Research Coordinator job available at Northwestern University's Cognitive
Neurology and Alzheimer's Disease Center in Chicago, IL.
The research assistant will be responsible for analysis of neuroimaging
datasets, in order to contribute to neuroscientific studies of normal aging
and pathological
Hi Doug,
Thanks you for directing me to my mistake in step 3 (see below new cmd line
in step 3). What I did is the following -
1) dt_recon --i /usr/local/freesurfer/subjects/Anatomy0981/DTI/I160.dcm --s
Anatomy0981 --o /usr/local/freesurfer/subjects/Anatomy0981/DTI --b
You must have already run this subject once with an expert-options file?
Once you've already run recon-all once on a subject with an expert-options file, you don't include it again in future invocations of recon-all. The expert options that you've previously used will automatically get used
it's just a measure of how far each point is from the sphere that we use
to guide some of the spherical transformation. It is a perfectly normal
part of recon-all
cheers
Bruce
On
Thu, 20 Mar 2014, chenchunhuichina wrote:
Dear Freesurfers,
I am new to freesurfer and I am afraid of doing
Hi Michael
I believe it is telling you that once the file expert.opts exists in the
scripts dir of a subject it will be used by default, and you don't need
to specify it on the command line.
cheers
Bruce
On Thu, 20 Mar 2014, Michael Green wrote:
I've been calling up an expert options file
try it like this
recon-all -s 002 -expert 002/scripts/expert.opts -xopts-overwrite
On 03/20/2014 12:30 AM, Michael Green wrote:
I've been calling up an expert options file which contains the text
mri_normalize -gentle but I'm having trouble executing it with this
command:
recon-all -s 002
Hello Freesurfer Expert,
Can you share the freesurfer sample named *bert* information such as
age,M/F and other details.
Thanks in advance,
cheers
Saurabh Thakur,
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
why do you need to know this? bert, and the rest of the distributed
data, are for tutorial purposes only.
doug
On 03/20/2014 09:57 AM, Saurabh Thakur wrote:
Hello Freesurfer Expert,
Can you share the freesurfer sample named *bert* information such as
age,M/F and other details.
1) Use the feat2surf script
2) I have not used mris_pmake myself. I'm guessing it will *work* on the
sphere in that it will return a path, but the distances between vertices
have no relationship to anatomy. It might fail on a flat map because it
is a patch.
doug
On 03/20/2014 10:43 AM,
Dear Surfers,
At moment I'm dealing with a huge dataset, preprocessed (with and without
smoothing) and statistically analyzed in FSL FEAT.
I used the reg-feat2anat to project functional EPI on inflated MPRAGE
(recon-all).
Because I'm interested in measuring Euclidian distances between peak
Hi,
I'm testing mri_convert for our dicom conversion needs; one thing that
would be fantastic is to be able to feed it a .tar.gz (or .zip)
containing a dicom series we'd like to convert. Is there a way to do
that?
Alternately, if there were a way to make it use stdin, I could just
pipe the
Hi,
Can you send us a screenshot of the original MRI before skull stripping?
Thanks!
Markus
On 20 mars 2014, at 14:46, Saurabh Thakur srbht...@gmail.com wrote:
Hello Freesurfer expert ,
I am sending you the image of brain.mgz screen-shot.
Is the area highlighted is part of cortex or it
what kind of points? Almost certainly yes, but it will also be
interesting debugging information for us to see whether it works or not
On
Thu, 20 Mar 2014, Borzello, Mia wrote:
I haven't checked that yet- would i still be able to pick points in freeview?
Hi Saurabh
those are eye sockets not brain. If the surfaces don't include them then
don't worry about them.
cheers
Bruce
On Thu, 20 Mar 2014, Saurabh Thakur wrote:
Hello Freesurfer expert ,
I am sending you the image of brain.mgz screen-shot.
Is the area highlighted is part of cortex or
I haven't checked that yet- would i still be able to pick points in freeview?
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, March 19, 2014 7:16
I would use step 3 for the wmparc instead of vol2vol.
you need both --seg and --seg-erode
--seg-erode 1 --seg
/usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz
doug
On 03/20/2014 04:43 AM, Rotem Saar wrote:
Hi Doug,
Thanks you for directing me to my mistake in step 3 (see
no, sorry
doug
On 03/20/2014 11:28 AM, Nate Vack wrote:
Hi,
I'm testing mri_convert for our dicom conversion needs; one thing that
would be fantastic is to be able to feed it a .tar.gz (or .zip)
containing a dicom series we'd like to convert. Is there a way to do
that?
Alternately, if
Thanks! If you're ever looking for a feature request, then, that's mine :)
Best,
-Nate
On Thu, Mar 20, 2014 at 12:10 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
no, sorry
doug
On 03/20/2014 11:28 AM, Nate Vack wrote:
Hi,
I'm testing mri_convert for our dicom conversion needs; one
I see. Try it in freeview then
Bruce
On Thu, 20 Mar 2014, Borzello, Mia wrote:
picking the electrode points for an intracranial patient. I can usually do it
pretty easily in tkmedit, but I'm just getting an odd contrast with this CT.
From:
Just to get some comparative result with subject which we have.
