Re: [Freesurfer] mri_binarize error for thalamic nuclei during trac-all prep

External Email - Use Caution Hi Freesurfer Developers, I believe I found a work around for the mri_binarize error I was running into regarding the thalamic nuclei segmentation during trac-all prep as described in greater detail in my previous message (

[Freesurfer] mri_binarize error for thalamic nuclei during trac-all prep

External Email - Use Caution Hi Freesurfer Developers, I'm trying to troubleshoot an error message during TRACULA preprocessing that seems to be related to the mri_binarize command used to create the /dlabel/anatorig/aparc+aseg+thalnuc.nii.gz file. I'm using FS v7.3.2 on OS

[Freesurfer] mri_binarize error when using trac-all -prep

External Email - Use Caution Hello Freesurfer Experts, I am currently attempting to process a single subject via Tracula v7.2. Previously, I used v6.0 to process this same dataset through all three steps of Tracula (prep, bedp, and path) with equivalent parameters with no

Re: [Freesurfer] mri_binarize --replace

no, not really. You can use multiple --replace optoins, eg, --replace -117 2 --replace -118 2 ... On 3/27/19 6:08 PM, Song, Da-Yea wrote: > > External Email - Use Caution > > Hello, > > I have a set of binary mask files that I’m trying to assign different > values to. Currently I’m

[Freesurfer] mri_binarize --replace

External Email - Use Caution Hello, I have a set of binary mask files that I'm trying to assign different values to. Currently I'm doing: mri_binarize --i sub001.nii.gz --o final_sub001.nii.gz --replace -117 2 mri_binarize --I sub002.nii.gz --o final_sub002.nii.gz --replace

Re: [Freesurfer] mri_binarize

It was just an oversight on my part when I wrote the program. I've just updated the file in our repository and put a copy here: https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize You can also specify all the structures you want by using the --match flag On 7/20/18 10:00 AM, John

[Freesurfer] mri_binarize

External Email - Use Caution Dear Freesurfer experts, I would like to inquire about the flag --subcort-gm in mri_binarize. It seems that the final product of this flag create a mask include the brain stem which is largely white matter. Why it was included in the subcortical gray

Re: [Freesurfer] mri_binarize

you can do it in two steps. First, use mri_binarize to create a mask of the structutures you want. Then use mri_mask to apply the mask to the aparc.DKT file On 12/03/2017 07:44 AM, John Anderson wrote: > Dear FS experts, > I want to use mri_binarize to create (binarized and free of CSF and >

[Freesurfer] mri_binarize

Dear FS experts, I want to use mri_binarize to create (binarized and free of CSF and ventricles) mask from "aparc.DKTatlas+aseg". How can I substract CSF and ventricles from teh atlas using mri_binarize? Thanks John___ Freesurfer mailing list

Re: [Freesurfer] mri_binarize/mri_mask command help

.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Monday, August 14, 2017 9:36 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_binarize/mri_mask command help > > mri_binarize needs a mask or segmentation as input (eg, aparc+aseg.

Re: [Freesurfer] mri_binarize/mri_mask command help

-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, August 14, 2017 9:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_binarize/mri_mask command help mri_binarize needs a mask

Re: [Freesurfer] mri_binarize/mri_mask command help

mri_binarize needs a mask or segmentation as input (eg, aparc+aseg.mgz). can you elaborate on what you are trying to do? what do you mean by a template? On 08/11/2017 03:01 PM, Yagmur Ozdemir 19 wrote: > > Dear FreeSurfer experts, > > I am trying to use the following command to merge the

Re: [Freesurfer] mri_binarize --gm

try making it executable, chmod a+x mri_binarize then run rehash and see if it work On 2/24/17 12:13 AM, Jinsong Tang wrote: Dear all, I am trying to run a mri_binarize command on FS 5.3 mri_binarize --i aparc+aseg.mgz --gm --o gmmask.mgz I obtain this: ERROR: Option –gm unknown

