Freesurfer people,
I have a label file that I want to make into a volume file only in the white
matter to use in diffusion tractography.
I was told to use mri_aparc2aseg to put the labels onto the WM surface and make
them into a volume. I made the label files into annotation files using the
fol
Hello,
I am having an issues with freeview ROIs. When I use the command line to load
the orig and the ROIs by themselves they display correctly, however when I
display the orig volume and the volume versions of the ROIs- the label ROIs
suddenly change to be in the wrong plane. I have done this s
Freesurfers,
I am trying to use a cortical label to label wm. I am using the following
command line:
mri_aparc2aseg --s $patient --annot 8V1 –labelwm
And most of the time in most subjects this works, however sometimes the output
file doesn’t label any wm with the 3000+N or 4000+N like it usuall
Douglas Greve
Reply-To: Freesurfer support list
Date: Saturday, February 3, 2018 at 1:12 PM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm
Can you send the terminal output of one of the runs that fails?
On 1/31/18 4:10 PM, Sims, Sa
question about how to remove
non-wm labels or is this a new submission? If a new subj, can you
describe the problem you are having?
On 02/05/2018 01:23 PM, Sims, Sara A wrote:
>
> This is the whole process output from a rerun on a subject that didn’t
>
/register_edit.dat
--o $subjects/$patient/mri/8V1_diffROI.nii --inv --nearest
I would appreciate any help!
Sara Sims
Graduate Research Fellow
University of Alabama at Birmingham
Department of Psychology
205-975-4060
sno...@uab.edu
On 2/5/18, 5:02 PM, "Sims, Sara A" wrote:
Doug,
Doug,
I am sorry that I wasn’t clear before, here is all the info about it all in one
place.
I am trying to transfer a cortical label to label wm by using the following
commands:
subjects=/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon;
unset SUBJECTS_DIR
SUBJECTS_DIR=$subjects
export
Hello,
I am trying to use Glasser’s parcellation to create a correlation matrix that
compares all parcels to all parcels.
I am new to FSFAST, but so far I have gotten the data preprocessed and ready to
go. But I am unsure how to proceed.
I have rh and lh annotation files of the parcellation in f
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Hello,
I have outputs from FSL probtrackx that I would like to display on Freesurfer
surfaces. If I put the volume into freesurfer space how can I get it to sample
onto a surface when the values are in white matter and not grey matter? To
rephrase, h
ive projdist in mri_vol2surf
cheers
Bruce
On Tue, 26 Jun 2018, Sims,
Sara A wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I have outputs from FSL probtrackx that I would like to display on
Freesurfer surface
.harvard.edu on behalf of
Bruce Fischl" wrote:
Hi Sara
check out the help (with --help). For example you could use:
--projdist-avg min max del : average along normal
cheers
Bruce
On Tue, 26 Jun
2018, Sims, Sara A wrote:
>Exter
understand all the
options so I can use them appropriately.
Thanks,
Sara Sims
On 7/9/18, 3:15 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce
Fischl" wrote:
I think it is short for "delta" - how far about the samples are
On Mon,
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Hello,
I am trying to put a mask that I made on the MNI brain (that had been run
through recon) into individual subject space. I have already created a
registration matrix using the following command:
mni152reg --s $patient --o $registration/$patient/
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Hello!
I would like to output the location and value of each vertex on a surface to a
text file. How could I go about doing this?
Thanks,
Sara Sims
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Freesurfer@nmr.mgh.harvard.edu
10/03/2018 11:48 AM, Sims, Sara A wrote:
>
> External Email - Use Caution
>
> Hello!
>
> I would like to output the location and value of each vertex on a
> surface to a text file. How could I go about doing this?
e:
Hi Sara
something like:
mris_convert -c lh.your_overlay lh.white lh.your_overlay.asc
should do the trick
cheers
Bruce
On Mon, 8 Oct
2018, Sims, Sara A wrote:
>External Email - Use Caution
>
> Doug,
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Hello,
I am trying to do a paired difference analysis of two runs of probtrackx (I
have already put them on the surface). The two conditions are “central” and
“far” for each subject. I have already checked the individual subjects data and
it does ind
External Email - Use Caution
Hello,
I am trying to do a paired difference analysis of two runs of probtrackx (I
have already put them on the surface). The two conditions are “central” and
“far” for each subject. I have already checked the individual subjects data and
it does ind
External Email - Use Caution
I have now gotten this to run on 3 subjects. However I have 786 subjects and
need to find the bad apple. Is there a way I can do quality checks on each
subject’s difference map in fsaverage space that mris_preproc has made?
Basically I want to cycle
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Freesurfers,
I am trying to use mri_mask using surface overlays. I made a label into a
volume and then into a surface with 1s inside the label and 0s outside the
label. I want to make a connectivity map surface overlay with values only
within my labe
d.edu on behalf of
Bruce Fischl" wrote:
Hi Sara
we will need to know the actual commands and the screen output from them
that you ran
cheers
Bruce
On Mon, 14 Oct 2019, Sims, Sara A (Campus) wrote:
>
> External Ema
External Email - Use Caution
Hello!
I have 786 subjects that I am trying to do a paired difference analysis using
mri_glm. I am getting stuck at the mris_preproc stage. I have tried running it
on a handful of subjects and it works wonderfully. However, when I run it on
all the s
here: /autofs/space/nihilus_001/CICS/ACRsoftware/ACRcurrent
On 3/18/19 11:12 AM, Sims, Sara A (Campus) wrote:
External Email - Use Caution
Hello!
I have 786 subjects that I am trying to do a paired difference analysis using
mri_glm. I am getting stuck at the mris_preproc stage. I have tr
ck on that and then click on a point in the surface, you should be
able to see a waveform of the measurements for all inputs. See if there
is one that is always 0. If you don't find any, then repeat with
--paired-diff
On 3/19/19 3
u just cut and paste them into the email. And are you sure
you're running the new command?
On 3/29/19 6:59 PM, Sims, Sara A (Campus) wrote:
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I have attached them here.
Sara Sims
Graduate Research Fellow
University of Alabama at Birmingham
Departme
, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Greve, Douglas N.,Ph.D." wrote:
Can you run it with --debug as the first option, capture the terminal
output, and send it to me?
On 4/2/19 4:02 PM, Sims, Sara A (Campus) wrote:
>
> External Ema
External Email - Use Caution
Hello!
I have a surface overlay that I want to extract the mean of the values within a
label and export to a text file. How can I do that?
I was looking into mris_anatomical_stats, but does mris_anatomical_stats let
you tell it what file to pull the d
2:07 PM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Extracting mean of values within a lable
look at mri_segstats. Run it with --help to get examples. Note that if your
input volume has multiple frames, you can use --avgwf to get means of all the
frames
On 4/19/2019 4:46 PM,
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