Hello Developers
I am trying to run recon-all on a number of MP2RAGE T1 images but I fail.
Using tkmedit, I noticed that orig/001.mgz looks fine but orig.mgz is all-0.
Also, mri_convert assumes TE=0, which is false.
Do you have any advice for me?
The recon-all.log is attached
FreeSurfer frees
Hello FreeSurfer Developers,
I'm attempting to convert only one file.label in one file.annot.
I'm using the command MRIS_LABEL2ANNOTATION.
mris_label2annot --s fsaverage --h lh --l
'/home/mlucignani/Desktop/TUTTO/merge/MERGE_AREA_1/originali_lh/lh_FILE_1.label'
ERROR: need to specify color tabl
Hello FreeSurfer Developers,
I'm attempting to convert only one file.label in one file.annot.
I'm using the command MRIS_LABEL2ANNOTATION.
export SUBJECTDIR= /home/mlucignani/Desktop/TUTTO
mris_label2annot --s fsaverage --h lh --l
'/usr/local/freesurfer/subjects/bert/label/aparc.annot.DKTatl
is the rawavg.mgz also empty? The TE=0 only means that nifti doesn't store
the MR parameters - it shouldn't change anything. If the rawavg.mgz is not
empty look at what the values are - maybe they (or the nifti) are too low
and the conversion to uchar sets them to 0?
On Tue, 18 Jul 2017,
clem
Dear Freesurfer users,
i have to run vertex by vertex analysis of cortical thickness across subjects.
As of now i have processed my data using the recon-all command and then the
mris_preproc (separately for each hemisphere). I have now two .mgh file but i
don’t know where to find the info that i
If you load it as an overlay on a surface, then freeview will give you
the coordinates in fsaverage space/MNI305 space.
On 7/18/17 11:27 AM, Giuliano Giari wrote:
> Dear Freesurfer users,
> i have to run vertex by vertex analysis of cortical thickness across
> subjects. As of now i have process
I tried the following, but the program seems to seg fault. No output files
are created. Please help! Thank you.
Alternatively, is there a way to generate the "nopvc" image in RBV space?
Thanks!
*>>mri_gtmpvc --i pet.nii.gz --reg pet2mri.lta --psf 6 --seg gtmseg.mgz
--no-reduce-fov --o pvcout*
sy
Hi,
Yes, I am trying to use skull stripping from another package, since -gcut
option did not work on our data for appropriate skull stripping, and as a
result there is too much pial matter included as white matter.
a) Is brainmask.mgz an appropriate input file for recon-all -all? for
example, sho
no, you don't use brainmask as input, you just put it in the subject's
mri dir. recon-all should then recognize that it is different than
brainmask.auto.mgz, assume it has been manually edited, and preserve
those edits
On Tue, 18 Jul 2017, Michelle VanTieghem wrote:
Hi,
Yes, I am trying to u
The rawavg.mgz is not empty. Many values are around 0 but there are also values
between 0.2 and 0.5 (and values between -0.4 and -0.5 in CSF).
It really seems like orig.mgz is all 0. How low do the values need to be for
the conversion to set them to 0?
Is there anything I can do to use recon-al
you need to scale them. WHy do you have negative values? I would scale
them so that the min is 0 and the mean is around 100 or so. In matlab it
would be something like:
first copy 001.mgz to 001.orig.mgz
thne in matlab do:
[v,M,mr] = load_mgh('001.orig.mgz') ;
v = (v - min(v(:))) * 100;
save_
After some investigation, I found that that command will not work. You
can run it in the normal way, and then run
mri_vol2vol --mov rbv.nii.gz --targ pet.nii.gz --regheader --fill-average
This will average all the rbv voxels that fall into a pet voxel (or you
could use --interp nearest|trilin|c
Do you mean to get each subject's value with nuisance regressors
removed? If so, you'd have to do that in matlab. If you want the values
of the contrast (ie, mean values, not individual subject), then you can
get those from the gamma.mgh file for the contrast (let me know if you
need more i
Dear experts in freesurfer,
I myself am a very beginner in freesurfer but I come with a difficult question
to answer. As you can see from the script below, I am trying to obtain the Bold
in CVS35MNI152 template space which hopefully has better properties for
accuracy and determination of locati
sorry, what is SPC?
On 07/14/2017 02:15 PM, Maria A Infante wrote:
> Hi everyone,
>
> I have a questions concerning the SPC values for an individual brain
> region. I am looking at group differences (3 groups) in SPC in surface
> and found one region that was significant after correcting for
>
Have you tried passing the fs registration matrix to mri_vol2vol instead
of the fsl matrix?
On 07/13/2017 05:02 PM, Paul Glad Mihai wrote:
> Hello,
>
> I'm getting two different results from the coregistration step. When I run
> bbregister on the mean epi it coregisters properly and writes out
Can you send me the input volume and seg at our filedrop?
https://gate.nmr.mgh.harvard.edu/filedrop2
On 07/17/2017 06:34 AM, M Janani wrote:
> Hi Douglas Greve,
> Yes, I’m getting the same result as mentioned below.
> Regards,
> Janani
> --
Not sure. It might be more accurate. Once you have the FWHM you want,
you can run mri_glmfit-sim with --fwhm-override
On 07/17/2017 05:43 PM, Jordi Pegueroles wrote:
> Dear FS experts,
>
> I was wondering if someone had performed multiple comparisons (ie
> monte-carlo) with the LME analyses. I
try
mri_vol2vol --gcam 005.mc.nii boldregister.dat
$SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0
output.nii.gz
This will sample it down to a 2mm space within the CVS atlas (should
overlap pretty well wi
you need another "--l" before your second label
On 07/18/2017 06:17 AM, francesca bottino wrote:
> Hello FreeSurfer Developers,
>
> I'm attempting to convert only one file.label in one file.annot.
> I'm using the command MRIS_LABEL2ANNOTATION.
> export SUBJECTDIR= /home/mlucignani/Desktop/TUTTO m
symmetrized percent change
M. Alejandra Infante, Ph.D.
Postdoctoral Fellow
UC San Diego Department of Psychiatry
Adolescent Brain Cognitive Development (ABCD) Study
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on
Hi all,
We are making manual white matter edits using the "voxel edit" tool in freeview
with “recon editing” selected. These edits are being saved to wm.mgz but not
applied to the white matter surfaces (using the command: recon-all
-autorecon2-wm -autorecon3 -subjid).
We are using FreeSurfer v
Hi Yuwen - This file is generated by the command dmri_paths, which is run
before the dmri_pathstats command. You can see the exact command lines in
scripts/trac-all.cmd (and the full output in scripts/trac-all.log).
Best,
a.y
From: freesurfer-boun...@nm
Hi Colleen - Do the DWIs of your subjects have any slices that are in the brain
but look very dark, almost like the background? That's what those measures
capture, and not all subjects have that. If your subjects don't have that, then
there's nothing to be concerned about!
Best,
a.y
_
Hi Anastasia or Krish,
Is there a version of tractstats2table floating around that allows me to
apply a binarized mask to extract stats for sub-sections of tracts? If not,
I can write my own—just wanting to see if such a function already exists so
that I don’t reinvent the wheel…
Derek Pisner
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