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.
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.
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:
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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:
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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:
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:
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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:
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:
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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:
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:
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:
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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. >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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:
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:
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:
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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The error message is "data and bvals/bvecs do not contain the same number of entries". This doesn't necessarily mean that the bvecs and bvals don't agree with each other, but that the bvecs and bvals don't agree with the DWI data.
Based on this line in the log file, there are 130 frames in the DWI dicoms, so I suspect that you may have two repetitions of your 65 directions:
INFO: (120 120 50), nframes = 130, ismosaic=0
You can confirm this my looking at the images. If that is the case, you need to have two repetitions in the bvecs/bvals files too.
On Thu, 3 Jul 2014, Pedro Rosa wrote:
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:
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:
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:
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Thank you once again! Yes, that is true. The bval and bvec file were doubled, so I removed half the values (and also the empty spaces) and the fMRIframe: frame >= nframes stopped from happening. A converted the dcm to nii using dcm2nii software, and used its bval and bvec files as input to TRACULA. Is it frequent to have a repetition of directions? I now included the doubled bvec and bval files, but it seems I have another error: [server:/MRI/Tracula-test] pedrogomesrosa% trac-all -prep -c config -no-isrunning INFO: SUBJECTS_DIR is /MRI/Tracula-test INFO: Diffusion root is /MRI/Tracula-test Actual FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/Freesurfer5.3/freesurfer Previous: /Volumes/Data/Freesurfer_5.3/freesurfer trac-preproc -c /MRI/Tracula-test/ESNA149/scripts/dmrirc.local -log /MRI/Tracula-test/ESNA149/scripts/trac-all.log -cmd /MRI/Tracula-test/ESNA149/scripts/trac-all.cmd -no-isrunning #------------------------------------- /Applications/Freesurfer5.3/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fri Jul 4 07:00:19 BRT 2014 mri_convert /MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155.dcm /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz mri_convert /MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155.dcm /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155.dcm... Getting Series No INFO: Found 6607 files in /MRI/Tracula-test/149 INFO: Scanning for Series Number 3 Scanning Directory INFO: found 6500 files in series INFO: loading series header info.
RunNo = 2 INFO: sorting. INFO: (120 120 50), nframes = 130, ismosaic=0 PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;
FileName /MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004780512604280.dcm Identification NumarisVer syngo MR B15 ScannerModel Espree PatientName XXXXXX Date and time StudyDate 20120613 StudyTime 074845.171000 SeriesTime 080047.531000 AcqTime 080046.267500 Acquisition parameters PulseSeq *ep_b0 Protocol DIF 64 2NEX 2.7mmX2mm Trigger (Ax Puro) PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 110 InversionTime -1 RepetitionTime 8000 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 2 SeriesNo 3 ImageNo 1 NImageRows 120 NImageCols 120 NFrames 130 SliceArraylSize 50 IsMosaic 0 ImgPos 116.6747 79.4248 -34.6722 VolRes 2.0000 2.0000 2.7000 VolDim 120 120 50 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 -0.0052 Vs -0.0000 -0.0052 1.0000 VolCenter -3.3253 -40.9270 32.1985 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=8000.00, TE=110.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.999986, -0.00523596) k_ras = (-0, -0.00523596, 0.999986) writing to /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz... mri_probedicom --i /MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155.dcm > /MRI/Tracula-test/ESNA149/dmri/dcminfo.dat cp /MRI/Tracula-test//bvec.bvec /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvecs cp /MRI/Tracula-test//bval2.bval /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvals ERROR: Found 130 b-values but 108.333 gradient vectors Darwin server.macbookpro.com 13.2.0 Darwin Kernel Version 13.2.0: Thu Apr 17 23:03:13 PDT 2014; root:xnu-2422.100.13~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Fri Jul 4 07:04:02 BRT 2014
Pedro Rosa
On Friday, July 4, 2014 at 5:18 AM, Anastasia Yendiki wrote:
The error message is "data and bvals/bvecs do not contain the same number of entries". This doesn't necessarily mean that the bvecs and bvals don't agree with each other, but that the bvecs and bvals don't agree with the DWI data.
Based on this line in the log file, there are 130 frames in the DWI dicoms, so I suspect that you may have two repetitions of your 65 directions:
INFO: (120 120 50), nframes = 130, ismosaic=0
You can confirm this my looking at the images. If that is the case, you need to have two repetitions in the bvecs/bvals files too.
