Dear Lilla and freesurfers,
I hvae tried to rub the mri_CVS_register and got the following error:
VolumeMorph load - failed to open input stream.
I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Any idea how to fix this>
Log file atttached
Thanks!
Shani
On Fri, Oct 30, 2015 at 11:17 P
Dear FreeSurfer group,
I have a question regarding timepoints and analysis.
For example, lets say we have a data-set of 80 subjects with the following
timepoints: baseline, 6 weeks, 6 months, 1 year and 2 years follow-up.
Two different studies on the same data needs to be performed.
a) Study_1 w
Hi Kasper,
generally the answer is yes, include all time point in the base, qc/edit
and do whatever analysis you want on the final .long.base directories.
This will guarantee a few nice things:
1. you will only need to do 1 pass through with QC and editing
2. information from other time points
I used freesurfer v5.3. We have about 5 subjects that had this kind of
error. We tried to fix on the wm and the result seemed good but we have no
clue to deal with the aseg. Here is the link to my subject directory (no
fix).
http://www.mediafire.com/download/xm2igrdo33mdgmm/NCP140575_1_recon.rar
T
Hi Ray
the ascii format is pretty barebones and doesn't have e.g. ras2vox info
that freeview uses to display the surfaces properly. It's for ease of
conversion and such.
cheers
Bruce
On Mon, 2 Nov 2015, Razlighi, Qolamreza R. wrote:
> Hi Guys,
> Why converting a surface to .asc format change
Hello all,
I was wondering if anyone with knowledge of the new hippocampal subfield
segmentation that is going to be released with version 6.0 could answer a quick
question. We have previously processed subjects in v5.3 and would like to use
the new hippocampal seg algorithm. How "standalone" is
Dear all,
I am very new to using TRACULA and Freesurfer. I am trying to apply tracula
on the provided tutorial data. When I ran the command trac-all -prep -c
dmrirc.tutorial, after eddy current correction, I get this error:
--
D.
___
Freesurfer mailing
Dear all,
I am very new to using TRACULA and Freesurfer. I am trying to apply tracula
on the provided tutorial data. When I ran the command trac-all -prep -c
dmrirc.tutorial, after eddy current correction, I get this error:
mv -f
/data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.
Dear FreeSurfer group,
I have tested the data output on the same subjects using the same
FreeSurfer version but on different machines, a MacPro and a iMac. The
output are different, which argues that it is important to run freesurfer
on the same computer on all your subjects.
Is it due to a rando
Dear Kasper,
This is due to the different operating systems you are running not
differences in the computers. Your iMac is running ~10.7 and your
MacPro is running ~10.9.
You should always run your analysis on the same operating system,
however you should get no differences on different computers
Can you try this version?
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.mac
If that fails, can you send me your dicoms through our filedrop?
https://gate.nmr.mgh.harvard.edu/filedrop2
doug
On 11/02/2015 11:14 AM, Biekman, Brian Darnell wrote:
>
>
>
>
> -
Hi experts,
I am having trouble performing a Monte Carlo correction using mri_glmfit-sim.
My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. I
then ran mri_glmfit on the data.
I want to do my analysis/correction only in auditory cortex (AC) so I did my
own simulation
Dear FreeSurfer experts,
I have a number of *.cluster.mgh files and I would like to calculate their
difference and peak coordinate etc like in fslmaths or fslstats in FSL.
For example, given two images, I want to know the brain regions in image1 but
not in image2.
Could you please recommend th
Hi Daniel
you can always convert to nifti via:
mri_convert cluster.mgh cluster.nii
and you will be able to use the FSL tools
cheers
Bruce
On Tue, 3 Nov 2015, Yang, Daniel
wrote:
> Dear FreeSurfer experts,
>
> I have a number of *.cluster.mgh files and I would like to calculate their
> diff
Hi Bruce,
Yes, that’s perfect! Thanks for the reply!! :)
Best,
Daniel
On 11/2/15, 8:48 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl" wrote:
>Hi Daniel
>
>you can always convert to nifti via:
>
>mri_convert cluster.mgh cluster.nii
>
>and you will be able to use the FSL
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