Can you verify that that run has the proper number of frames (eg, it
does not have a single frame)? Did it create fmcpr.mcdat and/or
mcdat2extreg.log? In the projectdir/log folder, there should be a file
with a name like /mc-subjectname-bold.log. Can you send that?
mcdat2extreg.log? In the projectdir/log folder, there should be a file
with a name like /mc-subjectname-bold.log. Can you send that?
with a name like /mc-subjectname-bold.log. Can you send that?
On 4/10/19 4:30 PM, Mcnorgan, Christopher wrote:
>
> External Email - Use Caution
>
> Hello, I���ve been trying to get to the bottom of why selxavg3-sess is
> failing for lack of a mcprextreg motion correction parameters file for
> one or more of the functional runs.
> I have 6 runs of BOLD data, and following the last failed attempt, we
> cleared out the run folders to start again from scratch with
> preprocess on the f.nii volumes.
>
> We are running preproc-sess on a per-run basis:
> preproc-sess -sSUBJECTNAME -per-run -surface fsaverage lhrh -mni305 -fsd
> bold-fwhm 4 -sliceorder up
> After doing this, we find that the folders for runs 1,2,3,4 and 6
> contain the file mcprextreg, but run 5 does not. Consequently,
> selxavg3-sess throws an error and aborts when it fails to find this
> file for run 5. Prior to our do-over, we had the same issue, so it
> appears that this file is reliably not being generated only for run 5.
> To further the mystery, a second dataset (different participant) was
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> Hello, I���ve been trying to get to the bottom of why selxavg3-sess is
> failing for lack of a mcprextreg motion correction parameters file for
> one or more of the functional runs.
> I have 6 runs of BOLD data, and following the last failed attempt, we
> cleared out the run folders to start again from scratch with
> preprocess on the f.nii volumes.
>
> We are running preproc-sess on a per-run basis:
> preproc-sess -sSUBJECTNAME -per-run -surface fsaverage lhrh -mni305 -fsd
> bold-fwhm 4 -sliceorder up
> After doing this, we find that the folders for runs 1,2,3,4 and 6
> contain the file mcprextreg, but run 5 does not. Consequently,
> selxavg3-sess throws an error and aborts when it fails to find this
> file for run 5. Prior to our do-over, we had the same issue, so it
> appears that this file is reliably not being generated only for run 5.
> To further the mystery, a second dataset (different participant) was
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> failing for lack of a mcprextreg motion correction parameters file for
> one or more of the functional runs.
> I have 6 runs of BOLD data, and following the last failed attempt, we
> cleared out the run folders to start again from scratch with
> preprocess on the f.nii volumes.
>
> We are running preproc-sess on a per-run basis:
> preproc-sess -sSUBJECTNAME -per-run -surface fsaverage lhrh -mni305 -fsd
> bold-fwhm 4 -sliceorder up
> After doing this, we find that the folders for runs 1,2,3,4 and 6
> contain the file mcprextreg, but run 5 does not. Consequently,
> selxavg3-sess throws an error and aborts when it fails to find this
> file for run 5. Prior to our do-over, we had the same issue, so it
> appears that this file is reliably not being generated only for run 5.
> To further the mystery, a second dataset (different participant) was
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> one or more of the functional runs.
> I have 6 runs of BOLD data, and following the last failed attempt, we
> cleared out the run folders to start again from scratch with
> preprocess on the f.nii volumes.
>
> We are running preproc-sess on a per-run basis:
> preproc-sess -sSUBJECTNAME -per-run -surface fsaverage lhrh -mni305 -fsd
> bold-fwhm 4 -sliceorder up
> After doing this, we find that the folders for runs 1,2,3,4 and 6
> contain the file mcprextreg, but run 5 does not. Consequently,
> selxavg3-sess throws an error and aborts when it fails to find this
> file for run 5. Prior to our do-over, we had the same issue, so it
> appears that this file is reliably not being generated only for run 5.
> To further the mystery, a second dataset (different participant) was
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> I have 6 runs of BOLD data, and following the last failed attempt, we
> cleared out the run folders to start again from scratch with
> preprocess on the f.nii volumes.
>
> We are running preproc-sess on a per-run basis:
> preproc-sess -sSUBJECTNAME -per-run -surface fsaverage lhrh -mni305 -fsd
> bold-fwhm 4 -sliceorder up
> After doing this, we find that the folders for runs 1,2,3,4 and 6
> contain the file mcprextreg, but run 5 does not. Consequently,
> selxavg3-sess throws an error and aborts when it fails to find this
> file for run 5. Prior to our do-over, we had the same issue, so it
> appears that this file is reliably not being generated only for run 5.
