Hi Doug,
Thanks very much!!
Best,
Daniel
On Jul 16, 2013, at 9:14 PM, Douglas Greve
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:
use
$FREESURFER_HOME/average/mni152.register.dat
doug
On 7/16/13 8:36 PM, Yang, Daniel wrote:
Dear FreeSurfer Experts,
I am interested in a
Thanks Anastasia,
IT HELPED!
On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Amirhossein - I'm attaching sample files.
a.y
On Tue, 16 Jul 2013, amirhossein manzouri wrote:
Hi Anastasia,
I have tried both , 3-row and 3-column format and still
Hello freesurfers,
I’ve been trying to run tracula on freesurfer and it seems that when I get to
the point where it uses FSL’s flirt I receive an error. I looked into it
further and it seems I am missing a file to run flirt:
$FREESURFER_HOME/bin/flirt.fsl
It seems that I somehow do not have
Hello,
I have a question about propagating changes to segmentation. Once I have
saved my edits what is the appropriate command to propagate these changes
for both cortical and subcortical changes that I have made.
The workflow instructs that after segmentation edits are made to run
Dear Freesurfer experts,
I have a question regarding the installation/running of FreeSurfer.
I have been trying to install freesurfer in a macbook pro (snow leopard) but no
success.
I followed the webpage from freesurfer (link below).
Dear Freesurfer experts,
I tried running the kvlQuantifyHippocampalSubfieldSegmentations.sh script
and get two text files (left right stats) but the only information in the
text files is the subject ID number.
However, on my terminal window, I can see the volume output for each
subfield and for
Pablo,
That page describes how to setup a personal laptop for usage in the
Freesurfer course. It does not apply to a standard freesurfer
installation.
Try opening a new terminal and typing bash before the export and
source commands you give below.
-Zeke
On 07/17/2013 10:27 AM, pablo najt
Hi Jasmeet,
what modification did you exactly make? Whih version of FreeSurfer is this?
Cheers,
/Eugenio
On 07/17/2013 10:22 AM, Jasmeet Hayes wrote:
Dear Freesurfer experts,
I tried running the kvlQuantifyHippocampalSubfieldSegmentations.sh
script and get two text files (left right stats)
Good to hear! Can you please share with all of us what was wrong with your
original files? It may help others who have the same problem in the
future. Thanks!
On Wed, 17 Jul 2013, amirhossein manzouri wrote:
Thanks Anastasia,
IT HELPED!
On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki
Hi Eugenio,
We are using version 5.1. I attached our script. We added to line 60,
setting the subject directory. We also changed the statFileName (see line
291 on the attached script). I should also note that the volumeStats_left
and right text files within each subject's mri folder is empty.
Hi Panos
sorry, I think this is pretty far outside our expertise, and it would be
hard in any case to try to figure out what happened to give you these
strange looking results. I certainly don't have any insight
sorry,
Bruce
On Wed, 17 Jul
2013, Fotiadis, Panagiotis wrote:
Hi FS Community,
OK, then the question is why kvlQuantifyPosteriorProbabilityImages is
producing an empty file
I think the problem is that
kvlQuantifyHippocampalSubfieldSegmentations.sh behaves in a different
way depending on the number arguments, etc. I would suggest that you go
back to the original
Hi Doug,
Can I ask a basic question about mri_label2vol? in mri_label2vol, what should
be the input for --temp? I understand it's supposed to be the template image.
If it's the native space, should it be rawavg.mgz or orig.mgz for that
individual?
Great thanks!
Best,
Daniel
--
Yung-Jui
does htis answer your question? It is from running mri_label2vol with --help
doug
--temp tempvolid
Template volume. The output volume will have the same size and geometry
as the template. Template must have geometry information (ie, direction
cosines and voxel sizes). Required.
On 07/17/2013
Hello,
Individuals who downloaded Freesurfer v5.3 for snow leopard (32bit) will
be missing six fsl routines. A patch has been created and can be
downloaded from this link:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer_fsl.tar.gz
To apply the patch, simply extract the
That worked, thanks for your help!