On Thu, 3 Jul 2014, Pedro Rosa wrote:
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
ERROR: Found 130 b-values but 108.333 gradient vectors
If the b-value table has 130 entries, then the gradient table should have 130*3 entries (one x,y,z direction vector for each b-value). This error means that there are fewer entries in the gradient table than there should be. Run wc -w on these text files to check for yourself.
On Fri, 4 Jul 2014, Pedro Rosa wrote:
Thank you once again! Yes, that is true. The bval and bvec file were doubled, so I removed half the values (and also the empty spaces) and the fMRIframe: frame >= nframes stopped from happening. A converted the dcm to nii using dcm2nii software, and used its bval and bvec files as input to TRACULA. Is it frequent to have a repetition of directions? I now included the doubled bvec and bval files, but it seems I have another error:
[server:/MRI/Tracula-test] pedrogomesrosa% trac-all -prep -c config -no-isrunning
INFO: SUBJECTS_DIR is /MRI/Tracula-test
INFO: Diffusion root is /MRI/Tracula-test
Actual FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /Applications/Freesurfer5.3/freesurfer
Previous: /Volumes/Data/Freesurfer_5.3/freesurfer
trac-preproc -c /MRI/Tracula-test/ESNA149/scripts/dmrirc.local -log /MRI/Tracula-test/ESNA149/scripts/trac-all.log -cmd /MRI/Tracula-test/ESNA149/scripts/trac-all.cmd -no-isrunning
#-------------------------------------
/Applications/Freesurfer5.3/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Fri Jul 4 07:00:19 BRT 2014
mri_convert/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155. dcm /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz
mri_convert/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155. dcm /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155. dcm...
Getting Series No
INFO: Found 6607 files in /MRI/Tracula-test/149
INFO: Scanning for Series Number 3
Scanning Directory
INFO: found 6500 files in series
INFO: loading series header info.
RunNo = 2
INFO: sorting.
INFO: (120 120 50), nframes = 130, ismosaic=0
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.000 0.000 0.000 0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
FileName/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004780512604280. dcm
Identification
NumarisVer syngo MR B15
ScannerModel Espree
PatientName XXXXXX
Date and time
StudyDate 20120613
StudyTime 074845.171000
SeriesTime 080047.531000
AcqTime 080046.267500
Acquisition parameters
PulseSeq *ep_b0
Protocol DIF 64 2NEX 2.7mmX2mm Trigger (Ax Puro)
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 110
InversionTime -1
RepetitionTime 8000
PhEncFOV 240
ReadoutFOV 240
Image information
RunNo 2
SeriesNo 3
ImageNo 1
NImageRows 120
NImageCols 120
NFrames 130
SliceArraylSize 50
IsMosaic 0
ImgPos 116.6747 79.4248 -34.6722
VolRes 2.0000 2.0000 2.7000
VolDim 120 120 50
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 -0.0052
Vs -0.0000 -0.0052 1.0000
VolCenter -3.3253 -40.9270 32.1985
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
INFO: no Siemens slice order reversal detected (good!).
TR=8000.00, TE=110.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -0, 0)
j_ras = (-0, -0.999986, -0.00523596)
k_ras = (-0, -0.00523596, 0.999986)
writing to /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz...
mri_probedicom --i/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155. dcm > /MRI/Tracula-test/ESNA149/dmri/dcminfo.dat
cp /MRI/Tracula-test//bvec.bvec /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvecs
cp /MRI/Tracula-test//bval2.bval /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvals
ERROR: Found 130 b-values but 108.333 gradient vectors
Darwin server.macbookpro.com 13.2.0 Darwin Kernel Version 13.2.0: Thu Apr 17 23:03:13 PDT 2014; root:xnu-2422.100.13~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Fri Jul 4 07:04:02 BRT 2014
Pedro Rosa
On Friday, July 4, 2014 at 5:18 AM, Anastasia Yendiki wrote:
The error message is "data and bvals/bvecs do not contain the same number of entries". This doesn't necessarily mean that the bvecs and bvals don't agree with each other, but that the bvecs and bvals don't agree with the DWI data.
Based on this line in the log file, there are 130 frames in the DWI dicoms, so I suspect that you may have two repetitions of your 65 directions:
INFO: (120 120 50), nframes = 130, ismosaic=0
You can confirm this my looking at the images. If that is the case, you need to have two repetitions in the bvecs/bvals files too.
