Try using /Users/MarjaCaverle/Desktop/MRI as the path in your -i
> On Oct 20, 2016, at 6:03 PM, Marja Caverlé wrote:
>
> /Users/MarjaCaverle/Desktop/MRI
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Dear Doug,
Thank you very much for this detailed explaination. I highly appreciate your help
Kindly I have the following question:
The command mri_vol2vol ran smoothly without any errors
The command mri_mask output the following :
mri_mask suvr.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage
Hi Cleo
can you upload a subject before and after editing so we can replicate what
you are seeing? And what version of FreeSurfer are you using? Does the WM
after editing get signifcantly >110? If so, you may have accidentally
placed a control point in a gray matter voxel
cheers
Bruce
On T
I guess you could compute the intersection of the cortex labels. Easy
enough to do in matlab once you map them all to a common space. Not sure if
we have anything that will do it, but we might. Perhaps someone else knows?
cheers
Bruce
cheers
Bruce
On Thu, 20 Oct
2016, Taha Abdullah wrote:
yes, I believe that is true
On Thu, 20 Oct 2016, Nicholas Heugel wrote:
So just to be clear, If the individual cortical parcellations are accurate then
what we observe isn't
due to some quirk from the cross subject registration?
Nicholas HeugelBiomedical Engineering Ph.D Candidate
Marquette
So just to be clear, If the individual cortical parcellations are accurate
then what we observe isn't due to some quirk from the cross subject
registration?
Nicholas Heugel
Biomedical Engineering Ph.D Candidate
Marquette University
On Thu, Oct 20, 2016 at 4:32 PM, Bruce Fischl
wrote:
> Hi Nicho
bash-3.2$ pwd
/Users/MarjaCaverle/Desktop/MRI
(this means that I am in the right one right?)
Not really someone near, furthermore, almost no one uses mac. I did some
analysis a few months back, and it worked just fine, but now I get these
errors. I intentionally did not update to Sierra yet, beca
All,
Last week I downloaded the Windows installation version (Virtualbox) from
this webpage: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall.
After completion ~ 90 minutes later, it was quite confusing what got
downloaded and where. There might be 2 potential issues I wanted to
you probably aren't in the MRI dir. What does the command:
pwd
return? And are there any mac-savvy users that can help you out nearby?
cheers
Bruce
On Thu, 20 Oct
2016, Marja Caverlé wrote:
Hi Bruce,
After downloading, I have put the files in those folders, and I can see them.
Furtherm
Hi Bruce,
After downloading, I have put the files in those folders, and I can see
them. Furthermore, when I go to the folder and then do the ls command, they
are listed as being there. however the command looking for all files with
the .nii extension says there are no files there. I don't understa
Hi Nicholas
I wouldn't think so. Look at the cortical parcellations and see if they
are accurate. If they are it means that the cross-subject registration
must be pretty good
Bruce
On Thu, 20 Oct 2016, Nicholas Heugel wrote:
I am encountering an odd effect when using the Freesurfer maps in B
I am encountering an odd effect when using the Freesurfer maps in
Brainstorm. I have Individual activity for multiple subjects where the
activity generally seems to look generally well spread across teh gyrus and
sulcus in task relevant areas. However, when I map the individual subjects
onto the
We do not have such a tool, sorry
On 10/20/2016 12:50 PM, John Anderson wrote:
>
> Hi FS experts,
> I wanted to inquire if there are any tools in FS that can help to
> de-identify DICOMs?
> Thank you for any comment
> John
>
>
> ___
> Freesurfer mailin
What do you mean? You have your own CSF segmentation and you want to use
that instead of the one created by gtmseg?
On 10/20/2016 11:32 AM, Adam Martersteck wrote:
> Hi FreeSurfer team,
>
> Hopefully Doug or someone familiar with the new PET PVC implementation
> can answer a few things I can't
Hi Dr. Fischl and Dr. Greve,
So moving the mouse over the medial wall seems to have all vertices within
that to have a zero mm thickness as expected. The yellow outline is the
lh.cortex.label and it seems to look good to me i.e. majority of the medial
wall is properly masked. To be noted, this was
Hi FS experts,
I wanted to inquire if there are any tools in FS that can help to de-identify DICOMs?
