Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? Thanks
On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp bakk.hbg@googlemail.com wrote: Dear Michele,
I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval?
Good luck, Barbara
On 28/08/2014 22:47, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz
I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries
The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors.
I am enclosing a zip folder with attachments: 1) original bvecs and bvals files organized in rows and columns 2) bvecs and bvals files generated by tracula 3) error logs
Let me know if you need any other information. Thanks in advance for your help.
_______________________________________________ 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
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 Michele,
Do you use the dicoms or the nifti files as input to TRACULA? Also, I think the complete trac-all.log could be even more helpful. I am a newbie myself but I am having a similar problem, so I am trying to find a solution as well :).
Best, Barbara
On Fri, Aug 29, 2014 at 4:48 PM, Michele Cavallari miches@bwh.harvard.edu wrote:
Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? Thanks
On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp bakk.hbg@googlemail.com wrote: Dear Michele,
I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval?
Good luck, Barbara
On 28/08/2014 22:47, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz
I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries
The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors.
I am enclosing a zip folder with attachments:
- original bvecs and bvals files organized in rows and columns
- bvecs and bvals files generated by tracula
- error logs
Let me know if you need any other information. Thanks in advance for your help.
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
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
Hi Michele,
This might be the solution - try the command 'more' in unix on your column bvec and bval, they should each have one (bval) and three (bvec) columns and no strange symbols. But you have these symbols in the bvec-file (probably because you have extra formatting information, that is not needed and an obstacle to Tracula).
more original_columns.bval
0
0
0
0
0
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
NEURO-222:tracula_help NEURO-222$ more original_columns.bvec
0 0 0
0 0 0 ^M0 0 0 ^M0 0 0 ^M0 0 0 ^M-1 0 0 ^M-0.166 0.986 0 ^M0.11 0.664 0.74 ^M-0.901 -0.419 -0.11 ^M0.169 -0.601 0.781 ^M0.815 -0.386 0.433 ^M-0.656 0.366 0.66 ^M^M-0.582 0.8 0.143 ^M-0.9 0.259 0.35 ^M-0.693 -0.698 0.178 ^M-0.357 -0.924 -0.14 ^M-0.543 -0.488 -0.683 ^M0.525 -0.396 0.753 ^M0.639 0.689 0.341 ^M0.33 -0.013 -0.944 ^M0.524 -0.783 0.335 ^M-0.609 -0.065 -0.791 ^M-0.22 -0.233 -0.947 ^M0.004 -0.91 -0.415 ^M0.511 0.627 -0.589 ^M-0.414 0.737 0.535 ^M0.679 0.139 -0.721 ^M-0.884 -0.296 0.362 ^M-0.262 0.432 0.863 ^M-0.088 0.185 -0.979 ^M-0.294 -0.907 0.302 ^M-0.887 -0.089 -0.453 ^M-0.257 -0.443 0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504 -0.025
You are ending up with multiple columns in the second row, please make sure they are 3 columns.
Good luck,
Barbara
On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp bakk.hbg@googlemail.com wrote:
Hi Michele,
Do you use the dicoms or the nifti files as input to TRACULA? Also, I think the complete trac-all.log could be even more helpful. I am a newbie myself but I am having a similar problem, so I am trying to find a solution as well :).
Best, Barbara
On Fri, Aug 29, 2014 at 4:48 PM, Michele Cavallari <miches@bwh.harvard.edu
wrote:
Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? Thanks
On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp bakk.hbg@googlemail.com wrote: Dear Michele,
I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval?
Good luck, Barbara
On 28/08/2014 22:47, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz
I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries
The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors.
I am enclosing a zip folder with attachments:
- original bvecs and bvals files organized in rows and columns
- bvecs and bvals files generated by tracula
- error logs
Let me know if you need any other information. Thanks in advance for your help.
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
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
Hi Barbara, thanks again for your help. I checked the bvecs file using the 'more' command, and (as you pointed out) there was some extra text. This was likely due to MS-excel formatting, which I have used to reshape the bvecs file from row to column configuration. Such extra text was not part of the original bvecs file organized in rows though, but tracula was not giving errors as well. So, take home message#1 It is not true that FreeSurfer 5.3 allows both rows and columns configuration of the bvecs (as stated in the wiki page). Or at least that's not true for all the scanners. I'd recommend a column configuration of the bvecs, even with FreeSurfer 5.3. Also - take home message#2 verify that there's no extra text due to excel formatting in the reshaped bvecs file.
That said, now this lead me to the next error! It seems that there's a problem with the recon-all output that I'm using (?). However, both the log file and the output of the recon-all processing seem fine to me. Here is the detail of the error message I am getting ERROR: fio_pushd: path/to/dlabel/mni And attached are the log files of both tracula pre-processing (with errors) and recon-all (apparently without errors).