At least this can be made available for public domain.
cheers
Saurabh Thakur,
On Thu, Mar 20, 2014 at 8:11 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
why do you need to know this? bert, and the rest of the
Hello Freesurfers,
I am interested in taking a volume file that is in fsaverage MNI305 space
and converting this volume to each subject's volume. How can this be done?
Thanks!
Best,
Omar
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
picking the electrode points for an intracranial patient. I can usually do it
pretty easily in tkmedit, but I'm just getting an odd contrast with this CT.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of
Just to clarify a bit further, in the asegstats2table there are values given
for TotalGrayVol. I am assuming this includes both subcortical and cortical
measures for GM along with cerebellar values, etc. Likewise, I am looking for
TotalWhiteVol or a way of calculating both cortical and
mri_vol2vol should do the trick using the inverse (I think) of the
mri/transforms/talairach.xfm file. Doug can confirm
cheers
Bruce
On Thu, 20 Mar 2014, Omar Singleton wrote:
Hello Freesurfers,
I am interested in taking a volume file that is in fsaverage MNI305 space
and converting this
Hi Amy
if you run it with at the end of the line, it shouldn't end when you
close the terminal window. Of course it will stop if the computer goes to
sleep though.
To rerun a recon that has partially finished, try using the -make all
directive on the recon-all command line instead of any
Hi!
If the cortical surface outlines are fine, but there is an overinclusion of
brain volume during segmentation, how should I fix this? Can we calculate
brain volume based on the cortical surface outlines -- if so, how?
Thanks!
Christina
___
Hi Christina
if the aseg is incorrect but the surfaces are right, then you don't need
to worry about it. This is the reason we typically use the surfaces
instead of the aseg for things like brain volume/cortex modeling.
cheers
Bruce
On Thu, 20
Mar 2014, Christina Chen wrote:
Hi!
If the
Hi Freesurfer Experts,
we are looking for a good way to remove subject names and dates of birth
from Siemens DICOM headers. Is there something implemented in Freesurfer?
Matlab's Image Processing Toolbox has a function to anonymize DICOM files (
no, sorry
doug
On 03/20/2014 05:29 PM, Caspar M. Schwiedrzik wrote:
Hi Freesurfer Experts,
we are looking for a good way to remove subject names and dates of
birth from Siemens DICOM headers. Is there something implemented in
Freesurfer?
Matlab's Image Processing Toolbox has a function to
cortical stats reported by asegstats2table use the surfaces, not the
cortical segmentation in aseg.mgz
doug
On 03/20/2014 05:29 PM, Christina Chen wrote:
Thanks a lot!! I have a follow up question:
We use the command
asegstats2table
to output the subcortical volumes (and other whole
I think there was an anonymization tool developed through the BIRN and
distributed by Ron Kikinis' group at the BWH. I'll cc Karl Helmer who
probably knows
cheers
Bruce
On Thu, 20 Mar 2014, Douglas N Greve wrote:
no, sorry
doug
On 03/20/2014 05:29 PM, Caspar M. Schwiedrzik wrote:
Hi
Hi Caspar,
I can't address your question regarding a specific tool, but wanted to mention a note of caution.
You need to make sure that you scrub any identifying info from Siemen's custom DICOM fields (not just the obvious public DICOM fields).
The challenge of doing that is why the safest
Also, for what it's worth, here's a little script that wraps this up:
https://gist.github.com/njvack/9674025
Best,
-Nate
On Thu, Mar 20, 2014 at 12:29 PM, Nate Vack njv...@wisc.edu wrote:
Thanks! If you're ever looking for a feature request, then, that's mine :)
Best,
-Nate
On Thu, Mar
Thanks a lot!! I have a follow up question:
We use the command
asegstats2table
to output the subcortical volumes (and other whole brain volumes) to
table. If the aseg is incorrect, can we still believe those values?
Thanks,
Christina
On Thu, Mar 20, 2014 at 1:27 PM, Bruce Fischl
Hello Freesurfer experts,
I am getting some unusual results with the lme pipeline, and I would
appreciate help with identifying the most likely step in which the problem
may have originated.
Running lme_fit_FS.m on a single vertex, followed by lme_F on the output of
that (stats) yields a p-value
FYI, you can also get the first file like this:
first_file=$(tar ztf ${in_file} | head -1)
It will be much faster than 'find'.
On 03/20/2014 05:18 PM, Nate Vack wrote:
Also, for what it's worth, here's a little script that wraps this up:
https://gist.github.com/njvack/9674025
Best,
-Nate
OK, so I can use the following command to go from MNI305 to subject space?
mri_vol2vol --mov AL15/mri.2mm/orig.mgz --targ lh.AItou_fs_2mm.nii.gz
--reg AL15/mri/transforms/talairach.xfm --invertmtx --inv --o
lh.aitou.ac15.2mm.nii.gz
I ran that command and got this error:
regio_read_register():
Hi Eric
I don’t see
any fundamental problem with this analysis. It looks like a regular lme
computation.
The p-value is essentially zero (to the extent of numeric precision). Even
under the null hypothesis p-values
distribute uniform(0,1). When signal is present in the data the distribution of
38 matches
Mail list logo
