Here's the exact code that I used:
surface:
mri_label2vol --annot aparc.a2009s.annot --regheader $1/$2/mri/orig.mgz --o
$1/$2/roi/mask_lh.nii --temp $1/$2/mri/orig.mgz --subject $2 --hemi lh
--proj frac 0 1 .1
same for the right hemisphere.
volumetric:
mri_label2vol --seg
Dear all,
I'm performing a study about the variability of the execution time of
recon-all. I noticed that the execution of recon-all in Freesurfer 5.3 for
two identical MRIs (two copies of the same MRI), takes different execution
time.
I'm performing the execution using GPUs capability, but the
Dear FS experts
in a former email
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg23322.html
it has been recommended that we should not map clusters found in an analysis
in the standard space
back to the individual space due to resampling issues.
In one of our study, we
Dear Freesurfers,
I have problems converting .nii.gz files into .mgh files needed e.g. for
performing ROI analysis.
I used mri_vol2surf and mri_vol2vol to produce .mgh files either to visualize
contrast estimates and significance maps on volumes or surfaces
I think the problem is due to voxel
Hi Guo,
Simply run recon-all again and add the flag -cw256. Then load up the
orig.mgz and make sure the head is fully visible.
HTH
D
On 7/1/15 9:48 PM, 宾果 wrote:
Dear Freesurfer team:
I am here want to ask for your help for some problems in
Freesurfer when I was processing my
I would just use the 2nd command since aparc.a2009s+aseg.mgz will have
already resolved the issues of overlap that you mention.
doug
On 07/02/2015 04:07 AM, Martin Hebart wrote:
Here's the exact code that I used:
surface:
mri_label2vol --annot aparc.a2009s.annot --regheader
click on the link at the bottom of every post, or go to the mailing
list link on the wiki:
http://surfer.nmr.mgh.harvard.edu/fswiki
this link on that page:
http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
hth
d
On Thu, Jul 2, 2015 at 8:57 AM, Mojdeh Zamyadi mojde...@gmail.com wrote:
Dear experts,
I am preparing seeds for a later tractography analysis in fsl (sorry about
this). I am bit concerned about the location of my final seed regions and
wanted to ask you if there is something wrong in my pipeline.
I first started using recon-all -subject HC015 -i HC015.nii.gz -all.
How did you create the EX.sm5.lh analysis? It is probably the case that
it is already on the surface in which case you don't need to run vol2surf.
doug
On 07/02/2015 04:54 AM, Milde, Christopher wrote:
Dear Freesurfers,
I have problems converting .nii.gz files into .mgh files needed e.g.
Could someone please tell me how to unsubscribe from this list? I couldn't
find it on the website.
Thanks
On Jul 2, 2015 4:56 AM, Milde, Christopher
christopher.mi...@zi-mannheim.de wrote:
Dear Freesurfers,
I have problems converting .nii.gz files into .mgh files needed e.g. for
performing
I think that might have been fixed in 5.3. Can you try 5.3 on that one
subject to see? Thanks for the kudos.
doug
On 07/01/2015 08:23 PM, joseph veliz wrote:
leopard i686 stable pub v5.1.0
As an aside I watched your introductory videos and found you to be
very knowledgeable, well-spoken and
There are inevitable issues around the boundaries of the cluster. For
small clusters, this can be a big deal. I would probably just use the
fsaverage clusters on the control group after they have been mapped to
fsaverage space (ie, run mris_preproc on the control group to get a
stack, smooth
Dear Doug,
thanks for the immediate response. Actually I checked the registration with
freeview/tkregister2 and print out the quality values which are perfectly fine
I did the following fMRI-analysis steps
FSFAST
1. Preproc-sess (for smoothwm as well as fsaverage space) --
Sorry, can you backup and tell me what you are trying to accomplish?
doug
On 07/02/2015 10:05 AM, Milde, Christopher wrote:
Dear Doug,
thanks for the immediate response. Actually I checked the registration with
freeview/tkregister2 and print out the quality values which are perfectly fine
Hi,
I’m trying to run the ‘beta’ version of FS6, centos4, and encountered the
error: ‘ERROR: Flag -hippocampal-subfields-T1 unrecognized’. I setenv and
source just as described for previous versions.
Also, I have Matlab 2014b downloaded on the computer (obviously comes with
runtime) but am
take a look at this
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 07/02/2015 09:05 AM, Yuval Harpaz wrote:
Dear FS group
I am looking for a way to compare left to right locations. I searched
previous posts and found little there, except a hint that I might use
the lh / rh.sphere.reg.
I
Hi Doug,
Thanks a lot. But aren't the aparc.a2009s+aseg.mgz the volume-based ROIs
and aren't they less accurate than the surface-based ones?
Best,
Martin
Am 02.07.2015 14:47 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu:
I would just use the 2nd command since aparc.a2009s+aseg.mgz will
We have quite a large data set we have processed in this study on v5.1.0
and have been previously advised to not switch versions in-between
processing data sets.
I do have a macbook pro running v5.3, I will attempt to recon on this
subject.
But are there any other options on v5.1?
Why is it
Ok, I think now I see the misunderstanding. I thought Freesurfer creates
both volume-based *cortical* ROIs and in a later step surface-based
cortical ROIs, but if I get it right the aparc is already based on the
surface. Do I understand this correctly?
Best,
Martin
Am 02.07.2015 21:24 schrieb
I could not find the function, can you tell me why and how I use this function?
Thanks!
On Jul 2, 2015, at 14:30, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Yun Wang
if you've run mris_expand you will need to run mris_compute_layer_fractions I
believe (and
freesurfer-Darwin-lion-stable-pub-v5.3.0 version
I use Mac Pro OS X Yosemite
On Jul 2, 2015, at 14:39, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
they are binaries. What version of FreeSurfer do you have, and what
hardware/software environment?
On Thu, 2 Jul 2015, Yun Wang wrote:
Hi All,
I am trying to segment gray matters (anatomical) into 5 layers and then
extracting different layers’ functional MRI data. I have got 5 surfaces using
mir_expand function and finish the registration of fMRI to anatomical data. I
want to make 5 masks and then extract the time series,
Hi Yun Wang
if you've run mris_expand you will need to run
mris_compute_layer_fractions I believe (and mris_compute_layer_intensities
if you want to account for partial volume effects)
cheers
Bruce
On Thu, 2
Jul 2015, Yun Wang wrote:
Hi All,
I am trying to segment gray matters
they are binaries. What version of FreeSurfer do you have, and what
hardware/software environment?
On Thu,
2 Jul 2015, Yun Wang wrote:
I could not find the function, can you tell me why and how I use this function?
Thanks!
On Jul 2, 2015, at 14:30, Bruce Fischl
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