Any help/suggestions? Thanks.
On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp bakk.hbg@googlemail.com wrote:
Hi Michele,
This might be the solution - try the command 'more' in unix on your column bvec and bval, they should each have one (bval) and three (bvec) columns and no strange symbols. But you have these symbols in the bvec-file (probably because you have extra formatting information, that is not needed and an obstacle to Tracula).
more original_columns.bval
0
0
0
0
0
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
NEURO-222:tracula_help NEURO-222$ more original_columns.bvec
0 0 0
0 0 0 ^M0 0 0 ^M0 0 0 ^M0 0 0 ^M-1 0 0 ^M-0.166 0.986 0 ^M0.11 0.664 0.74 ^M-0.901 -0.419 -0.11 ^M0.169 -0.601 0.781 ^M0.815 -0.386 0.433 ^M-0.656 0.366 0.66 ^M^M-0.582 0.8 0.143 ^M-0.9 0.259 0.35 ^M-0.693 -0.698 0.178 ^M-0.357 -0.924 -0.14 ^M-0.543 -0.488 -0.683 ^M0.525 -0.396 0.753 ^M0.639 0.689 0.341 ^M0.33 -0.013 -0.944 ^M0.524 -0.783 0.335 ^M-0.609 -0.065 -0.791 ^M-0.22 -0.233 -0.947 ^M0.004 -0.91 -0.415 ^M0.511 0.627 -0.589 ^M-0.414 0.737 0.535 ^M0.679 0.139 -0.721 ^M-0.884 -0.296 0.362 ^M-0.262 0.432 0.863 ^M-0.088 0.185 -0.979 ^M-0.294 -0.907 0.302 ^M-0.887 -0.089 -0.453 ^M-0.257 -0.443 0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504 -0.025
You are ending up with multiple columns in the second row, please make sure they are 3 columns.
Good luck,
Barbara
On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp < bakk.hbg@googlemail.com> wrote:
Hi Michele,
Do you use the dicoms or the nifti files as input to TRACULA? Also, I think the complete trac-all.log could be even more helpful. I am a newbie myself but I am having a similar problem, so I am trying to find a solution as well :).
Best, Barbara
On Fri, Aug 29, 2014 at 4:48 PM, Michele Cavallari < miches@bwh.harvard.edu> wrote:
Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? Thanks
On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp bakk.hbg@googlemail.com wrote: Dear Michele,
I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval?
Good luck, Barbara
On 28/08/2014 22:47, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz
I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries
The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors.
I am enclosing a zip folder with attachments:
- original bvecs and bvals files organized in rows and columns
- bvecs and bvals files generated by tracula
- error logs
Let me know if you need any other information. Thanks in advance for your help.
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
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
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 Michele,
You would have to make sure that the files are written to the same folder for both commands (recon-all and trac-all) Right now it seems you wrote the output of recon-all to /PHShome/my738/FSout/FSout_P00000401_e20130813_s002_Cor7minMDEFT_T1_b/
and trac-all output to /Users/michele/Desktop/tracula/sages_diff_test_tracula/SD000040_1/
This is what the code was looking for but did not find: Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz
What path did you specify for the T1 segmentations (by recon-all) in your configuration file?
Hope it helps, All the best, Barbara
On 03.09.14 17:31, Michele Cavallari wrote:
Hi Barbara, thanks again for your help. I checked the bvecs file using the 'more' command, and (as you pointed out) there was some extra text. This was likely due to MS-excel formatting, which I have used to reshape the bvecs file from row to column configuration. Such extra text was not part of the original bvecs file organized in rows though, but tracula was not giving errors as well. So, take home message#1 It is not true that FreeSurfer 5.3 allows both rows and columns configuration of the bvecs (as stated in the wiki page). Or at least that's not true for all the scanners. I'd recommend a column configuration of the bvecs, even with FreeSurfer 5.3. Also - take home message#2 verify that there's no extra text due to excel formatting in the reshaped bvecs file.
That said, now this lead me to the next error! It seems that there's a problem with the recon-all output that I'm using (?). However, both the log file and the output of the recon-all processing seem fine to me. Here is the detail of the error message I am getting ERROR: fio_pushd: path/to/dlabel/mni And attached are the log files of both tracula pre-processing (with errors) and recon-all (apparently without errors).
Any help/suggestions? Thanks.
