Dear. Freesurfer team.
Hi.
I'm using freesurfer 4.5 version.
While doing the motion correction, an error occurred.
the command I used: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003
the error I have: /home/jbang/Projects/replay/epi/replay01/bold_retino 3dvolreg -verbose -dfile 025/fmc.mcdat -base 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 025/tmp.mc-afni2.32291/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868 degrees from plumb. ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 degrees from plumb. ++ centers of base and input datasets are 9.09 mm apart ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD don't have same dimensions! Input: nx=74 ny=74 nz=32 Base: nx=74 ny=74 nz=33 ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command.
I think it's because the volume size is different.
The volume size for bold_retino is: number of slices 32 The volume size for bold_decode: number of slices 33
What should I do to correct this error?
Thank you for taking your time.
Best, Ji Won
Dear. Freesurfer team.
I'd appreciate any advice from you.
When doing the motion correction, I'd like to align all EPI data(bold_retino) to the first EPI of target run(bold_decode/003). However, the number of slices for target run(33) and the number of slices(32) for input run(bold_retino) are different.
When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003
Freesurfer says that: ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command.
These two kinds of run (bold_decode, bold_retino) were collected in one scan per subject, so the head position should not be too different...
Do you have any suggestions for fixing this error?
Should I do 3dWarp -deoblique?
Thank you so much.
Best, Ji Won
2016-02-08 16:30 GMT-05:00 Ji Won Bang kirstens03@gmail.com:
Dear. Freesurfer team.
Hi.
I'm using freesurfer 4.5 version.
While doing the motion correction, an error occurred.
the command I used: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003
the error I have: /home/jbang/Projects/replay/epi/replay01/bold_retino 3dvolreg -verbose -dfile 025/fmc.mcdat -base 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 025/tmp.mc-afni2.32291/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868 degrees from plumb. ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 degrees from plumb. ++ centers of base and input datasets are 9.09 mm apart ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD don't have same dimensions! Input: nx=74 ny=74 nz=32 Base: nx=74 ny=74 nz=33 ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command.
I think it's because the volume size is different.
The volume size for bold_retino is: number of slices 32 The volume size for bold_decode: number of slices 33
What should I do to correct this error?
Thank you for taking your time.
Best, Ji Won
Dear. Freesurfer team.
As another attempt, I run the motion correction without the argument -targrun:
mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
However, I get the same error message again.
Why is that?
Thanks so much for your effort and time.
I appreciate it a lot.
Best, Ji Won
2016-02-08 17:16 GMT-05:00 Ji Won Bang kirstens03@gmail.com:
Dear. Freesurfer team.
I'd appreciate any advice from you.
When doing the motion correction, I'd like to align all EPI data(bold_retino) to the first EPI of target run(bold_decode/003). However, the number of slices for target run(33) and the number of slices(32) for input run(bold_retino) are different.
When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003
Freesurfer says that: ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command.
These two kinds of run (bold_decode, bold_retino) were collected in one scan per subject, so the head position should not be too different...
Do you have any suggestions for fixing this error?
Should I do 3dWarp -deoblique?
Thank you so much.
Best, Ji Won
2016-02-08 16:30 GMT-05:00 Ji Won Bang kirstens03@gmail.com:
Dear. Freesurfer team.
Hi.
I'm using freesurfer 4.5 version.
While doing the motion correction, an error occurred.
the command I used: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003
the error I have: /home/jbang/Projects/replay/epi/replay01/bold_retino 3dvolreg -verbose -dfile 025/fmc.mcdat -base 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 025/tmp.mc-afni2.32291/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868 degrees from plumb. ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 degrees from plumb. ++ centers of base and input datasets are 9.09 mm apart ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD don't have same dimensions! Input: nx=74 ny=74 nz=32 Base: nx=74 ny=74 nz=33 ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command.
I think it's because the volume size is different.
The volume size for bold_retino is: number of slices 32 The volume size for bold_decode: number of slices 33
What should I do to correct this error?
Thank you for taking your time.
Best, Ji Won
In 4.5 I don't think there is a way to run it when different runs have different number of slices. Version 5+ will handle it properly. If you really want to use 4.5, then you'll have to put it in a different functional subdir (FSD, eg, bold), and create a new analysis for it, then combine them together after analysis. A bit of a hassle.
