There might be something wrong with the dicom, so first, try to convert
the dicom to nii.gz with mri_convert
On 5/10/2022 3:23 AM, m-maiw...@web.de wrote:
External Email - Use Caution
Hi all,
I try to run dt_recon on my dicom files, acquired with a siemens
scanner unsing the command
Hello Antti,
It may be possible that you’ve run out of space and the full volumes were not
written. You can check by using: df -h /path/to/file
Similarly, you can run mri_info on the input files to see how many frames there
are and where the discrepancy between the volumes set to x and y are ari
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It might be an issue with the current freesurfer dev version because when I
change it back to the Freesurfer 6.0 version it works perfectly fine? And
has no issues reading them.
On Tue, Apr 2, 2019 at 1:51 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard
It is having problems reading both the bvals and the bvecs
On 4/2/19 9:34 AM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am running dt_Recon with the following specifications and am running
> into this issue? I wasn't running into this issue previously. Two
>
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Thanks!
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
On Fri, Feb 15, 2019 at 11:18 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harva
Can you do this in two steps? First, convert the dicom to a volume format (eg,
mgz or nii.gz) with
mri_convert image001.dcm dwi.nii.gz
This may or may not create bvals and bvecs. If not, then you will have to
supply them. If they are created, look at them and make sure they are right.
Next ru
Hi Rito.
It is not finding information about the gradient table that was used for
the acquisition. If you have that information you can use the below option
to manually include it
--b bvals bvecs
If you do not you could try using load_dicom in order to grab that
information.
Lilla
On Mon,
The registration completed fine.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Wednesday, May 28, 2014 11:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dt_recon error
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Tuesday, May 27, 2014 6:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] dt_recon error
>
>
> Did it actually fail? If not
Greve
Sent: Tuesday, May 27, 2014 6:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dt_recon error
Did it actually fail? If not, does the registration look ok? That msg should
just be a warning doug
On 05/27/2014 02:06 PM, Weber, Wade (weberw) wrote:
>
> Hi all,
>
Did it actually fail? If not, does the registration look ok? That msg
should just be a warning
doug
On 05/27/2014 02:06 PM, Weber, Wade (weberw) wrote:
>
> Hi all,
>
> I have been trying to work with DTI data in FreeSurfer for the first
> time. We acquire our data on a 4T Varian and reconstruct
ay, February 12, 2014 8:24 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] dt_recon error for Siemens mosaics image
>
> has it been anonymized?
>
> On 02/11/2014 02:23 PM, Gennan Chen wrote:
>> HI! All,
>>
>> I got an error when I ran dt_recon
>
Subject: Re: [Freesurfer] dt_recon error for Siemens mosaics image
has it been anonymized?
On 02/11/2014 02:23 PM, Gennan Chen wrote:
> HI! All,
>
> I got an error when I ran dt_recon
>
> WARNING: file /Users/gnchen/tmp/3011_DTI/orig/MR01.dcm does not
> contain a Siemens AS
has it been anonymized?
On 02/11/2014 02:23 PM, Gennan Chen wrote:
> HI! All,
>
> I got an error when I ran dt_recon
>
> WARNING: file /Users/gnchen/tmp/3011_DTI/orig/MR01.dcm does not
> contain a Siemens ASCII header
>
> has this file been anonymized?
>
> ERROR: cannot unpack mosiacs without
Hi Yuko, i'm guessing that something is fishy with your bval and bvec
files. Make sure that there is a new line after the last entry. How did
you make the files?
doug
On 12/13/11 11:22 PM, Yuko Yotsumoto wrote:
> Hi Doug,
>
> I thought I figured this out, but I was wrong...
>
> my b-values are
Hi Doug,
I thought I figured this out, but I was wrong...
my b-values are 700, and number of directions is 64.
Number of images with b=0 is 1.
Text file for bvals has 65 rows, first row has 0, followed by 64 of 700.
0
700
700
700
...
Text file for bvecs has 65 rows and three columns. The first
Doug,
Never mind. I think I just figured it out!0
Yuko
On Dec 12, 2011, at 6:18 PM, Yuko Yotsumoto wrote:
> Thanks Doug,
>
> In the dt_recon help,
>
>> The bvalues are in a simple text file, one for each direction
>> (including b=0). The bvectors (gradient directions) are also in a
>> simple
Thanks Doug,
In the dt_recon help,
> The bvalues are in a simple text file, one for each direction
> (including b=0). The bvectors (gradient directions) are also in a
> simple text file with three components on each row. These also include
> the b=0 values. There must be as many rows in the bval
Hi Yuko, it will get the bvals and bvecs from a set of tables
distributed with FS. But the dicom has to have some information in it
that tells it which table to use. It looks like your dicom did not have
this information (it is not in the info dump created from the dicom). So
you'll have to cre
Hi Doug,
Thank you for your reply.
> If so, then it cannot extract the bvecs and bvals. If you supply them in a
> file on the command line
I don't quite understand how --b works with dt_recon.
I did:
dt_recon --i
/Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm --s AGY11
-
Hi Yuko, your dicom file might be from a different versioned scanner
than dt_recon is used to seeing. If so, then it cannot extract the bvecs
and bvals. If you supply them in a file on the command line, it should
run properly.
doug
Yuko Yotsumoto wrote:
> Hello,
>
> I'm having a problem with dt
what's your command-line? It's probably looking for the acq paraemeters.
If you can't get this fixed, then you'll just have to supply the bvalues
and bvects on the command-line.
Zhen Zonglei wrote:
Dear Thomas and all:
When I processed the DTI data with dt_recon command, I encountered
the
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