On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp <bakk.hbg@googlemail.com mailto:bakk.hbg@googlemail.com> wrote:
Hi Michele, This might be the solution - try the command 'more' in unix on your column bvec and bval, they should each have one (bval) and three (bvec) columns and no strange symbols. But you have these symbols in the bvec-file (probably because you have extra formatting information, that is not needed and an obstacle to Tracula). more original_columns.bval 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 NEURO-222:tracula_help NEURO-222$ more original_columns.bvec 0 0 0 0 0 0 ^M0 0 0 ^M0 0 0 ^M0 0 0 ^M-1 0 0 ^M-0.166 0.986 0 ^M0.11 0.664 0.74 ^M-0.901 -0.419 -0.11 ^M0.169 -0.601 0.781 ^M0.815 -0.386 0.433 ^M-0.656 0.366 0.66 ^M^M-0.582 0.8 0.143 ^M-0.9 0.259 0.35 ^M-0.693 -0.698 0.178 ^M-0.357 -0.924 -0.14 ^M-0.543 -0.488 -0.683 ^M0.525 -0.396 0.753 ^M0.639 0.689 0.341 ^M0.33 -0.013 -0.944 ^M0.524 -0.783 0.335 ^M-0.609 -0.065 -0.791 ^M-0.22 -0.233 -0.947 ^M0.004 -0.91 -0.415 ^M0.511 0.627 -0.589 ^M-0.414 0.737 0.535 ^M0.679 0.139 -0.721 ^M-0.884 -0.296 0.362 ^M-0.262 0.432 0.863 ^M-0.088 0.185 -0.979 ^M-0.294 -0.907 0.302 ^M-0.887 -0.089 -0.453 ^M-0.257 -0.443 0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504 -0.025 You are ending up with multiple columns in the second row, please make sure they are 3 columns. Good luck, Barbara On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp <bakk.hbg@googlemail.com <mailto:bakk.hbg@googlemail.com>> wrote: Hi Michele, Do you use the dicoms or the nifti files as input to TRACULA? Also, I think the complete trac-all.log could be even more helpful. I am a newbie myself but I am having a similar problem, so I am trying to find a solution as well :). Best, Barbara On Fri, Aug 29, 2014 at 4:48 PM, Michele Cavallari <miches@bwh.harvard.edu <mailto:miches@bwh.harvard.edu>> wrote: Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? Thanks On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp <bakk.hbg@googlemail.com <mailto:bakk.hbg@googlemail.com>> wrote: Dear Michele, I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval? Good luck, Barbara On 28/08/2014 22:47, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors. I am enclosing a zip folder with attachments: 1) original bvecs and bvals files organized in rows and columns 2) bvecs and bvals files generated by tracula 3) error logs Let me know if you need any other information. Thanks in advance for your help. _______________________________________________ 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 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 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
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 Barbara, I checked the path. The folder with the trac-all output is is the very same folder of the dwi dicoms. Attached is the dmrirc file I am using, with all the specs. Thanks
On Wed, Sep 3, 2014 at 12:59 PM, Barbara Kreilkamp bakk.hbg@googlemail.com wrote:
Hi Michele,
You would have to make sure that the files are written to the same folder for both commands (recon-all and trac-all) Right now it seems you wrote the output of recon-all to /PHShome/my738/FSout/FSout_P00000401_e20130813_s002_Cor7minMDEFT_T1_b/
and trac-all output to /Users/michele/Desktop/tracula/sages_diff_test_tracula/SD000040_1/
This is what the code was looking for but did not find: Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz
What path did you specify for the T1 segmentations (by recon-all) in your configuration file?
Hope it helps, All the best, Barbara
On 03.09.14 17:31, Michele Cavallari wrote:
Hi Barbara, thanks again for your help. I checked the bvecs file using the 'more' command, and (as you pointed out) there was some extra text. This was likely due to MS-excel formatting, which I have used to reshape the bvecs file from row to column configuration. Such extra text was not part of the original bvecs file organized in rows though, but tracula was not giving errors as well. So, take home message#1 It is not true that FreeSurfer 5.3 allows both rows and columns configuration of the bvecs (as stated in the wiki page). Or at least that's not true for all the scanners. I'd recommend a column configuration of the bvecs, even with FreeSurfer 5.3. Also - take home message#2 verify that there's no extra text due to excel formatting in the reshaped bvecs file.
That said, now this lead me to the next error! It seems that there's a problem with the recon-all output that I'm using (?). However, both the log file and the output of the recon-all processing seem fine to me. Here is the detail of the error message I am getting ERROR: fio_pushd: path/to/dlabel/mni And attached are the log files of both tracula pre-processing (with errors) and recon-all (apparently without errors).
Any help/suggestions? Thanks.