On 2/8/16 5:58 PM, Ji Won Bang wrote:
Dear. Freesurfer team.
As another attempt, I run the motion correction without the argument -targrun:
mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
However, I get the same error message again.
Why is that?
Thanks so much for your effort and time.
I appreciate it a lot.
Best, Ji Won
2016-02-08 17:16 GMT-05:00 Ji Won Bang <kirstens03@gmail.com mailto:kirstens03@gmail.com>:
Dear. Freesurfer team. I'd appreciate any advice from you. When doing the motion correction, I'd like to align all EPI data(bold_retino) to the first EPI of target run(bold_decode/003). However, the number of slices for target run(33) and the number of slices(32) for input run(bold_retino) are different. When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003 Freesurfer says that: ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command. These two kinds of run (bold_decode, bold_retino) were collected in one scan per subject, so the head position should not be too different... Do you have any suggestions for fixing this error? Should I do 3dWarp -deoblique? Thank you so much. Best, Ji Won 2016-02-08 16:30 GMT-05:00 Ji Won Bang <kirstens03@gmail.com <mailto:kirstens03@gmail.com>>: Dear. Freesurfer team. Hi. I'm using freesurfer 4.5 version. While doing the motion correction, an error occurred. the command I used: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003 the error I have: /home/jbang/Projects/replay/epi/replay01/bold_retino 3dvolreg -verbose -dfile 025/fmc.mcdat -base 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 025/tmp.mc-afni2.32291/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868 degrees from plumb. ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 degrees from plumb. ++ centers of base and input datasets are 9.09 mm apart ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD don't have same dimensions! Input: nx=74 ny=74 nz=32 Base: nx=74 ny=74 nz=33 ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command. I think it's because the volume size is different. The volume size for bold_retino is: number of slices 32 The volume size for bold_decode: number of slices 33 What should I do to correct this error? Thank you for taking your time. Best, Ji Won
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear. Freesurfer team.
Thanks so much your help and advice.
Based on the comments, I'm trying freesurfer version 5.3.0 instead of 4.5.0 now.
In our experiment, each participant is scanned twice on different days and the functional scan's brain volume are different (some scans have 33 number of slices, some have 32 number of slices).
Since participants moved a bit between scans on the same day, and the head position is different between different days, my advisor advised me to do co-registration between different functional scans and then do co-registration between anatomical and functional scans.
My question is this.
If I do motion-correction such that we align all EPI data to the first EPI of the first functional scan, will it be enough for co-registration between different functional scans and different days? Or should I do coregistration-specific process such as mri_robust_register, mri_robust_template etc?
Or I guess the method I choose should depend on how much the participant moved between scans and how much different the head position was between different days? For example, if the participant was very still between runs and the head position was not that too different, this motion correction is enough for coregistration between functional scans. However, if not, I should do coregistration-specific process such as mri_robust_register, mri_robust_template etc?
I'd appreciate any of your advice.
Please feel free to let me know your thoughts.
Best, Ji Won
2016-02-08 22:31 GMT-05:00 Douglas Greve greve@nmr.mgh.harvard.edu:
In 4.5 I don't think there is a way to run it when different runs have different number of slices. Version 5+ will handle it properly. If you really want to use 4.5, then you'll have to put it in a different functional subdir (FSD, eg, bold), and create a new analysis for it, then combine them together after analysis. A bit of a hassle.
On 2/8/16 5:58 PM, Ji Won Bang wrote:
Dear. Freesurfer team.
As another attempt, I run the motion correction without the argument -targrun:
mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
However, I get the same error message again.
Why is that?
Thanks so much for your effort and time.
I appreciate it a lot.
Best, Ji Won
2016-02-08 17:16 GMT-05:00 Ji Won Bang kirstens03@gmail.com:
Dear. Freesurfer team.
I'd appreciate any advice from you.
When doing the motion correction, I'd like to align all EPI data(bold_retino) to the first EPI of target run(bold_decode/003). However, the number of slices for target run(33) and the number of slices(32) for input run(bold_retino) are different.
