Hi! Thanks! It helped, but now I have another error… I attached the log, and both the bvec and bval files that served as inputs (without any empty space in the end) and the ones generated by the script in the $subject/dmri (which turns out to have empty spaces in the end). All these 4 files have 65 entries (bval with 65 for each one of the three sequences). Can you spot the error? Regards
Pedro Rosa
On Thursday, July 3, 2014 at 3:05 AM, Anastasia Yendiki wrote:
Hi Pedro - Have you specified not to do eddy current compensation? It looks like it's being skipped. In that case, you need to also skip the QA step (by adding -noqa to your trac-all command line). That's because the QA step requires the output of the eddy current compensation to assess how much motion there is in the data.
Hope this helps, a.y
On Thu, 3 Jul 2014, Pedro Rosa wrote:
Anastasia, I was finding the same error as Jun, and your help fixed it. Thank you very much. However, I am now finding a new error (attached). Can you help me? Thank you again. Regards, Pedro Rosa.
On Wednesday, July 2, 2014 at 10:49 PM, Jun Shinozaki wrote:
Hi Anastasia,
You are right! There are empty spaces at the end of the lines in original bvecs and bvals. I could fix the error and finish trac-preproc without error by eliminating these spaces. Thank you so much!
Regards, Jun Shinozaki
2014-07-02 15:21 GMT+09:00 Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu (mailto:ayendiki@nmr.mgh.harvard.edu)>:
There are probably some empty spaces at the end of the lines of the original files that confuses it into introducing those zeros. If you attach the original files, I can take a look at them.
On Wed, 2 Jul 2014, Jun Shinozaki wrote:
Hi Anastasia,
I created bvals.txt and bvecs.txt using dcm2nii. These original files were text files and set in dmrirc profile as "set bvalfile = /path/to/bvals.txt".
I checked word count for these files # wc -w bvals.txt bvecs.txt 65 bvals.txt 195 bvecs.txt 260 total
However, when I run "trac-all -prep -c dmrirc", then freesurfer creates bvals and bvecs automatically in dmri folder.
Then, I check word count # wc -w bvals bvecs 65 bvals 198 bvecs 263 total
Now, freesurfer adds 3 extra entries in the bvecs file. As you said, there is an extra column of zeros in the end.
So, I cannot fix the error.
Regards, Jun Shinozaki
2014-07-01 15:56 GMT+09:00 Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu (mailto:ayendiki@nmr.mgh.harvard.edu)>:
Hi Jun - By a simple word count on these files:
% wc -w bvals bvecs 65 bvals 198 bvecs 263 total
As you can see, there are 3 extra entries in the bvecs file. If you then open the file, you'll see that there is an extra column of zeros in the end. Not sure if that's what's causing the problem, but you might want to look for empty lines at the end of your original gradient table.
a.y
On Tue, 1 Jul 2014, Jun Shinozaki wrote:
Hi Anastasia, Thank you for your e-mail. I took 65 DWIs (5 b0 volumes and 60 direction DWIs).
I checked dwi.nii.gz in the dmri folder, and dwi.nii.gz had 65 images. Also, I checked bvals and bvecs in the dmri folder, and they have 65 counts. It seems consistent. I attach bvals and bvecs. These files were created by freesurfer automatically.
Regards, Jun Shinozaki
2014-06-30 18:38 GMT+09:00 Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu (mailto:ayendiki@nmr.mgh.harvard.edu)>:
Hi Jun - It's failing at the point where it tries to extract the low-b images from the DWI series. I suspect that the number of frames in the 4D DWI volume that is extracted from your dicom does not match the number of frames that it expects to find based on how many gradient vectors or b-values it's looking for. So I'd check these DWI, gradient vector and b-value files to make sure they are all consistent.
Hope this helps, a.y
On Mon, 30 Jun 2014, Jun Shinozaki wrote:
Dear All,
I am trying to run a single subject in TRACULA (trac-all -prep -c dmrirc), but exited with ERRORS.
ERROR: fMRIframe: frame >= nframes
The attached file is a log file.
Can anyone help me? Thank you in advance.
Regards, Jun Shinozaki.
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