On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp <bakk.hbg@googlemail.com
wrote:
Hi Michele,
This might be the solution - try the command 'more' in unix on your column bvec and bval, they should each have one (bval) and three (bvec) columns and no strange symbols. But you have these symbols in the bvec-file (probably because you have extra formatting information, that is not needed and an obstacle to Tracula).
more original_columns.bval
0
0
0
0
0
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
NEURO-222:tracula_help NEURO-222$ more original_columns.bvec
0 0 0
0 0 0 ^M0 0 0 ^M0 0 0 ^M0 0 0 ^M-1 0 0 ^M-0.166 0.986 0 ^M0.11 0.664 0.74 ^M-0.901 -0.419 -0.11 ^M0.169 -0.601 0.781 ^M0.815 -0.386 0.433 ^M-0.656 0.366 0.66 ^M^M-0.582 0.8 0.143 ^M-0.9 0.259 0.35 ^M-0.693 -0.698 0.178 ^M-0.357 -0.924 -0.14 ^M-0.543 -0.488 -0.683 ^M0.525 -0.396 0.753 ^M0.639 0.689 0.341 ^M0.33 -0.013 -0.944 ^M0.524 -0.783 0.335 ^M-0.609 -0.065 -0.791 ^M-0.22 -0.233 -0.947 ^M0.004 -0.91 -0.415 ^M0.511 0.627 -0.589 ^M-0.414 0.737 0.535 ^M0.679 0.139 -0.721 ^M-0.884 -0.296 0.362 ^M-0.262 0.432 0.863 ^M-0.088 0.185 -0.979 ^M-0.294 -0.907 0.302 ^M-0.887 -0.089 -0.453 ^M-0.257 -0.443 0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504 -0.025
You are ending up with multiple columns in the second row, please make sure they are 3 columns.
Good luck,
Barbara
On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp < bakk.hbg@googlemail.com> wrote:
Hi Michele,
Do you use the dicoms or the nifti files as input to TRACULA? Also, I think the complete trac-all.log could be even more helpful. I am a newbie myself but I am having a similar problem, so I am trying to find a solution as well :).
Best, Barbara
On Fri, Aug 29, 2014 at 4:48 PM, Michele Cavallari < miches@bwh.harvard.edu> wrote:
Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? Thanks
On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp bakk.hbg@googlemail.com wrote: Dear Michele,
I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval?
Good luck, Barbara
On 28/08/2014 22:47, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz
I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries
The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors.
I am enclosing a zip folder with attachments:
- original bvecs and bvals files organized in rows and columns
- bvecs and bvals files generated by tracula
- error logs
Let me know if you need any other information. Thanks in advance for your help.
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
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
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 listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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.
-- Barbara Kreilkamp
PhD Candidate
Magnetic Resonance and Image Analysis Research Center
University of Liverpool B.Kreilkamp@Liverpool.ac.uk http://www.liverpool.ac.uk
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 Michele,
Yes, tracula would have complained at the very first call, if the dwi data was not there.
So here is the problem, you write: setenv /Users/michele/Desktop/tracula/sages_diff_test_tracula/SD000040_1/FSout_P00000401_e20130813_s002_Cor7minMDEFT_T1_b
in the very first line in your config file, it should read
setenv SUBJECTS_DIR /Users/michele/Desktop/tracula/sages_diff_test_tracula/SD000040_1/FSout_P00000401_e20130813_s002_Cor7minMDEFT_T1_b
The problem was that recon-all files were not found (because the path was never set to the right environment variable SUBJECTS_DIR. Try now.
