We are currently working on a solution that brings FreeSurfer in the cloud.
Unfortunately, we are facing a lot of problems. Hopefully, someone can help me:
I want to run FreeSurfer on Ubuntu 14.04 or 14.10. What package is required to
download (CentOS 4 x86_64 (64b))? Does it work anyway on the
Dear Jens,
I can offer just a bit of information and I also have a question.
We are using Fedora 11.0 on an x86_64 box and both the Centos 4 and Centos 6
compiles work.
The package appears to be self-contained as I have seen no faults on failures
to find shared libraries.
We simply untar
Dear group,
I am new to FS and the ADNI protocol, thus my question: is it ok to have a
slice thickness of 1.2 mm and in-plane resolution of 1.05 mm for cortical
segmentation and brain volume analyses? This seems to be a sequence
suggested on the FreeSurferWiki (I am using a GE750 3T).
Doesn't
Hi Jens
you could estimate it, but it might not be exactly right. There's no way to
know how long it will take to converge as it depends on the details of the
anatomy. If the current output is not verbose enough for you, you can turn
on more output by:
setenv DIAG 0x04040
if you run some
Hi Gunjan
you need to give us more details. What are you trying to do? Why not just
run recon-all -all? That will be much easier than trying to ru individual
steps
chers
Bruce
On Wed, 19 Nov 2014, Gunjan Gautam wrote:
Hi,
I am facing few issues. I will be thankful if you can help me out.
Hi Antonio
yes, that should be fine. It probably reduces sensitivity in some regions,
but given the complexity of the folds I would expect it to average out.
That said, no one has ever done such a study so we really don't know.
cheers
Bruce
On Wed, 19 Nov 2014, Antonio Algaze Beato wrote:
I have corresponding setup modules for auto-deployment and configuration in the
cloud, but it still takes some time (even in the local cloud network) to
transfer the archive from the fileserver to the virtual machine and especially
to untar that archive. A manual untar took nearly 20 minutes,
Actually, I have two volumes, belong to the same subject. One volume is the
ground truth which will be considered as standard for the second volume
which is the processed one or the extracted brain. To perform a perfect
comparison between both volumes, these must generate equal number of slices
in
hi jens,
if you search the archives, there is a post that lists the minimal set of
files needed for running recon-all.
i used a tool called cde to create it: http://www.pgbovine.net/cde.html
this reduces the archive down to about 650MB comprising binaries and
atlases.
this wouldn't be for
Hi Gunjan
FreeSurfer has been designed to work as a pipeline. Picking out individual
pieces and running them may or may not work, and certainly won't be as
reliable. I would advise you to run recon-all -all, then you can use the
contents of the subject directory to do whatever analyses you
Ok I try this out.
Did you answer my Query 1(related to cropped output of mri_convert command
? I probably did not understand.
On Nov 19, 2014 8:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Gunjan
FreeSurfer has been designed to work as a pipeline. Picking out individual
pieces
no, because I don't know what the volume are that you are using
On Wed, 19
Nov 2014, Gunjan Gautam wrote:
Ok I try this out.
Did you answer my Query 1(related to cropped output of mri_convert command ?
I probably did not understand.
On Nov 19, 2014 8:10 PM, Bruce Fischl
I have attached both the volumes (reference and input) with my mail.
Its the last step of my work, I'm stuck at and not finding any solution. I
read that FreeSurfer can solve my problem.
I will be obliged if you find some time for this.
Best Regards,
Gunjan
On Nov 19, 2014 8:19 PM, Bruce Fischl
Hi Gunjan
you need to give us more information. What are the two volumes? Why is
one ground truth? What in general are you trying to achieve?
cheers
Bruce
On Wed, 19
Nov 2014, Gunjan Gautam wrote:
I have attached both the volumes (reference and input) with my mail.
Its the last step of
Try swapping a and b. Or use mri_vol2vol with your reference volume as
target
On 11/19/14 7:41 AM, Gunjan Gautam wrote:
Hi,
I am facing few issues. I will be thankful if you can help me out.*
*
*
Query 1)* I used mri_convert a.nii a.resliced.nii -rl b.nii in order
to generate slices so
Dear Freesurfer experts,
I'm not sure how to apply cluster-wise correction for multiple comparisons when
one is not interested in doing group statistics.
