Re: [Freesurfer] error in motion correction

[Ji Won Bang]

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 :

> 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 :
>
>> 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 < 
>> kirsten...@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.

Re: [Freesurfer] error in motion correction

[Douglas N Greve]

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  >:
>
> 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 > >:
>>
>> 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 > >:
>>
>> 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 

Re: [Freesurfer] error in motion correction

[Douglas N Greve]

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 > >:
>>
>> 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 :
>>>
>>> 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 :
>>>
>>> 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
>>>  

Re: [Freesurfer] error in motion correction

[Douglas Greve]

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 >:


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 >:

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





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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] error in motion correction

[Ji Won Bang]

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 :

> 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
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] error in motion correction

[Ji Won Bang]

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 :

> 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 :
>
>> 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
>>
>
>
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Re: [Freesurfer] Error with motion-correction session(ms-sess)

[Doug Greve]

Looks like matlab is having trouble running from the shell. I have no 
idea what causes this, you may have to ask your system administrator for 
help.


doug

 wrote:


Hi, Mr or Ms

My name is Kenta in Japan. I'm undergraduate student.
Please help me!
I've tried some things to solve the error with mc-sess.
But I could not solve this error.

The mc-sess processing didn't completely run and  following message 
showed up.


I'm using matlab R2007a, macOS10.5.5, and freesurfer ver4.0.5.
If you want some information about this error or another things, let 
me know.


==
- INFO: northog = 6, pct = 100
2008-12-02 
20:08:06.237 MATLAB[1256:60b] Process manager already initialized -- 
can't fully enable headless mode.

==

Yours sincerely.

Kenta



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Douglas N. Greve, Ph.D.
MGH-NMR Center
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