On Wed, Jul 17, 2013 at 12:00 PM, Juan Eugenio Iglesias
igles...@nmr.mgh.harvard.edu wrote:
OK, then the question is why kvlQuantifyPosteriorProbabilityImages is
producing an empty file
I think the problem is that
Hi Bruce,
Don't worry about it!
In addition, I was wondering about something else as well. I've been using
MRIcron to analyze some of my Susceptibility Clinical Scans and even though
they used to open fine, some of them (like the one I have attached in this
email) appear distorted in a way. In
Hello--
We have a set of scans with bad artifact throughout the temporal lobe and
the superior cortex. We've had to do the normalization steps (n3
correction, normalization) manually on most of these scans to preserve the
gm/wm boundary. Now, when we run mri_segment, it leaves out some gray
Hi,
I have some trouble running recon-all longitudinal pipelines. When
recon-all comes to mri_register_ca it crashes without giving a message,
even tough 8g ram was available. I have run the program with -debug. Is
there any other option I may use? The system is running Rocks 6.0
(Mamba), and
I implemented the ROI percent signal change formula following the MarsBaR FAQ
(http://marsbar.sourceforge.net/faq.html) but the values I'm getting seem too
small (on the order of .0002%). Basically the formula is the (beta * peak
absolute value of the canonical HRF regressor * 100)/(run mean).
then I get on the order of .02% difference between the contrasted conditions.
The run mean values are in my expected ballpark of about 100 or so.
The condition betas are just very very small.
Or perhaps this is typical of FSFAST analyses?
On Jul 17, 2013, at 2:00 PM, Douglas N Greve
Hi Yune
you are better off using the ?h.cortex.label file to mask in what is
needed for each subject
cheers
Bruce
On Wed, 17 Jul 2013, Yune Lee wrote:
Hello freesurfer experts,
For visualization purpose (i.e., displaying group maps), I applied a mask
for medial wall regions using the
Hello Erin,
Thank you so much for asking. I have been curious to know this, too.
Sincerely,
Ye
On Wed, Jul 17, 2013 at 12:41 PM, Erin Browning brown...@uwm.edu wrote:
Hello--
We have a set of scans with bad artifact throughout the temporal lobe and
the superior cortex. We've had to do the
It's a boxcar design so 20.265.
mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface fsaverage lh
-fwhm 5 -event-related -paradigm CPA1.par -nconditions 20 -spmhrf 0 -TR 2
-refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg nuisreg2.dat 7
-tpexclude tpexclude.dat
On Jul 17,
It's a little complicated. Basically there were eight runs, comprising four
conditions (me, we, you1, you2) each with two adjoining runs. For the
analysis, I merged each of the pairs into a single run and added a nuisance
regressor to account for the difference in run means. There were a
Dear Freesurfer experts, I am
interested in running cortical surface area on longitudinal data from MRI scans
and run multisubject comparisons (patients vs controls). I would like to ask
you where could I find either a tutorial or a guide for performing
Dear FreeSurfer experts,
I was wondering if there is anywhere a table or hint, suggesting which
particular steps of all the recon-all steps (i.e.
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) are part
of the volume-based or the surface-based stream or both? I also found
this
Oh, right, the nuisance regressors are given a separate regressor for
each run. I had forgotten!
On 07/17/2013 04:55 PM, Joseph Dien wrote:
On Jul 17, 2013, at 4:50 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
On 07/17/2013 04:48 PM, Joseph Dien
Dear Bruce,
Could you please let me know whether my message of last week, in which I
uploaded the subject's volssurfs, have reached the list? I haven't
received a reply about those questions and was wondering whether that email
maybe got rejected due to the large size of the attachments. The
Hi Tudor,
yes, it got through. It's on our list of things to get to, we just
haven't gotten there yet
Bruce
On Wed, 17 Jul 2013, Tudor Popescu wrote:
Dear Bruce,
Could you please let me know whether my message of last week, in which I
uploaded the subject's volssurfs, have reached the list?
30 matches
Mail list logo