> To further the mystery, a second dataset (different participant) was
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> cleared out the run folders to start again from scratch with
> preprocess on the f.nii volumes.
>
> We are running preproc-sess on a per-run basis:
> preproc-sess -sSUBJECTNAME -per-run -surface fsaverage lhrh -mni305 -fsd
> bold-fwhm 4 -sliceorder up
> After doing this, we find that the folders for runs 1,2,3,4 and 6
> contain the file mcprextreg, but run 5 does not. Consequently,
> selxavg3-sess throws an error and aborts when it fails to find this
> file for run 5. Prior to our do-over, we had the same issue, so it
> appears that this file is reliably not being generated only for run 5.
> To further the mystery, a second dataset (different participant) was
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> preprocess on the f.nii volumes.
>
> We are running preproc-sess on a per-run basis:
> preproc-sess -sSUBJECTNAME -per-run -surface fsaverage lhrh -mni305 -fsd
> bold-fwhm 4 -sliceorder up
> After doing this, we find that the folders for runs 1,2,3,4 and 6
> contain the file mcprextreg, but run 5 does not. Consequently,
> selxavg3-sess throws an error and aborts when it fails to find this
> file for run 5. Prior to our do-over, we had the same issue, so it
> appears that this file is reliably not being generated only for run 5.
> To further the mystery, a second dataset (different participant) was
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
>
> We are running preproc-sess on a per-run basis:
> preproc-sess -sSUBJECTNAME -per-run -surface fsaverage lhrh -mni305 -fsd
> bold-fwhm 4 -sliceorder up
> After doing this, we find that the folders for runs 1,2,3,4 and 6
> contain the file mcprextreg, but run 5 does not. Consequently,
> selxavg3-sess throws an error and aborts when it fails to find this
> file for run 5. Prior to our do-over, we had the same issue, so it
> appears that this file is reliably not being generated only for run 5.
> To further the mystery, a second dataset (different participant) was
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> preproc-sess -sSUBJECTNAME -per-run -surface fsaverage lhrh -mni305 -fsd
> bold-fwhm 4 -sliceorder up
> After doing this, we find that the folders for runs 1,2,3,4 and 6
> contain the file mcprextreg, but run 5 does not. Consequently,
> selxavg3-sess throws an error and aborts when it fails to find this
> file for run 5. Prior to our do-over, we had the same issue, so it
> appears that this file is reliably not being generated only for run 5.
> To further the mystery, a second dataset (different participant) was
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> bold-fwhm 4 -sliceorder up
> After doing this, we find that the folders for runs 1,2,3,4 and 6
> contain the file mcprextreg, but run 5 does not. Consequently,
> selxavg3-sess throws an error and aborts when it fails to find this
> file for run 5. Prior to our do-over, we had the same issue, so it
> appears that this file is reliably not being generated only for run 5.
> To further the mystery, a second dataset (different participant) was
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> bold-fwhm 4 -sliceorder up
> After doing this, we find that the folders for runs 1,2,3,4 and 6
> contain the file mcprextreg, but run 5 does not. Consequently,
> selxavg3-sess throws an error and aborts when it fails to find this
> file for run 5. Prior to our do-over, we had the same issue, so it
> appears that this file is reliably not being generated only for run 5.
> To further the mystery, a second dataset (different participant) was
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> contain the file mcprextreg, but run 5 does not. Consequently,
> selxavg3-sess throws an error and aborts when it fails to find this
> file for run 5. Prior to our do-over, we had the same issue, so it
> appears that this file is reliably not being generated only for run 5.
> To further the mystery, a second dataset (different participant) was
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> selxavg3-sess throws an error and aborts when it fails to find this
> file for run 5. Prior to our do-over, we had the same issue, so it
> appears that this file is reliably not being generated only for run 5.
> To further the mystery, a second dataset (different participant) was
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> file for run 5. Prior to our do-over, we had the same issue, so it
> appears that this file is reliably not being generated only for run 5.
> To further the mystery, a second dataset (different participant) was
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> appears that this file is reliably not being generated only for run 5.
> To further the mystery, a second dataset (different participant) was
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> To further the mystery, a second dataset (different participant) was
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> I notice that the runs with the missing motion correction parameter
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> each contain a tmpdir.mcdat2extreg.##### folder, which suggests that
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> the process might have not completed, though it���s odd that it would
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> I was hoping someone might have some suggestions for debugging why
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> this file might not be getting generated, as well as what steps might
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> be taken to force its creation. I���m going to start by deleting the
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> *
> * University at Buffalo,
> * The State University of New York
> *
> * The State University of New York
> *
> *
* http://ccnlab.buffalo.edu/
> * Office: 716.645.0236
> * Lab: 716.645.0222
> **********************************************/
> **********************************************/
************************/