Re: [Freesurfer] mri_binarize --gm

Hello. I have installed the new version of mri_binarize. However, I got a new problem. -- GNU libc version: 2.19 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's

[Freesurfer] mri_binarize --gm

Dear all, I am trying to run a mri_binarize command on FS 5.3 mri_binarize --i aparc+aseg.mgz --gm --o gmmask.mgz I obtain this: ERROR: Option –gm unknown I found there was a previous post suggest to use the new mri_binarize from

Re: [Freesurfer] mri_binarize --gm option unknown

try this version https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize On 11/02/2016 12:37 PM, HOSSU Gabriela wrote: > > Hello everyone, > > I am trying to run a mri_binarize command on FS v 5.2, Linux 64bit, > but when I use the option —gm (also for –subcort-gm). > > I am getting an

[Freesurfer] mri_binarize --gm option unknown

Hello everyone, I am trying to run a mri_binarize command on FS v 5.2, Linux 64bit, but when I use the option -gm (also for -subcort-gm). I am getting an error that says the -gm option is not recognized. Here is the command line and the following error (from the mri folder of a subject):

Re: [Freesurfer] mri_binarize --rmax option unknown

Thanks very much, Doug! That version works perfectly. Just out of curiosity now, is there potentially a way to create a binarized mask in the other way that I mentioned? That is, to generate a mask that cuts maintains the middle 95% of the data (i.e. +- 2SDs of the signal mean) as a way to

Re: [Freesurfer] mri_binarize --rmax option unknown

That was a bug which I have not fixed. Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize On 06/09/2016 03:53 PM, Lakhani, Bimal wrote: > Good afternoon, > > I am trying to run a fairly simple mri_binarize command on FS v 5.3, > Linux 64bit, but when I use

Re: [Freesurfer] mri_binarize --rmax option unknown

Alternatively, is there another way to calculate the binzarized threshold min and max based on multiples of the standard deviation of the global mean? Thanks! On June 9, 2016 at 12:54:25 PM, Lakhani, Bimal (bimal.lakh...@ubc.ca) wrote: Good afternoon, I am

[Freesurfer] mri_binarize --rmax option unknown

Good afternoon, I am trying to run a fairly simple mri_binarize command on FS v 5.3, Linux 64bit, but when I use the option — rmax, I am getting an error that says the —rmax option is not recognized. It is made weirded because —rmin works perfectly. Here is the command line and the following

Re: [Freesurfer] mri_binarize

Hi Mohamad, I don't know why that would be. Note that the aseg does not have individual cortical labels. You should use aparc+aseg.mgz On 03/12/2016 04:19 PM, Alshikho, Mohamad J. wrote: > > Hi Doug, > > I would like to inquire about the command “ mri_binarize”. In the > past, this command

Re: [Freesurfer] mri_binarize

ct: Re: [Freesurfer] mri_binarize Hi Mohamad can you send us the command lines and screen outputs from doing it both ways? The output format shouldn't change things - there is no reason you shouldn't be able to write directly to nifti cheers Bruce On Sat, 12 Mar 2016, Alshikho, Mohamad J. wrote: Hi Do

Re: [Freesurfer] mri_binarize

...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Saturday, March 12, 2016 4:40 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_binarize Hi Mohamad can you send us the command lines and screen outputs from

Re: [Freesurfer] mri_binarize

Hi Mohamad can you send us the command lines and screen outputs from doing it both ways? The output format shouldn't change things - there is no reason you shouldn't be able to write directly to nifti cheers Bruce On Sat, 12 Mar 2016, Alshikho, Mohamad J. wrote: Hi Doug, I would like

[Freesurfer] mri_binarize

Hi Doug, I would like to inquire about the command " mri_binarize". In the past, this command was able to create a binarized nifti mask from aseg.mgz, wmparc.mgz etc without the need to convert the output "mgz" files to nifti. In other words If I want to create a mask for the precentral

Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh

Hi Erik, please remember to include previous correspondence. Can you upload the file for me? https://gate.nmr.mgh.harvard.edu/filedrop2 On 01/29/2016 02:17 AM, Erik Lindberg wrote: > Dear Bruce and Freesurfer, > > Yes, that is what I am saying! This what appears in the commandprompt > when

[Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh

Dear Bruce and Freesurfer, Yes, that is what I am saying! This what appears in the commandprompt when running the command: input cache.th13.abs.sig.cluster.mgh frame 0 nErode3d 0 nErode2d 0 output thresholded.mgh Binarizing based on threshold min1.3 max+infinity

Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

Dear Bruce and Freesurfers, I probably then go about this in the wrong way. My aim is to create a binary mask for regions that I found differences in - in a group-comparison. I then want to export the mask so I can use it as seed area in an fMRI analysis. Can this be done Thanks Eric Hi

Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

yes, but do you want to do the fMRI analysis on the surface or in the volume? There are lots of advantages to doing it on the surface. If your sig.cluster.mgh was a surface overlay then the threholded.mgh might be exactly what you want. Load it on an inflated surface and take a look cheers

Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

Hi Erik what is the dimensionality of sig.cluster.mgh? You can tell this with mri_info. It is problaby a surface overlay (so nvertices in one dimension), and can't be viewed in the volume but only on the surface. cheers Bruce On Mon, 25 Jan 2016, Erik Lindberg wrote: Dear Douglas and

Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

please remember to include previous correspondences. We can't remember every post ... On 1/25/16 3:39 AM, Erik Lindberg wrote: Dear Douglas and Freesufers, You suggested: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) I tried this and was expecting that

Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

Dear Douglas and Freesufers, You suggested: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) I tried this and was expecting that I would get a three-dimensional mask in which the statistical significant part would be white and the rest black. This seems not

[Freesurfer] mri_binarize error

Hi list I'm running mri_binarize --i aparc+aseg.mgz --match 1005 1008 1010 1025 1029 1031 --o lh.parietal.nii.gz and I get this error: $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $cwd /Applications/freesurfer/subjects/Control20cmdline mri_binarize --i aparc+aseg.mgz --match

Re: [Freesurfer] mri_binarize error

does that file exist and do you have read permissions? On 10/03/2014 04:02 PM, std...@virgilio.it wrote: Hi list I'm running mri_binarize --i aparc+aseg.mgz --match 1005 1008 1010 1025 1029 1031 --o lh.parietal.nii.gz and I get this error: $Id: mri_binarize.c,v 1.26.2.1 2011/04/08

Re: [Freesurfer] mri_binarize VS mri_extract_label

When you add --wm, you are telling mri_binarize is give you all of white matter (this include CC and cerebellar WM and hypointensities). When you pass just 2 and 41, you get only cerebral WM. doug Palzes, Vanessa wrote: Could someone please explain to me the difference between mri_binarize

[Freesurfer] mri_binarize VS mri_extract_label

Could someone please explain to me the difference between mri_binarize and mri_extract_label? I had been using mri_extract_label to create ROI masks of cerebral white matter (2 and 41). I recently became aware that this would give me a label with 0 and 128. I tried mri_binarize (with the same

[Freesurfer] mri_binarize download

Hi all, Where I can find a copy of the mri_binarize file? It doesn't seem to be included with 4.0.5, and based on a post from 2007 I looked in ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev/ to no avail. I've also checked the site. Since this is my first post

Re: [Freesurfer] mri_binarize download

Can you give me your platform? I'll see if I can put it online. -Krish On Nov 6, 2008, at 12:05 AM, Dominic Dwyer wrote: Hi all, Where I can find a copy of the mri_binarize file? It doesn’t seem to be included with 4.0.5, and based on a post from 2007 I looked in