When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003
Freesurfer says that: ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command.
These two kinds of run (bold_decode, bold_retino) were collected in one scan per subject, so the head position should not be too different...
Do you have any suggestions for fixing this error?
Should I do 3dWarp -deoblique?
Thank you so much.
Best, Ji Won
2016-02-08 16:30 GMT-05:00 Ji Won Bang < kirstens03@gmail.com kirstens03@gmail.com>:
Dear. Freesurfer team.
Hi.
I'm using freesurfer 4.5 version.
While doing the motion correction, an error occurred.
the command I used: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003
the error I have: /home/jbang/Projects/replay/epi/replay01/bold_retino 3dvolreg -verbose -dfile 025/fmc.mcdat -base 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 025/tmp.mc-afni2.32291/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868 degrees from plumb. ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 degrees from plumb. ++ centers of base and input datasets are 9.09 mm apart ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD don't have same dimensions! Input: nx=74 ny=74 nz=32 Base: nx=74 ny=74 nz=33 ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command.
I think it's because the volume size is different.
The volume size for bold_retino is: number of slices 32 The volume size for bold_decode: number of slices 33
What should I do to correct this error?
Thank you for taking your time.
Best, Ji Won
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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,
you should co register your structural scans with robust-register or robust-template (if you have more than 2). This can be done into the midspace to make sure both time points are mapped to avoid processing bias.
You can then register the functional scans to their corresponding structurals and concat the transforms to get everything into the same midspace.
Best, Martin
On 02/10/2016 12:48 PM, Ji Won Bang wrote:
Dear. Freesurfer team.
Thanks so much your help and advice.
Based on the comments, I'm trying freesurfer version 5.3.0 instead of 4.5.0 now.
In our experiment, each participant is scanned twice on different days and the functional scan's brain volume are different (some scans have 33 number of slices, some have 32 number of slices).
Since participants moved a bit between scans on the same day, and the head position is different between different days, my advisor advised me to do co-registration between different functional scans and then do co-registration between anatomical and functional scans.
My question is this.
If I do motion-correction such that we align all EPI data to the first EPI of the first functional scan, will it be enough for co-registration between different functional scans and different days? Or should I do coregistration-specific process such as mri_robust_register, mri_robust_template etc?
Or I guess the method I choose should depend on how much the participant moved between scans and how much different the head position was between different days? For example, if the participant was very still between runs and the head position was not that too different, this motion correction is enough for coregistration between functional scans. However, if not, I should do coregistration-specific process such as mri_robust_register, mri_robust_template etc?
I'd appreciate any of your advice.
Please feel free to let me know your thoughts.
Best, Ji Won
2016-02-08 22:31 GMT-05:00 Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
In 4.5 I don't think there is a way to run it when different runs have different number of slices. Version 5+ will handle it properly. If you really want to use 4.5, then you'll have to put it in a different functional subdir (FSD, eg, bold), and create a new analysis for it, then combine them together after analysis. A bit of a hassle. On 2/8/16 5:58 PM, Ji Won Bang wrote:Dear. Freesurfer team. As another attempt, I run the motion correction without the argument -targrun: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino However, I get the same error message again. Why is that? Thanks so much for your effort and time. I appreciate it a lot. Best, Ji Won 2016-02-08 17:16 GMT-05:00 Ji Won Bang <kirstens03@gmail.com <mailto:kirstens03@gmail.com>>: Dear. Freesurfer team. I'd appreciate any advice from you. When doing the motion correction, I'd like to align all EPI data(bold_retino) to the first EPI of target run(bold_decode/003). However, the number of slices for target run(33) and the number of slices(32) for input run(bold_retino) are different. When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003 Freesurfer says that: ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command. These two kinds of run (bold_decode, bold_retino) were collected in one scan per subject, so the head position should not be too different... Do you have any suggestions for fixing this error? Should I do 3dWarp -deoblique? Thank you so much. Best, Ji Won 2016-02-08 16:30 GMT-05:00 Ji Won Bang <kirstens03@gmail.com <mailto:kirstens03@gmail.com>>: Dear. Freesurfer team. Hi. I'm using freesurfer 4.5 version. While doing the motion correction, an error occurred. the command I used: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003 the error I have: /home/jbang/Projects/replay/epi/replay01/bold_retino 3dvolreg -verbose -dfile 025/fmc.mcdat -base 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 025/tmp.mc-afni2.32291/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868 degrees from plumb. ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 degrees from plumb. ++ centers of base and input datasets are 9.09 mm apart ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD don't have same dimensions! Input: nx=74 ny=74 nz=32 Base: nx=74 ny=74 nz=33 ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command. I think it's because the volume size is different. The volume size for bold_retino is: number of slices 32 The volume size for bold_decode: number of slices 33 What should I do to correct this error? Thank you for taking your time. Best, Ji Won _______________________________________________ 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
This is the right way to do it, but it may be over kill. I doubt the fMRI results are going to change much whether you use the anatomical from first day only, the 2nd day only, or a combination of the two.