Best, Barbara
On 03/09/2014 18:04, Michele Cavallari wrote:
Hi Barbara, I checked the path. The folder with the trac-all output is is the very same folder of the dwi dicoms. Attached is the dmrirc file I am using, with all the specs. Thanks
On Wed, Sep 3, 2014 at 12:59 PM, Barbara Kreilkamp <bakk.hbg@googlemail.com mailto:bakk.hbg@googlemail.com> wrote:
Hi Michele, You would have to make sure that the files are written to the same folder for both commands (recon-all and trac-all) Right now it seems you wrote the output of recon-all to /PHShome/my738/FSout/FSout_P00000401_e20130813_s002_Cor7minMDEFT_T1_b/ and trac-all output to /Users/michele/Desktop/tracula/sages_diff_test_tracula/SD000040_1/ This is what the code was looking for but did not find: Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz What path did you specify for the T1 segmentations (by recon-all) in your configuration file? Hope it helps, All the best, Barbara On 03.09.14 17:31, Michele Cavallari wrote:Hi Barbara, thanks again for your help. I checked the bvecs file using the 'more' command, and (as you pointed out) there was some extra text. This was likely due to MS-excel formatting, which I have used to reshape the bvecs file from row to column configuration. Such extra text was not part of the original bvecs file organized in rows though, but tracula was not giving errors as well. So, take home message#1 It is not true that FreeSurfer 5.3 allows both rows and columns configuration of the bvecs (as stated in the wiki page). Or at least that's not true for all the scanners. I'd recommend a column configuration of the bvecs, even with FreeSurfer 5.3. Also - take home message#2 verify that there's no extra text due to excel formatting in the reshaped bvecs file. That said, now this lead me to the next error! It seems that there's a problem with the recon-all output that I'm using (?). However, both the log file and the output of the recon-all processing seem fine to me. Here is the detail of the error message I am getting ERROR: fio_pushd: path/to/dlabel/mni And attached are the log files of both tracula pre-processing (with errors) and recon-all (apparently without errors). Any help/suggestions? Thanks. On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp <bakk.hbg@googlemail.com <mailto:bakk.hbg@googlemail.com>> wrote: Hi Michele, This might be the solution - try the command 'more' in unix on your column bvec and bval, they should each have one (bval) and three (bvec) columns and no strange symbols. But you have these symbols in the bvec-file (probably because you have extra formatting information, that is not needed and an obstacle to Tracula). more original_columns.bval 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 NEURO-222:tracula_help NEURO-222$ more original_columns.bvec 0 0 0 0 0 0 ^M0 0 0 ^M0 0 0 ^M0 0 0 ^M-1 0 0 ^M-0.166 0.986 0 ^M0.11 0.664 0.74 ^M-0.901 -0.419 -0.11 ^M0.169 -0.601 0.781 ^M0.815 -0.386 0.433 ^M-0.656 0.366 0.66 ^M^M-0.582 0.8 0.143 ^M-0.9 0.259 0.35 ^M-0.693 -0.698 0.178 ^M-0.357 -0.924 -0.14 ^M-0.543 -0.488 -0.683 ^M0.525 -0.396 0.753 ^M0.639 0.689 0.341 ^M0.33 -0.013 -0.944 ^M0.524 -0.783 0.335 ^M-0.609 -0.065 -0.791 ^M-0.22 -0.233 -0.947 ^M0.004 -0.91 -0.415 ^M0.511 0.627 -0.589 ^M-0.414 0.737 0.535 ^M0.679 0.139 -0.721 ^M-0.884 -0.296 0.362 ^M-0.262 0.432 0.863 ^M-0.088 0.185 -0.979 ^M-0.294 -0.907 0.302 ^M-0.887 -0.089 -0.453 ^M-0.257 -0.443 0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504 -0.025 You are ending up with multiple columns in the second row, please make sure they are 3 columns. Good luck, Barbara On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp <bakk.hbg@googlemail.com <mailto:bakk.hbg@googlemail.com>> wrote: Hi Michele, Do you use the dicoms or the nifti files as input to TRACULA? Also, I think the complete trac-all.log could be even more helpful. I am a newbie myself but I am having a similar problem, so I am trying to find a solution as well :). Best, Barbara On Fri, Aug 29, 2014 at 4:48 PM, Michele Cavallari <miches@bwh.harvard.edu <mailto:miches@bwh.harvard.edu>> wrote: Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? Thanks On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp <bakk.hbg@googlemail.com <mailto:bakk.hbg@googlemail.com>> wrote: Dear Michele, I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval? Good luck, Barbara On 28/08/2014 22:47, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors. I am enclosing a zip folder with attachments: 1) original bvecs and bvals files organized in rows and columns 2) bvecs and bvals files generated by tracula 3) error logs Let me know if you need any other information. Thanks in advance for your help. _______________________________________________ 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 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 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 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.-- Barbara Kreilkamp PhD Candidate Magnetic Resonance and Image Analysis Research Center University of Liverpool B.Kreilkamp@Liverpool.ac.uk <mailto:B.Kreilkamp@Liverpool.ac.uk> http://www.liverpool.ac.uk _______________________________________________ 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 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 Michelle - Try replacing this line: setenv /Users/michele/Desktop/tracula/sages_diff_test_tracula/SD000040_1/FSout_P00000401_e20130813_s002_Cor7minMDEFT_T1_b
with: setenv SUBJECTS_DIR /PHShome/my738/FSout
(Or whatever the location of your freesurfer recons is.)
