Sounds great, will try that!
Again, thank you very much for your help!
Bastian.
On 22 July 2014 01:53, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote:
Hi Bastian,
yes, lta are the (here rigid) transformations (dat files are deprecated).
you can use mri_convert -at lta
or mri_vol2vol for
Dear Experts,
I used ‘mri_surf2surf’ to get the area, thickness, volume of all the vertices
in the brain. I am wondering what functions can I use to get other information,
such as ‘curvind, foldind, gauscurv, meancurv, thicknessstd’ ? I know
FreeSurfer provides these statistic data according
Hi,
two years ago I processed a lot of data using freesurfer v5.1. Now I'm
using v5.3 on a different group of subjects, I'm wondering if I can use
together all the subjects from the different versions.
Or there is a way to re-run it using the last version? I suppose that I can
copy the
Hi Qiongmin
mris_anatomical_stats will do some of what you want, although not on a
vertex-by-vertex basis. Thickness, area, mean curvature and volume are all
stored in per-vertex files that you can use. The other curvatures can be
created useing mris_curvature I believe.
cheers
Bruce
On
Hi Anastasia,
By `compatible' I meant whether I could export tracula outputs into a
format recognized by DtiMap, with the LAS coordinates preserved.
My goal for this project is to use tracula outputs to prepare
probabilistic segmentations of the white matter including deep structures.
I was
Hi Gianluca
if you rerun recon-all it should preserve all your edits (unless you
explicitly tell it not to). We definitely do not recommend mixing
versions.
cheers
Bruce
On Tue, 22 Jul 2014, Gianluca Rambaldelli wrote:
Hi,
two years ago I processed a lot of data using freesurfer v5.1.
Can DTImap read nifti volumes? The output of tracula includes one nifti
volume with the probability distribution of each of the 18 pathways in
each subject.
On Tue, 22 Jul 2014, Shantanu Ghosh wrote:
Hi Anastasia,
By `compatible' I meant whether I could export tracula outputs into a
Dear Freesurfer Community,
Running Tracula preprocessing produces this error:
ERROR: Could not open
/home/elia/scripts/Tracula/LCL/dcmTimePoints_tar/T13D/timePoint1/dmri/bvals for
reading
I think the error described is the same as here:
Hi Elia - Have you searched for the libnetcdf error in the archives? I do
believe that a few people were getting that error when 5.3 was first
released.
a.y
On Tue, 22 Jul 2014, Elia S. wrote:
Dear Freesurfer Community,
Running Tracula preprocessing produces this error:
ERROR: Could not
Hi Shannon
not sure about freeview, Ruopeng should be able to answer that part, but it
should be easy enough in tksurfer. Just load the labels separately and give
them whatever color you want.
cheers
Bruce
On Mon, 21 Jul 2014, Shannon Buckley wrote:
Hi experts,
I’m trying to create a
Hi Shannon,
If I understand correctly, you are trying to load 2 ROIs on top of a layer of
annotations on surface? Can you show me the freeview command you run? Or did
you do everything on the GUI? BTW, are you using the latest dev build of
freeview or the released one in v5.3? If I remember
Aha Tksurfer, of course!
Will follow up with Ruopeng about freeview, but tksurfer satisfies the goal
nicely...
Thank you!
On Jul 22, 2014, at 7:53 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Shannon
not sure about freeview, Ruopeng should be able to answer that part, but it
Hi Ruopeng,
I just used the GUI while trying to figure this out... Was going to circle back
to build a proper cmd line once I have the pieces I need. I was wondering if
maybe my commands to build the annotation were faulty, but if it's just the
version at issue then that's not so bad...
In
Dear Anastasia,
With the new Tracula update installed, I ran the command:
trac-all –qa –c dmrirc_file with location of bval specified and received
the following error after ‘Loading
volume-to-baseline affine transformations’
Could not open ../dmri/
dwi.ecclog for reading.
It seems like
Hi all,
I was wondering how you go about looking at dtifit_V1 (the primary eigenvector
of the tensors) displayed as lines in freeview?
Emily
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Hello,
I am trying to convert my significant cluster from qdec into a .gii file, and I
have a couple of questions.
My mri_convert is not working, but it is my first time using it so I may be
missing something, but it just keeps opening up the usage and gives no errors.
mris_convert --annot
Hi FreeSurfer group,
I was wondering if there is a way to include control points in my command
line when I run recon-all. We are working with a large dataset and many of
the subjects have underestimations in the anterior temporal lobes so it
would be beneficial to expand the WM surface slightly
Hi Adam
I don't think so as how would we don't know where the anterior temporal
lobe at that stage in the process.
Bruce
On
Tue, 22 Jul 2014, Adam Mezher wrote:
Hi FreeSurfer group,
I was wondering if there is a way to include control points in my command
line when I run recon-all. We are
Hello All,
I was testing to see if the freesurfer program works and it does seem to work
for anything besides the free viewer program. I do not know what is wrong with
the others; do you have any ideas? Also I am trying to use the inhomogeneity
correction, convert the images that I have to
Hi Isaiah
what are the input images that you have? What format and what imaging
sequence? You should be able to just run recon-all on them (check out
recon-all -help)
cheers
Bruce
On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello All,
I was testing to see if the freesurfer program works
Hello Bruce,
Thanks for the response; I tried the inputs from the check freesurfer page. I
just tried to do the run recon-all and got the list of possible commands. The
input images are unix executable files separately, but I can convert them to
.hdr/.img or .nii using mricron. They are MRI
Hi Isaiah
recon-all -i input file -s subject identifier -sd dir to put subject
in -all
should do the trick. input file should be a *single* file in the right
dicom series, or a .nii file. Don't use analyze
Bruce
On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello Bruce,
Thanks for the
Hi Bruce,
Thank you for your message.
Yes, I rechecked the result and have tried it several times. It still seems to
be not working. However, our lab has used the watershed flag previously and it
had worked. Not sure what has changed.
Thank you for your help.
Sourav
Hi Sourav
can you explain what failed? Was too much removed? Too little? What did
you try to fix it?
Bruce
On Tue, 22 Jul 2014, SOURAV RANJAN KOLE wrote:
Hi Bruce,
Thank you for your message.
Yes, I rechecked the result and have tried it several times. It still seems
to be not working.
?Hi All,
I am new to freeSurfer and need your guidance for some of the doubts I have.
I have installed freeSurfer in a windows 7 machine using virtualBox. I am
trying to process some of my own sMRI data using freeSurfer software. The data
is skull-stripped and has cerebellum. The format of
Hi Bruce,
I do not see any improvement in the skull stripping by decreasing the height. I
have also tried using the multistrip flag but I do not see any changes no
matter the height. Also, it seems that after watershed, it is not respecting
the manual edits that I have made as you can see in
Hi Sourav
Can you explain exactly what you think is failing? Provide images in a couple
of different views (coronal, sagittal) with arrows showing what you think is
incorrect?
Cheers
Bruce
On Jul 22, 2014, at 8:11 PM, SOURAV RANJAN KOLE sourav.k...@utah.edu wrote:
Hi Bruce,
I do not
Hi Soumya
Can you include the full command and screen output of what you ran? Are you
sure that they are nifti and not analyze? Analyze is to be avoided as it
doesn't contain enough information to tell left from right
Cheers
Bruce
On Jul 22, 2014, at 8:01 PM, soumyabrata.dey
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