Hi everyone,
I have some problems trying to run TRACULA on some DWI data. It is a mosaic
Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and
bval files.
Then I run the trac-all -prep -c command and I get the following error :
WARNING: file /My/path/to/dicom does not
Hi everyone,
I’m reposting my problem if someone could help me I would really appreciate it.
I have some problems trying to run TRACULA on some DWI data. It is a mosaic
Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and
bval files.
Then I run the trac-all -prep -c c
Hi everyone,
It’s been two weeks that I’ve been facing some issues with Tracula. I hope you
could help me with that.
I run trac-all -prep -c on some DICOM files but I had the following error :
WARNING: file
/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.3680043.6.8878.2255
Hi Lars,
I had the same problem. You can notice in your bvec file that there are some
unusual blank spaces sometimes. Try to look at each space between two numbers
and make sure it’s fine. You can also make sure about the number of entries by
running wc -w on each of your bvec or bval file.
Hop
the original files used.
On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
mailto:ayend...@nmr.mgh.harvard.edu>> wrote:
Hi Ismail - Are you passing the nifti volume as input to trac-all? It's
hard to tell without looking at your configuration file.
Best,
a.y
On Tue, 28 Jun 2016, Koubiyr, Ism
fti volume, not the
> bvecs/bvals. Can you send the log file from scripts/trac-all.log?
>
> Thanks,
> a.y
>
> On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
>
>> Hi Anastasia,
>> Thank you for getting back to me.
>> Here are more details about my problem, I think it
ct the 32nd frame of your nifti file, but from the error
> message it looks like your nifti file doesn't have a 32nd frame. So either
> the nifti file has too few volumes, or the bvecs/bvals have too many lines.
> You'll have to figure that out.
>
> a.y
>
> On M
e number of frames that shows up?
>
> On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
>
>> Hi Anastasia,
>>
>> This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals.
>> So this shouldn’t be the reason.
>> Also why the DICOMs wouldn’t work a
?
ERROR: cannot unpack mosiacs without ASCII header
Any idea what this could be ?
Thanks,
Ismail
On Jul 4, 2016, at 3:15 PM, Koubiyr, Ismail
mailto:ikoub...@bwh.harvard.edu>> wrote:
It says 1 … I don’t understand why I get that knowing that when I open the
nifti I can go through the
Hi everyone,
I’m having some issues converting my DICOMs (DWI) into NIFTI using mri_convert.
I looked for other topics with people having the same kind of problem but
couldn’t find an answer.
Each time I run mri_convert on my DICOMs I get the following error :
WARNING: file MR.1.3.12.2.1107.5.2
The file has not been anonymized.
Thanks,
Ismail
> On Jul 5, 2016, at 11:20 AM, Douglas N Greve
> wrote:
>
> can you answer the question that it asks?
>
> On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
>> Hi everyone,
>>
>> I’m having some issues c
Hi,
This is a repost. Would anyone have a solution to this problem ?
Thanks for your help.
Best,
Ismail
> On Jul 5, 2016, at 11:24 AM, Koubiyr, Ismail wrote:
>
> The file has not been anonymized.
>
> Thanks,
>
> Ismail
>
>> On Jul 5, 2016, at 11:20
Hi Doug,
It is still an issue. I uploaded the DICOMs to you. Hope it could be useful.
Thanks.
Ismail
> On Jul 18, 2016, at 6:14 PM, Douglas N Greve
> wrote:
>
> Is this still a problem? If so, can you upload the dicom files to our
> file drop?
>
> On 07/05/2016 11:2
cluded -it dicom, the conversion did not have an error, but the
output had only one slice. Since these are mosaics, they need the
Siemens ascii header which is ignored with -it dicom. So ... don't use
-it dicom
On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote:
Hi Doug,
It is still an issue. I u
scii header, run
mri_probedicom --i MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
There should be a line like below
### ASCCONV BEGIN
On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote:
Hi Doug,
That’s weird because I can’t convert it using only mri_convert, here
is the error I get :
WA
but I used it on linux. Do you have a linux box with
FS installed that you can try it on?
On 7/19/16 1:57 PM, Koubiyr, Ismail wrote:
I used the same command line as you did. And when I check with mri_probedicom I
can see the ASCII header.
Here is the version of FS I am using :
freesurfer-i386
g to do with the ascii header when
unpacking skyra data on the mac, that might be it. Zeke, can you get
Ismail a version of mri_convert appropriate for his OS?
doug
On 7/20/16 10:34 AM, Koubiyr, Ismail wrote:
Hi Doug,
I tried it on the cluster and it worked, which is weird because it was
no
I think you can use mri_binarize and set the match values as you like.
Hope it can help.
Best,
Ismail
> On Jul 21, 2016, at 2:13 PM, Jinsong Tang wrote:
>
> Hello freesurfers,
>
> I want to select the subcortical structures (thalamus, pallidum, caudate,
> putamen, accumbens, hippocampus, and
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