Hi Bruce,
When I wanted to view them in freeview, simply nothing happened. Freeview
did not load the files, so I assumed it did not work with dicoms, that's
why I converted them.
Best,
Marja
On Tue, Jun 14, 2016 at 12:23 PM, Douglas Greve
wrote:
> What do you mean that FS did not accept the d
What do you mean that FS did not accept the dicom files? Can you provide
a command line and terminal output? You can use dcmunpack -src
/path/to/dicom to get a list of the series in a dicom folder
On 6/13/16 9:57 PM, Marja Caverlé wrote:
Hi Bruce,
I converted first of all because freesurfer d
sorry, I don't understand the question. It looks like the design matrix
is right. It looks like the contrasts tests for a diff between AD and
controls. What else do you need?
On 6/13/16 8:49 AM, Hao wen wrote:
Hello:
I am still confused about how to make the design matrix in FS for
group an
You can include a mask, eg
mri_segstats --i input.nii.gz --mask input.nii.gz --maskthresh .0001
On 6/10/16 11:59 AM, Lakhani, Bimal wrote:
Hello,
I am running mri_segstats to get the intensity mean of a custom image
volume, but I do not want zeroes to be included in the calculation of
t
Hi Bruce,
I converted first of all because freesurfer did not accept the dicom files.
Furthermore the dicom's consist of a lot of files of different scans, and
they are not named accordingly. The whole folder consists of files called
eg 1254890234, so I have no clue how to get the right files.
Th
Dear Experts:
I set up FS development version.
And now it shows error message:
--
GNU libc version: 2.17
ERROR: Systems running GNU glibc version greater than 2.15
require a newly formatted license file (it's free). Please
Hi Marja
why are you converting at all? Why not just give one of the dicom files in
the correct series to recon-all directly? I don't think we've ever seen an
orientation problem if you process that way
cheers
Bruce
On Tue, 14 Jun 2016, Marja Caverlé wrote:
No, when I view them in freeview
I'm trying to convert the dicom to the original 001.mgz file using the
following command on a Mac OSX Yosemite version 10.10.5. My
SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/
. My current working directory is /Users/csfinuf/Desktop/freesurfer/morerepeat/
. The following i
Latest freeview is just what comes with the developement version of
freesurfer. You can download the latest development verion from the
following page:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
On 06/13/2016 12:44 PM, Chiu, Bryan (PHTH) wrote:
Hello,
I would like to download the
Hello,
I would like to download the latest version of FreeView so I could use the
Recon Edit option. I've downloaded the latest version of FreeSurfer (v5.3), but
it seems that I have an older version of FreeView (v1.0). Could someone please
assist me in updating FreeView - I can't find the down
No, when I view them in freeview the orientation is the same as in the
original dicoms, but the results in the .stats files made me think that
left and right might be swapped. Of course this could just really be the
results of the correct hemispheres, but that is why I asked whether you are
aware o
so you convert from dicom to nifti, then view in freeview and you think
that the anatomical orientations are incorrect? That should definitely not
be the case
On Tue, 14 Jun 2016, Marja
Caverlé wrote:
Well the DICOMs I visualized in osiriX, and the niftis in both freesurfer
and fsl. And the
Hi Navena
hmmm, sounds like that subject didn't finish processing for some reason.
You could try rerunning just that step with:
recon-all -s N1 -sd /Users/navenalingum/Applications/freesurfer/subjects
-cortparc -cortparc2 -cortparc3
and see if that completes (it should only take a couple o
Dear FreeSurfer experts,
I am currently in the process of running the mris_anatomical_stats command line
to look at cortical thickness however, the output states that the annotation
file could not be read.
Please see below for command line and output:
navenalingum% mris_anatomical_stats -a
Well the DICOMs I visualized in osiriX, and the niftis in both freesurfer
and fsl. And there they seemed to match.
So my question is; is there a possibility that dimensions are swapped
during the recon -all? If not, then I am sure R=R and L=L.
Thanks!
On Tue, Jun 14, 2016 at 12:55 AM, Bruce Fisch
Hi Marja
what did you visualize it in? I would suggest freeview
cheers
Bruce
On Tue, 14 Jun 2016,
Marja Caverlé wrote:
Hi Bruce,
I converted the images with MRIconvert, then I swapped them in FSL with
swapdim.
I checked the images by opening the original dicoms and the converted
niftis, and
Hi Bruce,
I converted the images with MRIconvert, then I swapped them in FSL with
swapdim.
I checked the images by opening the original dicoms and the converted
niftis, and then visually compared them (since the heads are not very
symmetrical that was not too hard).
Best,
Marja
On Tue, Jun 14,
Hi Marja
how did you swap them? And more importantly, how did you check that
the orientations were correct after conversion?
cheers
Bruce
On Mon, 13 Jun 2016, Marja Caverlé wrote:
Hi guys,
Just a quick question; I have converted my original DICOMs into niftis.
After the conversion I manu
Hello:
I am still confused about how to make the design matrix in FS for group
analysis:
I want to create a design matrix like this: X = 1 + TermAge + TermGender *
TermGroup (this should be like
Age
Female
*
AD
Male
*
AD
Female
*
CN
Male
*
CN
)
There are just 5 columns,
Hej.
I recently tried to create a license file for a Unix-based installation of
FreeSurfer that previously had no license file associated with it. With the
help of our IT people, I have tried copying the lines I received via email into
a file named ‘license.txt’ and then following responses I
Hi guys,
Just a quick question; I have converted my original DICOMs into niftis.
After the conversion I manually checked whether the orientations were still
the same, and they were not, so I swapped them. After this I did a recon
-all.
A lot of my results are at one side while I expected them in t
Dear all,
I've a lot of patients and we are looking for the fastest solution to check
the output of Freesurfer. On the troubleshooting page (
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData)
there are a lot of steps to check, but I think not all of that should be
done to f
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