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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
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OK - I double checked, and even compared the new mkcontrast2 with the old
one to verify that I copied all as I should (see below). Still the
mkcontrast2 exits when checking $FS_MKCON_USE_BIN with the same error
message (no matter if this variable is
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
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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
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
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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
Your recon-all command line is not correct, try something like
recon-all -s mysubject -i
/home/regal/Data/Subjects/test_old_version/01C_dislebi_T1.nii -all
On 07/03/2018 01:29 PM, Bernardo Regal wrote:
>
> External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I have a
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Hello FreeSurfer Developers,
I have a problem to convert the files using the recon-all.
It appears, recon-all -s 1 exited with ERRORS.
Before I had the last version (stable v6.0.0). As I did not find a solution
of how to fix this problem, so I
questions answered below
On 07/03/2018 01:14 PM, Patrycja Naumczyk wrote:
>
> External Email - Use Caution
>
> Douglas,
>
> thanks a lot - unfortunately this still doesn't work - it stops at the
> same cause:
>
> mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0
> INFO:
I don't know anything mri2mesh. Have you tried contacting the developers
of that? Our equivalent tool is called mkheadsurf
On 06/26/2018 02:59 PM, Palig Mouradian wrote:
>
>
> Hi Freesurfer,
>
> I am working on creating head models using the add-on mri2mesh command
> that incorporates free
It is just a GLM fitter, so it will take any data. Is this fMRI? Why not
use a specific tool for that?
On 06/27/2018 08:51 AM, Evelyn Eger wrote:
>
>
> Dear Freesurfer experts,
>
> I would like to know whether mri_glmfit can be used to estimate
> first-level (single subject) models as well or
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Douglas,
thanks a lot - unfortunately this still doesn't work - it stops at the same
cause:
mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0
INFO: Found 2 Non-Null Conditions
INFO: Found 3 Delays
Condition Weights:
Is it really high res? Was there a big defect? Can you send the log file?
On 06/28/2018 12:44 PM, Ottavio Morciano wrote:
>
>
>
>
>
> Hi!I have a macbook pro MY 2014 with a Intel Core i7(quad core,2.7
> ghz) and 16 gb of ram with El Capitan.This Macbook to run recon-all it
> takes 47 hours with
Sorry for the delay. I've put a new version here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2
copy it to $FREESURFER_HOME/fsfast/bin
On 07/03/2018 12:13 PM, Patrycja Naumczyk wrote:
>
>
> Hi all,
>
> I'll repost - does FSv6 no longer support octave for FS-Fast processing?
>
>
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Hi all,
I'll repost - does FSv6 no longer support octave for FS-Fast processing?
Would appreciate clarification on this :)
Patrycja
2018-06-29 21:41 GMT+02:00 Patrycja Naumczyk :
> Hi all,
>
> I just switched from FS 5.3 to 6.0 on Gentoo Linux.
On 07/02/2018 01:48 AM, Soan Duong wrote:
>
>
> Dear FreeSurfer,
>
> My name is Soan Duong. I used FreeSurfer to segmentation some
> high-resolution T1w images (resolution of 0.5x0.533x0.533, size of
> 288x378x420), and got a couple of problems:
>
> 1.I ran the command: recon-all -i
possible but not easy. You will need to get the surface vertex index
number that maps to a given xyz. The easiest way to do that is to create
a label, then use mri_label2label with the --paint option. You will
still need to convert your xyz into the coordinates used on fsaverage.
See
How much did you smooth by? Is this thickness, area, or volume? Also, in
general, you should not be using dev since it is an uncontrolled
distribution (ie, there are many things in there that have not been
tested). Also, I'm encouraging people to use permutation rather than
monte-carlo-based
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Dear FreeSurfer experts,
I am trying to do vertex-wise comparisons for thickness, surface area and
volume between three groups with glmfit.
Currently I am using the dev version (
freesurfer-darwin-OSX-ElCapitan-dev-20180627-4a8f901 )
yes, you can run every step individually if you want to. Note that at the
very end of autorecon3 we do update the aseg using the surface locations,
which helps the voxel-based segmentation of cortical gray matter
significantly, but maybe that doesn't matter to you.
Check the recon-all --help
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Dear Sir,
I was able to generate segmentations as cited in the module , I am able
obtain segmentations for CA1 posterior Head and CA1 Posterior body , along
with CA1 head and CA1 body , what does non posterior parcellations of CA1
head and body
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Dear Freesurfers,
is it possible to convert a text file (containing x/y/z-coordinates and
corresponding values) into a Freesurfer surface file to display it on a
standard volume (e.g., fsaverage)?
Thanks in advance!
Luke
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Hi everybody!
I have an error in one of my subjects preprocessing
error opening file dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz
In the dlabel folder of this subject, the mni folder has the half of the
items that the rest of subjects have
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I was thinking it could be a corrupt MCR cache. Could you please:
a) Delete /tmp/MCR* directories
b) Make sure you've got enough space in /tmp/
Cheers,
/Eugenio
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
University College
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Yes!
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: Dev vasu
Sent: Tuesday, July 3, 2018 12:22:27 AM
To:
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Hi Bruce,
thank you for answering. The problem is that autorecon2 runs all the way to
step 23, and I only need up until step 12. Is there another way?
Regards,
Francisco
On Mon, Jul 2, 2018 at 9:08 PM, Bruce Fischl
wrote:
> Hi Francisco
>
> do
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