For group analysis you concatenate individuals into one file and use mri_glmfit
and mri_glmfit-sim to run general linear model and
Thank you very much for your response.
Out of curiosity, does someone know why the ADNI protocol has an
anisotropic voxel resolution?
I was wondering if it had to do with the increased SNR being more
beneficial for accurate segmentation than the gain in resolution from a 1mm
isotropic voxel...
Hi Antonio
probably both
Bruce
On Wed, 19 Nov 2014, Antonio Algaze Beato wrote:
Thank you very much for your response.
Out of curiosity, does someone know why the ADNI protocol has an anisotropic
voxel resolution?
I was wondering if it had to do with the increased SNR being more beneficial
I downloaded two volumes from BrainWeb database. One is treated as ground
truth because it has preassigned values(0-11) for each types of tissues and
by a simple coding binary brain mask can be achieved.
Another volume is the processed one using any brain extraction algorithm.
Now, I have two
Hello,
I just wanted to repost this to see if anyone had any thoughts on an
appropriate 'lesion' size for a pothole analysis performed on the surface.
We want to compare the average number of small surface lesions (estimated
from cortical thickness) across single subjects for a control group
Dear FreeSurfer experts,
There are some image processing tools from the MINC toolkit I have been testing
out on some FreeSurfer files, that all require the image to be in MINC format.
I am able to convert the *.mgz files to *.mgz, but I have been unable to
perform the conversion in the other
Hi Douglas, thanks for your reply. Is there a way to rerun only WM
segmentation with the threshold option, without going through the whole
time-consuming FS pipeline?
Thank you!
On Tue, Nov 18, 2014 at 10:37 PM, Douglas Greve gr...@nmr.mgh.harvard.edu
wrote:
The unsegmented is all the WM that
There are two ways you can do this.
1. Make an expert options file with the contents
mri_aparc2aseg --wmparc-dmax 100
Run run recon-all like
recon-all -s subject -wmparc -expert YourXOptsFile
2. Look in recon-all.log for the mri_aparc2aseg command, cut and paste
it into the terminal, add
Was the dicom anonymized? Also, mosaics are usually fMRI or DTI. Are you
sure this is a high-res anatomical that will be suitable for recon-all?
doug
On 11/19/2014 11:41 AM, Ashley Stillman wrote:
Hi Freesurfer team,
Any ideas for the below issue we are having?
We are having issues running
ok, thank you very much for your prompt reply!
will try to do that
On Wed, Nov 19, 2014 at 11:43 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
There are two ways you can do this.
1. Make an expert options file with the contents
mri_aparc2aseg --wmparc-dmax 100
Run run recon-all
Hi Michele
sorry, I don't think so. You need to run to the end. The good news is
that when we get V6 out you will find it is substantially faster (if you
have a multi-core machine)
cheers
Bruce
On Wed, 19 Nov 2014, Michele Cavallari wrote:
Hi Douglas, thanks for your reply. Is there a way
ok, so should I just re-run the recon-all with the wm option? i.e.
recon-all -all --wmparc-dmax 100
On Wed, Nov 19, 2014 at 12:07 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Michele
sorry, I don't think so. You need to run to the end. The good news is that
when we get V6 out you
I think Michele only wants to regenerate the wmparc.mgz, so just running
recon-all with --wmparc and the xopts should work
On 11/19/2014 12:07 PM, Bruce Fischl wrote:
Hi Michele
sorry, I don't think so. You need to run to the end. The good news is
that when we get V6 out you will find it
yes, I already have the FS outputs for all the subjects. Thanks
On Wed, Nov 19, 2014 at 12:36 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
oh, so it's already been run all the way through? Sorry, I didn't
understand that.
Bruce
On Wed, 19 Nov 2014, Douglas N Greve wrote:
I think
Hi satra,
I have tried to find some posts about the minimum files required to run
recon-all, but I cannot find anything. Could you please try to find the post in
the archives and provide me the link?
Thank you very much!
Gesendet: Mittwoch, 19. November 2014 um 15:23 Uhr
Von: Satrajit
hi jens,
here is the post - the links were all broken, but i've updated them below.
note that this run was from nov 2013. i would recommend doing a run with
all the current patches installed.
an update on the files needed for a vanilla recon-all run (evaluation done
using
Hi freesurfer experts,
Is there other methods for multiple comparison correction apart from Monte
carlo simulation in Freesurfer?
Thanks!
zhiwei___
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