@nmr.mgh.harvard.edu
Subject: [EXTERNAL] Re: [Freesurfer] mri_coreg threads parallel processing
clarification
While email attachments are a popular and convenient way to send documents,
they are also a common source of viruses. Use caution when opening attachments,
even if they appear to have been sent by
External Email - Use Caution
Dear Doug and team,
Thanks very much for your support. I’ve tried multiple different thread
numbers between 1 and 10 with no effect. I can successfully use multithreading
to accelerate other applications like mri_synthseg.
I tried adding combination
It looks like it is only using one thread, though you have correctly
specified 10. I often run it with more than 1, and it certainly uses as
many as I give it. It is possible that it is not allowed to have that
many threads. Have you been able to run other programs with multiple
threads? You ca
Does
/apps/freesurfer/7.4.1/subjects/002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/mri/brainmask.mgz,
exist?
Usually people are not putting their subjects in the FS subjects folder,
so I'm wondering if your SUBJECTS_DIR is set correctly.
it says it cannot find /XYZ/2123.nii
probably this file does not exist
On 2/28/19 10:09 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer community,
>
> when I run mri_coreg I get the following error.
> /XYZ/2123/mri/brainmask.mgz is in the specified location.
External Email - Use Caution
Dear Dr Greve – I am immensely impressed with the results. thank you so much
for all of your help!!!
Regards
john
You have to do it for each frame. Use reg.lta instead of reg.dat. You can apply
it with mri_vol2vol --mov frame1.nii --reg reg1.lta --o
You have to do it for each frame. Use reg.lta instead of reg.dat. You
can apply it with
mri_vol2vol --mov frame1.nii --reg reg1.lta --o frame1.reg.nii
This will use trilinear interpolation by default, but that is probably
ok here.
On 07/03/2018 02:29 PM, John Anderson wrote:
>
>
> Hi Dr Greve,
External Email - Use Caution
Hi Dr Greve,
If the individual PET frames are named: frame1.nii frame2.nii, frame3.nii ...
frame10.nii, and the mean for all the ten frames is "frames_mean.nii"
I ran mri_corg on one of the fames as follows:
mri_coreg --mov frame1.nii --ref frame
mri_coreg is the right one for that job
On 07/03/2018 01:51 PM, John Anderson wrote:
>
> Dear Freesurfer experts,
>
> I have ten PET frames for every subject in my database. these frames
> represent specific time during PET acquisition. Due to head motion
> during acquisition the frames are n
No, sorry. You have to use mri_vol2vol. Should be pretty simple
On 1/18/18 4:34 PM, John Anderson wrote:
Dear FS developers,
Are there any versions of "mri_coreg" that allows to output the
registered images. I mean flag "--out or -o" similar to spmregister?
Thanks for any guidance
John
Actually thank you for me as well for such a nice question! ;-)
This great response makes sense. Thank you very much Dr Greve for the follow up
> Original Message
> Subject: Re: [Freesurfer] mri_coreg
> Local Time: August 23, 2017 6:49 PM
> UTC Time: August 23, 2
Actually, it is on by default (thanks to Emma for pointing it out). The
smoothing helps to blur anatomical differences which reduces the chance
that it will get stuck in a local minimum. It will usually only smooth
the reference, and only if it is high res; this can help the reference
look a li
I don't think that is turned on by default. There is smoothing of the
NMI historgrams, but that is unrelated
On 08/21/2017 12:07 PM, John Anderson wrote:
> Dear Dr Greve,
> Kindly, I wanted to know why "mri_coreg" apples smoothing during
> registration. e.g.
>
> mri_coreg --s subject --mov temp
Hello ZK
Yes, Ubuntu is 32-bit. I installed it half-year ago, only had such
version. Does FreeSurfer provide 64-bit ubuntu version on Windows?
Best Regards
Frank Yu
On Thu, Dec 15, 2016 at 3:18 PM, Z K wrote:
> My guess is that your Ubuntu virtual machine is 32bit? If so it will not
> be ab
My guess is that your Ubuntu virtual machine is 32bit? If so it will not
be able to run our 64bit binaries. We no longer build 32bit binaries.
On 12/15/2016 12:07 PM, Frank Robert wrote:
> Hello FS experts
>
> I followed the instruction to download the mri_coreg file from website
>
>
> https://ga
rateful for this tool :)
> If I want to run the analyses of the various PET data in the same
> study, will it be of concern that I am using a mix of boundary-based
> (AV and PIB) and normalised mutual information (PK)?
> Best Wishes,
> Elijah
>
>
> Re: [Freesurf
Hi,
just wanted to mention that the --cost NMI (normalized mutual
information) and MI implementations in mri_robust_register are the same
as spm_coreg and now mri_coreg (if the -nosym flag is specified in
robust register, else it is registering in a symmetric midspace instead
into the target s
It is my implementation of the spm_coreg program written by John
Ashburner using normalized mutual information. I liked the spm program
so much that I put the effort into replicating its behavior in C. My
guess is that BBR was failing because the initialization was failing.
Still I like mri_co
18 matches
Mail list logo
