Re: [Freesurfer] Geometries-related error from base step & absent norm.mgz

[Tudor Popescu]

External Email - Use Caution

Quick follow-up note in case it will be helpful to anyone experiencing the
same problem: I got hold of a Linux machine and installed FreeSurfer 6.0 on
it; running these same commands there successfuly produced the norm.mgz
file.
Therefore, this appears to be a bug in FS v5.3.0 (which is sadly the only
version available to run on Windows, using a Linux Virtual Machine).
Cheers,
Tudor

On Wed, 27 Jun 2018 at 18:00, Tudor Popescu  wrote:

> Hi again,
>
> At a loss for more things to try here, I tried the following: for the
> first subject in my sample, I replaced the 'post' scan (01_2.nii.gz) with a
> copy of the pre (01_1.nii.gz ), to rule out the unlikely cause that an
> actual geometries problem is at the root here, as reported in the
> warning/error I mentioned earlier.
>
> While this removed the geometries message from the output of the base
> command, the error about norm.mgz not being there remained. Further
> searches of the FS mailing list revealed that this file's absence might be
> due to a bug in FS v6 (even though I am running 5.3.0, through
> VirtualBox, on Windows). Nevertheless, I followed the instructions
> for
> applying the bugfix patch, but when I redid everything (deleted subject
> folders, reissued the commands), the result was the same.
>
> It thus seems the base step expects norm.mgz to exist, whereas the
> previous steps ('-i' and 'cross') do not create it.
>
> I attach the recon-all logs for the pre, post and base of subject 01.
> Would remain thankful to anyone who can suggest what else I can try!
>
> Best wishes,
> Tudor
>
> On Thu, 21 Jun 2018 at 10:16, Tudor Popescu  wrote:
>
>> Dear FS list,
>>
>> ( Apologies for asking my question again which I am still struggling to
>> resolve and which I tried to clarify and condense below. )
>>
>> I have pre and post-intervention data for a single group of subjects, and
>> I'd like to extract the cortical thickness at both timepoints, for all
>> standard regions in the atlas. I followed the standard approach
>> for
>> longitudinal studies, however the third ('base') step immediately gives
>> this error:
>>
>> *"WARNING: Image geometries differ across time, maybe due to aquisition
>> changes? This can potentially bias a longitudinal study! "*
>>
>>
>> I don't think the acquisition parameters of the pre-post images actually 
>> differ:
>> I could verify that all images indeed have
>>   - identical voxel size (1x1x1)
>>   - identical image size (176x224x160)
>>   - a (0,0,0) point that overlaps well-enough on the anterior commissure
>>
>> This suggests trivial (if any) "geometry" differences, and at Bruce's
>> suggestion, I used  mri_convert to resample each subject's 'post' to
>> their 'pre' baseline:
>>
>> mri_convert -rl 01_1.nii.gz 01_2.nii.gz 01_2resampled.nii.gz
>>
>> (and renamed the resampled file to 01_2). However, the base step,
>>
>> recon-all -base 01 -tp 01_1 -tp 01_2 -all
>>
>> still gives the same error about geometries, and also in addition, this
>> one:
>>
>> mghRead(/media/FS/01_1/mri/norm.mgz, -1): could not open file
>> MultiRegistration::loadMovables: could not open input volume
>> /media/FS/01_1/mri/norm.mgz.
>>
>> Inside /media/FS/01_1/mri/ (where /media/FS is my $SUBJECTS_DIR), there
>> is indeed no norm.mgz, which suggests something in my previous commands for
>> subject1:
>>
>> recon-all -i 01_1.nii.gz -subjid 01_1
>> recon-all -i 01_2.nii.gz -subjid 01_2
>> recon-all -subjid 01_1 -all
>> recon-all -subjid 01_2 -all
>>
>> ..had gone wrong despite these having produced no errors. Although I
>> thought the base step already does autorecon1 as part of the longitudinal
>> pipeline, I tried doing it manually:
>>
>> recon-all -autorecon1 -subjid 01
>>
>> however this returns:
>>
>> ERROR: It appears that this subject ID is an existing base/template from
>> longitudinal processing (-base). Please make sure you pass all necessary
>> flags. For example, if you are trying to re-run a -base: \' -base
>>  -tp  ... \'
>>
>> ..whereas running autorecon1 and 2 for the first *timepoint *instead,
>>
>> recon-all -autorecon1  -autorecon2 -subjid 01_1
>>
>> returns
>>
>> mri_em_register: could not open input volume nu.mgz
>>
>>
>> Should I in fact use, in  mri_convert -rl , a *single *target for all
>> the pre images in the study, like the study-specific template
>> 
>>  used
>> by VBM? Or what else can I try to get the base step to continue? I'm
>> very grateful for any suggestions!
>>
>> Cheers,
>> Tudor
>>
>
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The information 

[Freesurfer] Geometries-related error from base step & absent norm.mgz

[Tudor Popescu]

External Email - Use Caution

 Dear FS list,

( Apologies for asking my question again which I am still struggling to
resolve and which I tried to clarify and condense below. )

I have pre and post-intervention data for a single group of subjects, and
I'd like to extract the cortical thickness at both timepoints, for all
standard regions in the atlas. I followed the standard approach
for
longitudinal studies, however the third ('base') step immediately gives
this error:

*"WARNING: Image geometries differ across time, maybe due to aquisition
changes? This can potentially bias a longitudinal study! "*


I don't think the acquisition parameters of the pre-post images
actually differ:
I could verify that all images indeed have
  - identical voxel size (1x1x1)
  - identical image size (176x224x160)
  - a (0,0,0) point that overlaps well-enough on the anterior commissure

This suggests trivial (if any) "geometry" differences, and at Bruce's
suggestion, I used  mri_convert to resample each subject's 'post' to their
'pre' baseline:

mri_convert -rl 01_1.nii.gz 01_2.nii.gz 01_2resampled.nii.gz

(and renamed the resampled file to 01_2). However, the base step,

recon-all -base 01 -tp 01_1 -tp 01_2 -all

still gives the same error about geometries, and also in addition, this one:

mghRead(/media/FS/01_1/mri/norm.mgz, -1): could not open file
MultiRegistration::loadMovables: could not open input volume
/media/FS/01_1/mri/norm.mgz.

Inside /media/FS/01_1/mri/ (where /media/FS is my $SUBJECTS_DIR), there is
indeed no norm.mgz, which suggests something in my previous commands for
subject1:

recon-all -i 01_1.nii.gz -subjid 01_1
recon-all -i 01_2.nii.gz -subjid 01_2
recon-all -subjid 01_1 -all
recon-all -subjid 01_2 -all

..had gone wrong despite these having produced no errors. Although I
thought the base step already does autorecon1 as part of the longitudinal
pipeline, I tried doing it manually:

recon-all -autorecon1 -subjid 01

however this returns:

ERROR: It appears that this subject ID is an existing base/template from
longitudinal processing (-base). Please make sure you pass all necessary
flags. For example, if you are trying to re-run a -base: \' -base
 -tp  ... \'

..whereas running autorecon1 and 2 for the first *timepoint *instead,

recon-all -autorecon1  -autorecon2 -subjid 01_1

returns

mri_em_register: could not open input volume nu.mgz


Should I in fact use, in  mri_convert -rl , a *single *target for all the
pre images in the study, like the study-specific template

used
by VBM? Or what else can I try to get the base step to continue? I'm very
grateful for any suggestions!

Cheers,
Tudor
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