a.y
On Wed, 3 Sep 2014, Michele Cavallari wrote:
Hi Barbara,I checked the path. The folder with the trac-all output is is the very same folder of the dwi dicoms. Attached is the dmrirc file I am using, with all the specs. Thanks
On Wed, Sep 3, 2014 at 12:59 PM, Barbara Kreilkamp bakk.hbg@googlemail.com wrote: Hi Michele,
You would have to make sure that the files are written to the same folder for both commands (recon-all and trac-all) Right now it seems you wrote the output of recon-all to /PHShome/my738/FSout/FSout_P00000401_e20130813_s002_Cor7minMDEFT_T1_b/ and trac-all output to /Users/michele/Desktop/tracula/sages_diff_test_tracula/SD000040_1/ This is what the code was looking for but did not find: Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz What path did you specify for the T1 segmentations (by recon-all) in your configuration file? Hope it helps, All the best, Barbara On 03.09.14 17:31, Michele Cavallari wrote: Hi Barbara, thanks again for your help.I checked the bvecs file using the 'more' command, and (as you pointed out) there was some extra text. This was likely due to MS-excel formatting, which I have used to reshape the bvecs file from row to column configuration. Such extra text was not part of the original bvecs file organized in rows though, but tracula was not giving errors as well. So, take home message#1 It is not true that FreeSurfer 5.3 allows both rows and columns configuration of the bvecs (as stated in the wiki page). Or at least that's not true for all the scanners. I'd recommend a column configuration of the bvecs, even with FreeSurfer 5.3. Also - take home message#2 verify that there's no extra text due to excel formatting in the reshaped bvecs file.
That said, now this lead me to the next error! It seems that there's a problem with the recon-all output that I'm using (?). However, both the log file and the output of the recon-all processing seem fine to me. Here is the detail of the error message I am getting ERROR: fio_pushd: path/to/dlabel/mni And attached are the log files of both tracula pre-processing (with errors) and recon-all (apparently without errors).
Any help/suggestions? Thanks.
On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp bakk.hbg@googlemail.com wrote: Hi Michele, This might be the solution - try the command 'more' in unix on your column bvec and bval, they should each have one (bval) and three (bvec) columns and no strange symbols. But you have these symbols in the bvec-file (probably because you have extra formatting information, that is not needed and an obstacle to Tracula).
more original_columns.bval
0
0
0
0
0
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
NEURO-222:tracula_help NEURO-222$ more original_columns.bvec
0 0 0
0 0 0 ^M0 0 0 ^M0 0 0 ^M0 0 0 ^M-1 0 0 ^M-0.166 0.986 0 ^M0.11 0.664 0.74 ^M-0.901 -0.419 -0.11 ^M0.169 -0.601 0.781 ^M0.815 -0.386 0.433 ^M-0.656 0.366 0.66 ^M^M-0.582 0.8 0.143 ^M-0.9 0.259 0.35 ^M-0.693 -0.698 0.178 ^M-0.357 -0.924 -0.14 ^M-0.543 -0.488 -0.683 ^M0.525 -0.396 0.753 ^M0.639 0.689 0.341 ^M0.33 -0.013 -0.944 ^M0.524 -0.783 0.335 ^M-0.609 -0.065 -0.791 ^M-0.22 -0.233 -0.947 ^M0.004 -0.91 -0.415 ^M0.511 0.627 -0.589 ^M-0.414 0.737 0.535 ^M0.679 0.139 -0.721 ^M-0.884 -0.296 0.362 ^M-0.262 0.432 0.863 ^M-0.088 0.185 -0.979 ^M-0.294 -0.907 0.302 ^M-0.887 -0.089 -0.453 ^M-0.257 -0.443 0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504 -0.025
You are ending up with multiple columns in the second row, please make sure they are 3 columns.
Good luck,
Barbara
On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp bakk.hbg@googlemail.com wrote: Hi Michele,
Do you use the dicoms or the nifti files as input to TRACULA? Also, I think the complete trac-all.log could be even more helpful. I am a newbie myself but I am having a similar problem, so I am trying to find a solution as well :). Best, BarbaraOn Fri, Aug 29, 2014 at 4:48 PM, Michele Cavallari miches@bwh.harvard.edu wrote: Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? Thanks
On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp <bakk.hbg@googlemail.com> wrote: Dear Michele, I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval? Good luck, Barbara On 28/08/2014 22:47, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors. I am enclosing a zip folder with attachments: 1) original bvecs and bvals files organized in rows and columns 2) bvecs and bvals files generated by tracula 3) error logs Let me know if you need any other information. Thanks in advance for your help. _______________________________________________ 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 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
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
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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail.