On Thu, 3 Jul 2014, Pedro Rosa wrote:
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:
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:
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:
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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Hi, Thanks a lot. I corrected the files as you suggested and now it finished without error. Best, Pedro Rosa.
On Jul 4, 2014, at 7:24 AM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
ERROR: Found 130 b-values but 108.333 gradient vectors
If the b-value table has 130 entries, then the gradient table should have 130*3 entries (one x,y,z direction vector for each b-value). This error means that there are fewer entries in the gradient table than there should be. Run wc -w on these text files to check for yourself.
On Fri, 4 Jul 2014, Pedro Rosa wrote:
Thank you once again! Yes, that is true. The bval and bvec file were doubled, so I removed half the values (and also the empty spaces) and the fMRIframe: frame >= nframes stopped from happening. A converted the dcm to nii using dcm2nii software, and used its bval and bvec files as input to TRACULA. Is it frequent to have a repetition of directions? I now included the doubled bvec and bval files, but it seems I have another error: [server:/MRI/Tracula-test] pedrogomesrosa% trac-all -prep -c config -no-isrunning INFO: SUBJECTS_DIR is /MRI/Tracula-test INFO: Diffusion root is /MRI/Tracula-test Actual FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/Freesurfer5.3/freesurfer Previous: /Volumes/Data/Freesurfer_5.3/freesurfer trac-preproc -c /MRI/Tracula-test/ESNA149/scripts/dmrirc.local -log /MRI/Tracula-test/ESNA149/scripts/trac-all.log -cmd /MRI/Tracula-test/ESNA149/scripts/trac-all.cmd -no-isrunning #------------------------------------- /Applications/Freesurfer5.3/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fri Jul 4 07:00:19 BRT 2014 mri_convert/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155. dcm /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz mri_convert/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155. dcm /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155. dcm... Getting Series No INFO: Found 6607 files in /MRI/Tracula-test/149 INFO: Scanning for Series Number 3 Scanning Directory INFO: found 6500 files in series INFO: loading series header info. RunNo = 2 INFO: sorting. INFO: (120 120 50), nframes = 130, ismosaic=0 PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004780512604280. dcm Identification NumarisVer syngo MR B15 ScannerModel Espree PatientName XXXXXX Date and time StudyDate 20120613 StudyTime 074845.171000 SeriesTime 080047.531000 AcqTime 080046.267500 Acquisition parameters PulseSeq *ep_b0 Protocol DIF 64 2NEX 2.7mmX2mm Trigger (Ax Puro) PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 110 InversionTime -1 RepetitionTime 8000 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 2 SeriesNo 3 ImageNo 1 NImageRows 120 NImageCols 120 NFrames 130 SliceArraylSize 50 IsMosaic 0 ImgPos 116.6747 79.4248 -34.6722 VolRes 2.0000 2.0000 2.7000 VolDim 120 120 50 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 -0.0052 Vs -0.0000 -0.0052 1.0000 VolCenter -3.3253 -40.9270 32.1985 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=8000.00, TE=110.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.999986, -0.00523596) k_ras = (-0, -0.00523596, 0.999986) writing to /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz... mri_probedicom --i/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155. dcm > /MRI/Tracula-test/ESNA149/dmri/dcminfo.dat cp /MRI/Tracula-test//bvec.bvec /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvecs cp /MRI/Tracula-test//bval2.bval /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvals ERROR: Found 130 b-values but 108.333 gradient vectors Darwin server.macbookpro.com 13.2.0 Darwin Kernel Version 13.2.0: Thu Apr 17 23:03:13 PDT 2014; root:xnu-2422.100.13~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Jul 4 07:04:02 BRT 2014 Pedro Rosa On Friday, July 4, 2014 at 5:18 AM, Anastasia Yendiki wrote: The error message is "data and bvals/bvecs do not contain the same number of entries". This doesn't necessarily mean that the bvecs and bvals don't agree with each other, but that the bvecs and bvals don't agree with the DWI data. Based on this line in the log file, there are 130 frames in the DWI dicoms, so I suspect that you may have two repetitions of your 65 directions: INFO: (120 120 50), nframes = 130, ismosaic=0 You can confirm this my looking at the images. If that is the case, you need to have two repetitions in the bvecs/bvals files too. On Thu, 3 Jul 2014, Pedro Rosa wrote:
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: 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: 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: 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . 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