Re: [Freesurfer] mri_coreg threads parallel processing clarification

@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

Re: [Freesurfer] mri_coreg threads parallel processing clarification

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

Re: [Freesurfer] mri_coreg threads parallel processing clarification

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

[Freesurfer] mri_coreg threads parallel processing clarification

External Email - Use Caution Dear experts, Thanks in advance for any help you can provide. I’m using “mri_coreg” and trying to accelerate it with the “--threads” (and/or “--nthreads”) flags. However in the subsequent command feedback it looks like it is still using just one thr

Re: [Freesurfer] mri_coreg error: could not open brainmask.mgz file to register PET image with anatomical

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.

Re: [Freesurfer] mri_coreg error

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.

[Freesurfer] mri_coreg error

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. Can you help me with this? Thanks! Boris mri_coreg --s 2123 --mov /XYZ/2123.nii --reg 2123.reg.lta Could not set loca

Re: [Freesurfer] mri_Coreg or bbregister

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

Re: [Freesurfer] mri_Coreg or bbregister

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,

Re: [Freesurfer] mri_Coreg or bbregister

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

Re: [Freesurfer] mri_Coreg or bbregister

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

[Freesurfer] mri_Coreg or bbregister

External Email - Use Caution 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 not fully overlapped on top of each other. I created tem

Re: [Freesurfer] mri_coreg

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

[Freesurfer] mri_coreg

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___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.

Re: [Freesurfer] mri_coreg

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

Re: [Freesurfer] mri_coreg

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

Re: [Freesurfer] mri_coreg

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

[Freesurfer] mri_coreg

Dear Dr Greve, Kindly, I wanted to know why "mri_coreg" apples smoothing during registration. e.g. mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta Are there any effects on the accuracy of smoothing if I turn off this default feature (specifically in pet surfer pipeline). mri

Re: [Freesurfer] mri_coreg question

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

Re: [Freesurfer] mri_coreg question

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

[Freesurfer] mri_coreg question

Hello FS experts I followed the instruction to download the mri_coreg file from website https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg put it on my virtual machine ubuntu \local\user\freesurfer\bin directory. But I run it and it say

Re: [Freesurfer] mri_coreg !

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

[Freesurfer] mri_coreg !

f 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: [Freesurfer] mri_coreg ! <http://www.mail-archive.com/search?l=free

Re: [Freesurfer] mri_coreg !

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

Re: [Freesurfer] mri_coreg !

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

[Freesurfer] mri_coreg !

Hi Doug, I just want to say that mri_coreg worked tremendously well for the registration of some very blurry PET-PK data. I was not getting any success with bbregister and init-fsl or mri_robust_register options. How does this technique differ from the boundary-based registration? Thanks a lot.