Thanks Anastasia. I figured out the right path, and I'm now running the 2nd step of tracula pipeline on that case. There was a problem with subdirectories (my fault). And also the missing 'SUBJECTS_DIR' syntax in the setenv command, as both you and Barbara pointed out. Thanks again for your help
On Thu, Sep 4, 2014 at 5:22 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Michelle - Try replacing this line: setenv /Users/michele/Desktop/tracula/sages_diff_test_ tracula/SD000040_1/FSout_P00000401_e20130813_s002_Cor7minMDEFT_T1_b
with: setenv SUBJECTS_DIR /PHShome/my738/FSout
(Or whatever the location of your freesurfer recons is.)
a.y
On Wed, 3 Sep 2014, Michele Cavallari wrote:
Hi Barbara,I checked the path. The folder with the trac-all output is is
the
very same folder of the dwi dicoms. Attached is the dmrirc file I am using, with all the specs. Thanks
On Wed, Sep 3, 2014 at 12:59 PM, Barbara Kreilkamp < bakk.hbg@googlemail.com> wrote: Hi Michele,
You would have to make sure that the files are written to the same folder for both commands (recon-all and trac-all) Right now it seems you wrote the output of recon-all to /PHShome/my738/FSout/FSout_P00000401_e20130813_s002_Cor7minMDEFT_T1_b/
and trac-all output to /Users/michele/Desktop/tracula/sages_diff_test_tracula/SD000040_1/ This is what the code was looking for but did not find: Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz What path did you specify for the T1 segmentations (by recon-all) in your configuration file? Hope it helps, All the best, Barbara On 03.09.14 17:31, Michele Cavallari wrote: Hi Barbara, thanks again for your help.I checked the bvecs file using the 'more' command, and (as you pointed out) there was some extra text. This was likely due to MS-excel formatting, which I have used to reshape the bvecs file from row to column configuration. Such extra text was not part of the original bvecs file organized in rows though, but tracula was not giving errors as well. So, take home message#1 It is not true that FreeSurfer 5.3 allows both rows and columns configuration of the bvecs (as stated in the wiki page). Or at least that's not true for all the scanners. I'd recommend a column configuration of the bvecs, even with FreeSurfer 5.3. Also - take home message#2 verify that there's no extra text due to excel formatting in the reshaped bvecs file.
That said, now this lead me to the next error! It seems that there's a problem with the recon-all output that I'm using (?). However, both the log file and the output of the recon-all processing seem fine to me. Here is the detail of the error message I am getting ERROR: fio_pushd: path/to/dlabel/mni And attached are the log files of both tracula pre-processing (with errors) and recon-all (apparently without errors).
Any help/suggestions? Thanks.
On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp bakk.hbg@googlemail.com wrote: Hi Michele, This might be the solution - try the command 'more' in unix on your column bvec and bval, they should each have one (bval) and three (bvec) columns and no strange symbols. But you have these symbols in the bvec-file (probably because you have extra formatting information, that is not needed and an obstacle to Tracula).
more original_columns.bval
0
0
0
0
0
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
NEURO-222:tracula_help NEURO-222$ more original_columns.bvec
0 0 0
0 0 0 ^M0 0 0 ^M0 0 0 ^M0 0 0 ^M-1 0 0 ^M-0.166 0.986 0 ^M0.11 0.664 0.74 ^M-0.901 -0.419 -0.11 ^M0.169 -0.601 0.781 ^M0.815 -0.386 0.433 ^M-0.656 0.366 0.66 ^M^M-0.582 0.8 0.143 ^M-0.9 0.259 0.35 ^M-0.693 -0.698 0.178 ^M-0.357 -0.924 -0.14 ^M-0.543 -0.488 -0.683 ^M0.525 -0.396 0.753 ^M0.639 0.689 0.341 ^M0.33 -0.013 -0.944 ^M0.524 -0.783 0.335 ^M-0.609 -0.065 -0.791 ^M-0.22 -0.233 -0.947 ^M0.004 -0.91 -0.415 ^M0.511 0.627 -0.589 ^M-0.414 0.737 0.535 ^M0.679 0.139 -0.721 ^M-0.884 -0.296 0.362 ^M-0.262 0.432 0.863 ^M-0.088 0.185 -0.979 ^M-0.294 -0.907 0.302 ^M-0.887 -0.089 -0.453 ^M-0.257 -0.443 0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504 -0.025
You are ending up with multiple columns in the second row, please make sure they are 3 columns.
Good luck,
Barbara
On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp bakk.hbg@googlemail.com wrote: Hi Michele,
Do you use the dicoms or the nifti files as input to TRACULA? Also, I think the complete trac-all.log could be even more helpful. I am a newbie myself but I am having a similar problem, so I am trying to find a solution as well :). Best, BarbaraOn Fri, Aug 29, 2014 at 4:48 PM, Michele Cavallari miches@bwh.harvard.edu wrote: Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? Thanks
On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp <bakk.hbg@googlemail.com> wrote: Dear Michele, I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval? Good luck, Barbara On 28/08/2014 22:47, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors. I am enclosing a zip folder with attachments: 1) original bvecs and bvals files organized in rows and columns 2) bvecs and bvals files generated by tracula 3) error logs Let me know if you need any other information. Thanks in advance for your help. _______________________________________________ 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 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
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
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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail.