Thank you for any comment
John
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So what I understand is that we can do the segmentation using the whole
brain MRI and then use the higher contrast MRI to refine the thalamus
segmentation? if so, can you explain more about it?
Thank you
Dorsa
On Thu, Oct 20, 2016 at 12:20 PM, Bruce Fischl
wrote:
> no, you need full brain cove
no, you need full brain coverage in at least one, but we do have some
prototype tools that use a smaller FOV image after a recon to segment
specific structures (including at least a bit of work on the STN).
As I said though, depending on the details of the 40 slice image I would be
cautious ab
After spmregister, you can run
mri_vol2vol --mov pet.nii --reg reg.dat --tal --talres 2 --talxfm
talairach.xfm --nearest --no-save-reg --o pet.tal2mm.nii
# mask out the cortical structures
mri_mask pet.tal2mm.nii
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
pet.tal2mm.subc.n
Dear Niels
the way Burkhard suggested works also on our Ubuntu16.04.
the new license file must have four lines two of which consists of numbers.
you mentioned that your license is the same as for FS 5.3.0.
HTH
Cheers
Jürgen
Am 20.10.2016 um 17:57 schrieb NIELS JANSSEN .:
> Hi Burkhard,
>
> Th
You can run recon-all -s subject -talairach -mc
to generate the talairach transform, and then
mri_segstats --talxfm subject/mri/transforms/talairach.xfm --etiv-only
should only take a few min per subject
On 10/20/2016 11:37 AM, Dev vasu wrote:
>
> Dear all,
>
> I would like to like obtain the
Hi Burkhard,
Thanks for the message but this does not solve my problem. I untarred as
root in /usr/local, and as myself in /home. I also requested a new license
file (which appears the same btw), and it does not matter. For all options
I am still getting the same error saying my license is invalid
Dear all,
I would like to like obtain the data values of IntraCranial Volume (ICV)
for 10 subjects , i know that recon-all automatically calls mri_segstats,
but i would like to know if there is any other method to obtain ICV
quickly, since running recon-all on each subject takes a lot of time.
Dear all,
I would like to like obtain the data values of IntraCranial Volume (ICV)
for 10 subjects , i know that recon-all automatically calls mri_segstats,
but i would like to know if there is any other method to obtain ICV
quickly, since running recon-all on each subject takes a lot of time.
Hi FreeSurfer team,
Hopefully Doug or someone familiar with the new PET PVC implementation can
answer a few things I can't seem to find on
http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer or either of Doug's PVC
publications (2013 or 2016).
1) Is the choroid plexus included in the binarized the
Hi Niels,
I also downloaded the development version recently. After untarring all files
are mine (my uid & gid). Did you unpack the tar file as root?
Then, I had to request a new license from the freesurfer team. Freesurfer did
not accept the old license anymore. But that was it - now it runs ag
Hi Marja
you need to figure out where the input files are! How do you know they
are there? Can you run:
ls -l /Desktop/MRI/*.nii*
cheers
Bruce
On Wed, 19 Oct 2016, Marja Caverlé wrote:
Hi Bruce,
that command also says there is no file or directory:
bash-3.2$ ls -l /Documents/MRI/L001.ni
Hi Dorsa
if you upload your subject I'll take a look. What is a 3TC image? I don't
know what contrast the image you sent is but I would be cautious about only
using it to assess the accuracy of the T1 segmentation
cheers
Bruce
On Wed, 19
Oct 2016, Dorsa Haji Ghaffari wrote:
I have attach
Dear users,
I have Ubuntu 16.04 (64bit) and I would like to use freesurfer.
I first installed version 5.3 but got the well-known 'nu_correct' error:
nu_correct: crashed while running nu_estimate_np_and_em (termination
status=65280)
Some searching revealed that this error is also described here:
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