Excerpts from recon-all.log
..
77 defects to be corrected
0 vertices coincident
reading input surface /home/#/subjects/./surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from
have you checked the skull stripping? It looked like it might be cutting
off some brain. If you upload the subject I'll take a look (although we
will need the volume before skull stripping). Why are you not stripping
within FS? That might make life easier for you
cheers
Bruce
p.s. I think
Thank you! Is there something similar to assign labels to functional cortices
eg. motor, visual, auditory?
Thanks
S
On Feb 28, 2013, at 10:47 AM, Rudolph Pienaar wrote:
After a conventional FS run you can do the following:
$mri_annotation2label --subject subj --hemi hemi --lobesStrict
Hi I got an error -lobesStrict unknown. I am running mri_annotation2label
version stable5.
Is there a workaround?
On Feb 28, 2013, at 10:47 AM, Rudolph Pienaar wrote:
After a conventional FS run you can do the following:
$mri_annotation2label --subject subj --hemi hemi --lobesStrict
It looks like you might be running a too-old version of
mri_annotation2label. What FS build/version are you running?
On Thu Feb 28 11:36:50 2013, Sudhin A. Shah wrote:
Hi I got an error -lobesStrict unknown. I am running mri_annotation2label
version stable5.
Is there a workaround?
On Feb
freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
On Feb 28, 2013, at 12:12 PM, Rudolph Pienaar wrote:
It looks like you might be running a too-old version of
mri_annotation2label. What FS build/version are you running?
On Thu Feb 28 11:36:50 2013, Sudhin A. Shah wrote:
Hi I got an
v5.0.0 is too old. I'd suggest grabbing the current 5.1.0 build and
then just using the 'mri_annotation2label' from that.
On Thu Feb 28 12:17:02 2013, Sudhin A. Shah wrote:
freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
On Feb 28, 2013, at 12:12 PM, Rudolph Pienaar wrote:
It looks
Dear Freesurfer,
I was wondering if there is any output from Tracula that quantifies
head motion (or the head motion correction performed). If so, is there
any standard in the field about an acceptable level or a cut-off point?
Thank you for your help,
Allison Gruber
Hi:
I need to compute the GM and WM volume for each lobe... I know that
for GM, I must use:
mri_annotation2label --subject bert --hemi rh --lobesStrict lobesfile
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.lobesfile.stats -b -a ../label/lh.lobesfile.annot bert
Hi Allison - There's no quantification of motion built in right now,
although we're looking into this issue and perhaps it'll be included in a
future version. You could look at the transformation matrices from
eddy_correct (in dmri/dwi.ecclog) and quantify the frame-by-frame motion
from that.
Dear FreeSurfers,
I am working on generating a functional map of electrophysiological activity on
a freesurfer pial surface and I've come across something that has stumped me. I
have the electrode coordinates in RAS space and I am trying to interpolate a
value at each surface vertex for the
Hi Ben, there are several things going on/wrong here. tksurfer reports
the coords from the orig surface (historical reasons) which will be
slightly different than the white surface in most casesand somewhat
different than the pial. These coordinates are in our special coordinate
system and
Hi Gonzalo, each of those commands has a --help flag which causes it to
print out documentation. Have you looked at that yet?
doug
On 02/28/2013 01:20 PM, Gonzalo Rojas Costa wrote:
Hi:
I need to compute the GM and WM volume for each lobe... I know that
for GM, I must use:
I am unable to download freesurfer from the ftp server.
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz
Looks like the server is down again.
Thanks,
Alexandru
yes, we are having some disk issues. Hopefully back up by tomorrow
Bruce
On Thu,
28 Feb 2013, Avram, Alexandru (NIH/NICHD) [F] wrote:
I am unable to download freesurfer from the ftp server.
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Linux
Hi Ashley, does that file exist? What is inside it? Did that subject
have errors during recon-all?
doug
On 02/27/2013 07:33 PM, Ashley Hannah wrote:
Hello,
I am trying to make a table of cortical volumes, however when I run
the command:
asegstats2table -subjects Sub1 Sub2 Sub3 --segno 17
Can you send me the Xtmp.mat file from the outputdirectory?
doug
On 02/28/2013 07:34 AM, Katie Bettencourt wrote:
Still looking for an answer why my analysis gives me an ill
conditioned error. I have run this analysis fine before, with a
timewindow of 22, but when I tried to change the time
Hi Sophie, check out this wiki page
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
doug
On 02/28/2013 10:18 AM, Sophie Maingault wrote:
Dear experts,
I would like to study cortical thickness asymmetries. According to old
messages it seems impossible so I would like to know if it is always
we are having disk problems. All downloads will be down for the next few
days.
sorry about that -- it's hurting us more than it hurts you:).
doug
On 02/28/2013 04:02 PM, Sudhin A. Shah wrote:
Hello,
Is there a link to the
Dear freesurfer experts,
I have a question regarding how to
incorporating bbregister coregistered mean image into the SPM batch.
After realignment step, I convert the mean functional image from the analyze
format to nii format (to avoid flipping brain using
Here it is for one of the failed runs. Let me know if you need anything
else.
Katie
On Thu, Feb 28, 2013 at 3:27 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Can you send me the Xtmp.mat file from the outputdirectory?
doug
On 02/28/2013 07:34 AM, Katie Bettencourt wrote:
Still
Went to download an updated version of Freesurfer today, and saw a posting
on the site that says:
ALL DOWNLOADS ARE OFFLINE WHILE WE DEAL WITH STORAGE ISSUES
Is there any estimate of when they might return? It looks like it's a
fairly new issue, based on the wiki history on the download page,
yes, we are hoping tomorrow
Bruce
On Thu, 28 Feb 2013, DT wrote:
Went to download an updated version of Freesurfer today, and saw a posting
on the site that says:
ALL DOWNLOADS ARE OFFLINE WHILE WE DEAL WITH STORAGE ISSUES
Is there any estimate of when they might return? It looks like
Hi Helen, it is not aligned. You will need to apply the registration
with mri_vol2vol or use the --o option to output a volume. I did not
follow how you are trying to incorporate this into the SPM pipeline.
Also note that if you are using SPM8, make sure to added --spm-nii or
else you will
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