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 Michelle - Based on your recon-all.log, your SUBJECTS_DIR that contains the freesurfer recon of your subject is /PHShome/my738/FSout. But based on you trac-all.log, you're using: SUBJECTS_DIR /Users/michele/Desktop/tracula/sages_diff_test_tracula
So tracula cannot find the freesurfer recon of your subject. This is what's causing the latest error.
About the confusion with the gradient table formats: The tutorials refer to the latest version of tracula, which has been updated since the 5.3 release. The newer features included in those updates are described here: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates
Hope this helps, a.y
On Wed, 3 Sep 2014, Michele Cavallari wrote:
Hi Barbara,thanks again for your help. I checked the bvecs file using the 'more' command, and (as you pointed out) there was some extra text. This was likely due to MS-excel formatting, which I have used to reshape the bvecs file from row to column configuration. Such extra text was not part of the original bvecs file organized in rows though, but tracula was not giving errors as well. So, take home message#1 It is not true that FreeSurfer 5.3 allows both rows and columns configuration of the bvecs (as stated in the wiki page). Or at least that's not true for all the scanners. I'd recommend a column configuration of the bvecs, even with FreeSurfer 5.3. Also - take home message#2 verify that there's no extra text due to excel formatting in the reshaped bvecs file.
That said, now this lead me to the next error! It seems that there's a problem with the recon-all output that I'm using (?). However, both the log file and the output of the recon-all processing seem fine to me. Here is the detail of the error message I am getting ERROR: fio_pushd: path/to/dlabel/mni And attached are the log files of both tracula pre-processing (with errors) and recon-all (apparently without errors).
Any help/suggestions? Thanks.
On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp bakk.hbg@googlemail.com wrote: Hi Michele, This might be the solution - try the command 'more' in unix on your column bvec and bval, they should each have one (bval) and three (bvec) columns and no strange symbols. But you have these symbols in the bvec-file (probably because you have extra formatting information, that is not needed and an obstacle to Tracula).
more original_columns.bval
0
0
0
0
0
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
NEURO-222:tracula_help NEURO-222$ more original_columns.bvec
0 0 0
0 0 0 ^M0 0 0 ^M0 0 0 ^M0 0 0 ^M-1 0 0 ^M-0.166 0.986 0 ^M0.11 0.664 0.74 ^M-0.901 -0.419 -0.11 ^M0.169 -0.601 0.781 ^M0.815 -0.386 0.433 ^M-0.656 0.366 0.66 ^M^M-0.582 0.8 0.143 ^M-0.9 0.259 0.35 ^M-0.693 -0.698 0.178 ^M-0.357 -0.924 -0.14 ^M-0.543 -0.488 -0.683 ^M0.525 -0.396 0.753 ^M0.639 0.689 0.341 ^M0.33 -0.013 -0.944 ^M0.524 -0.783 0.335 ^M-0.609 -0.065 -0.791 ^M-0.22 -0.233 -0.947 ^M0.004 -0.91 -0.415 ^M0.511 0.627 -0.589 ^M-0.414 0.737 0.535 ^M0.679 0.139 -0.721 ^M-0.884 -0.296 0.362 ^M-0.262 0.432 0.863 ^M-0.088 0.185 -0.979 ^M-0.294 -0.907 0.302 ^M-0.887 -0.089 -0.453 ^M-0.257 -0.443 0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504 -0.025
You are ending up with multiple columns in the second row, please make sure they are 3 columns.
Good luck,
Barbara
On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp bakk.hbg@googlemail.com wrote: Hi Michele,
Do you use the dicoms or the nifti files as input to TRACULA? Also, I think the complete trac-all.log could be even more helpful. I am a newbie myself but I am having a similar problem, so I am trying to find a solution as well :). Best, BarbaraOn Fri, Aug 29, 2014 at 4:48 PM, Michele Cavallari miches@bwh.harvard.edu wrote: Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? Thanks
On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp <bakk.hbg@googlemail.com> wrote: Dear Michele, I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval? Good luck, Barbara On 28/08/2014 22:47, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors. I am enclosing a zip folder with attachments: 1) original bvecs and bvals files organized in rows and columns 2) bvecs and bvals files generated by tracula 3) error logs Let me know if you need any other information. Thanks in advance for your help. _______________________________________________ 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 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
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@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Barbara Kreilkamp -
Michele Cavallari -
Michele Cavallari