On 02/10/2016 01:25 PM, Martin Reuter wrote:
Hi,
you should co register your structural scans with robust-register or robust-template (if you have more than 2). This can be done into the midspace to make sure both time points are mapped to avoid processing bias.
You can then register the functional scans to their corresponding structurals and concat the transforms to get everything into the same midspace.
Best, Martin
On 02/10/2016 12:48 PM, Ji Won Bang wrote:
Dear. Freesurfer team.
Thanks so much your help and advice.
Based on the comments, I'm trying freesurfer version 5.3.0 instead of 4.5.0 now.
In our experiment, each participant is scanned twice on different days and the functional scan's brain volume are different (some scans have 33 number of slices, some have 32 number of slices).
Since participants moved a bit between scans on the same day, and the head position is different between different days, my advisor advised me to do co-registration between different functional scans and then do co-registration between anatomical and functional scans.
My question is this.
If I do motion-correction such that we align all EPI data to the first EPI of the first functional scan, will it be enough for co-registration between different functional scans and different days? Or should I do coregistration-specific process such as mri_robust_register, mri_robust_template etc?
Or I guess the method I choose should depend on how much the participant moved between scans and how much different the head position was between different days? For example, if the participant was very still between runs and the head position was not that too different, this motion correction is enough for coregistration between functional scans. However, if not, I should do coregistration-specific process such as mri_robust_register, mri_robust_template etc?
I'd appreciate any of your advice.
Please feel free to let me know your thoughts.
Best, Ji Won
2016-02-08 22:31 GMT-05:00 Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
In 4.5 I don't think there is a way to run it when different runs have different number of slices. Version 5+ will handle it properly. If you really want to use 4.5, then you'll have to put it in a different functional subdir (FSD, eg, bold), and create a new analysis for it, then combine them together after analysis. A bit of a hassle. On 2/8/16 5:58 PM, Ji Won Bang wrote:Dear. Freesurfer team. As another attempt, I run the motion correction without the argument -targrun: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino However, I get the same error message again. Why is that? Thanks so much for your effort and time. I appreciate it a lot. Best, Ji Won 2016-02-08 17:16 GMT-05:00 Ji Won Bang <kirstens03@gmail.com>: Dear. Freesurfer team. I'd appreciate any advice from you. When doing the motion correction, I'd like to align all EPI data(bold_retino) to the first EPI of target run(bold_decode/003). However, the number of slices for target run(33) and the number of slices(32) for input run(bold_retino) are different. When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003 Freesurfer says that: ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command. These two kinds of run (bold_decode, bold_retino) were collected in one scan per subject, so the head position should not be too different... Do you have any suggestions for fixing this error? Should I do 3dWarp -deoblique? Thank you so much. Best, Ji Won 2016-02-08 16:30 GMT-05:00 Ji Won Bang <kirstens03@gmail.com>: Dear. Freesurfer team. Hi. I'm using freesurfer 4.5 version. While doing the motion correction, an error occurred. the command I used: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003 the error I have: /home/jbang/Projects/replay/epi/replay01/bold_retino 3dvolreg -verbose -dfile 025/fmc.mcdat -base 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 025/tmp.mc-afni2.32291/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868 degrees from plumb. ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 degrees from plumb. ++ centers of base and input datasets are 9.09 mm apart ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD don't have same dimensions! Input: nx=74 ny=74 nz=32 Base: nx=74 ny=74 nz=33 ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command. I think it's because the volume size is different. The volume size for bold_retino is: number of slices 32 The volume size for bold_decode: number of slices 33 What should I do to correct this error? Thank you for taking your time. Best, Ji Won _______________________________________________ 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.
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I'm not sure what you are trying to do in the long run. If you have two different scan days and you want to test for differences between them, then analyze each day separately in FSFAST (no problem about the different number of slices). Within a day, each run is separately registered to the anatomical, so there is no issue about aligning to the first time point of the first run. Each run is aligned to the middle time point of each run.
On 02/10/2016 12:48 PM, Ji Won Bang wrote:
Dear. Freesurfer team.
Thanks so much your help and advice.
Based on the comments, I'm trying freesurfer version 5.3.0 instead of 4.5.0 now.
In our experiment, each participant is scanned twice on different days and the functional scan's brain volume are different (some scans have 33 number of slices, some have 32 number of slices).
Since participants moved a bit between scans on the same day, and the head position is different between different days, my advisor advised me to do co-registration between different functional scans and then do co-registration between anatomical and functional scans.
My question is this.
If I do motion-correction such that we align all EPI data to the first EPI of the first functional scan, will it be enough for co-registration between different functional scans and different days? Or should I do coregistration-specific process such as mri_robust_register, mri_robust_template etc?
Or I guess the method I choose should depend on how much the participant moved between scans and how much different the head position was between different days? For example, if the participant was very still between runs and the head position was not that too different, this motion correction is enough for coregistration between functional scans. However, if not, I should do coregistration-specific process such as mri_robust_register, mri_robust_template etc?
I'd appreciate any of your advice.
Please feel free to let me know your thoughts.
Best, Ji Won
2016-02-08 22:31 GMT-05:00 Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
In 4.5 I don't think there is a way to run it when different runs have different number of slices. Version 5+ will handle it properly. If you really want to use 4.5, then you'll have to put it in a different functional subdir (FSD, eg, bold), and create a new analysis for it, then combine them together after analysis. A bit of a hassle. On 2/8/16 5:58 PM, Ji Won Bang wrote:Dear. Freesurfer team. As another attempt, I run the motion correction without the argument -targrun: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino However, I get the same error message again. Why is that? Thanks so much for your effort and time. I appreciate it a lot. Best, Ji Won 2016-02-08 17:16 GMT-05:00 Ji Won Bang <kirstens03@gmail.com <mailto:kirstens03@gmail.com>>: Dear. Freesurfer team. I'd appreciate any advice from you. When doing the motion correction, I'd like to align all EPI data(bold_retino) to the first EPI of target run(bold_decode/003). However, the number of slices for target run(33) and the number of slices(32) for input run(bold_retino) are different. When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003 Freesurfer says that: ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command. These two kinds of run (bold_decode, bold_retino) were collected in one scan per subject, so the head position should not be too different... Do you have any suggestions for fixing this error? Should I do 3dWarp -deoblique? Thank you so much. Best, Ji Won 2016-02-08 16:30 GMT-05:00 Ji Won Bang <kirstens03@gmail.com <mailto:kirstens03@gmail.com>>: Dear. Freesurfer team. Hi. I'm using freesurfer 4.5 version. While doing the motion correction, an error occurred. the command I used: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003 the error I have: /home/jbang/Projects/replay/epi/replay01/bold_retino 3dvolreg -verbose -dfile 025/fmc.mcdat -base 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 025/tmp.mc-afni2.32291/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868 degrees from plumb. ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 degrees from plumb. ++ centers of base and input datasets are 9.09 mm apart ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD don't have same dimensions! Input: nx=74 ny=74 nz=32 Base: nx=74 ny=74 nz=33 ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command. I think it's because the volume size is different. The volume size for bold_retino is: number of slices 32 The volume size for bold_decode: number of slices 33 What should I do to correct this error? Thank you for taking your time. Best, Ji Won _______________________________________________ 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.
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Douglas N Greve
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