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Hi Bruce,

Thanks for your answer! Before seeing this warning (rather: error, as no output is produced), I'd not have thought the pre-post images have different geometries, as I'm pretty sure their acquisition parameters were the same. The pre and post of any one subject, as well as the different subjects' images, all seem to have identical voxel size (1x1x1) and image size (176x224x160). Furthemore, the (0,0,0) point seems to always overlap well-enough on the anterior commissure...

This all suggests to me the geometry differences are trivial, so the resampling is worth a try. However, I'm unsure whether, in the call to *mri_convert -rl*, the target would have to be subject-specific (e.g. resample each 'post' to the 'pre' baseline), or if I should use a single target for all the pre&post images in the study, a bit like the study-specific template https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLVBM/UserGuide#C_-_Creating_the_template:_fslvbm_2_template used by VBM?

Cheers, Tudor

On 6 June 2018 at 16:37, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Tudor

if you are sure that the differences are trivial you can resample the images to all have exactly the same geometries and rerun (I think mri_convert -rl <target vol> <source vol> <source vol resampled>

should do it (-rl is "reslice like"). If they are not trivial though you may find effects that only reflect the acquisition differences.

cheers Bruce

On Wed, 6 Jun 2018, Tudor Popescu wrote:

...

    External Email - Use Caution

Hello, If any more information is needed to address my question, please do let me know. I hope to hear back and once again thanks a lot for any assistance with this.

Best wishes, Tudor

On 1 June 2018 at 16:07, Tudor Popescu tudor3@gmail.com wrote: Dear all, I have pre and post-intervention data for a single group of subjects, and I'd like to extract the cortical thickness pre and post, for all standard regions in the atlas, and use those in subsequent analyses.

Following the standard approach for longitudinal studies, I used the following types of commands:

1. recon-all -i 01_1.nii.gz -subjid 01_1 recon-all -i 01_2.nii.gz -subjid 01_2 recon-all -i 02_1.nii.gz -subjid 02_1 .. where e.g. 01 is the subj code, and _1 and _2 represent pre and post

scans 2. recon-all -subjid 01_1 -all recon-all -subjid 01_2 -all .. 3. recon-all -base 01 -tp 01_1 -tp 01_2 -all .. 4. recon-all -long 01_1 01 -all recon-all -long 01_2 01 -all .. However, the base step has led to warnings of the type: "WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! ", and consequently to an empty /stats folder -- even though my pre and post images are aligned and have similar acquisition parameters.

Have I done something wrong, and how can I fix this warning/error? Many thanks in advance for any help.

Best wishes, Tudor

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Hi Tudor

I think Martin is probably better able to sort this out than I am.

Bruce

On Mon, 11 Jun 2018, Tudor Popescu wrote:

External Email - Use Caution

Hi Bruce, I assumed a subject-specific target for the mri_convert, so I used this command to realign subject1's post to his pre: mri_convert -rl 01_1.nii.gz 01_2.nii.gz 01_2resampled.nii.gz

(and renamed the resampled file to 01_2). However, then the base step recon-all -base 01 -tp 01_1 -tp 01_2 -all

still gives the same warning about geometries differing across time; and also in addition, this error message (which might have been there earlier too but had gone unnoticed): 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: 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

..has 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 <templateid> -tp <tpNid> ... '

..and 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

Not sure what to do at this stage!.. Thanks again for any pointers!

Cheers, Tudor

On Thu, 7 Jun 2018 at 18:16, Tudor Popescu tudor3@gmail.com wrote: Hi Bruce, Thanks for your answer! Before seeing this warning (rather: error, as no output is produced), I'd not have thought the pre-post images have different geometries, as I'm pretty sure their acquisition parameters were the same. The pre and post of any one subject, as well as the different subjects' images, all seem to have identical voxel size (1x1x1) and image size (176x224x160). Furthemore, the (0,0,0) point seems to always overlap well-enough on the anterior commissure...

This all suggests to me the geometry differences are trivial, so the resampling is worth a try. However, I'm unsure whether, in the call to mri_convert -rl, the target would have to be subject-specific (e.g. resample each 'post' to the 'pre' baseline), or if I should use a single target for all the pre&post images in the study, a bit like the study-specific template used by VBM?

Cheers, Tudor

On 6 June 2018 at 16:37, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Tudor

  if you are sure that the differences are trivial you can resample the images to
  all have exactly the same geometries and rerun (I think mri_convert -rl <target
  vol> <source vol> <source vol resampled>

  should do it (-rl is "reslice like"). If they are not trivial though you may find
  effects that only reflect the acquisition differences.

  cheers
  Bruce

  On Wed, 6 Jun 2018, Tudor Popescu wrote:


                External Email - Use Caution        

        Hello,
        If any more information is needed to address my question, please do
        let me know. I hope to hear back and once again
        thanks a lot for any assistance with this.

        Best wishes,
        Tudor

        On 1 June 2018 at 16:07, Tudor Popescu <tudor3@gmail.com> wrote:
              Dear all,
        I have pre and post-intervention data for a single group of subjects,
        and I'd like to extract the cortical
        thickness pre and post, for all standard regions in the atlas, and use
        those in subsequent analyses.

        Following the standard approach for longitudinal studies, I used the
        following types of commands:
         1. recon-all -i 01_1.nii.gz -subjid 01_1
            recon-all -i 01_2.nii.gz -subjid 01_2
            recon-all -i 02_1.nii.gz -subjid 02_1
            ..
            where e.g. 01 is the subj code, and _1 and _2 represent pre and
        post scans
         2. recon-all -subjid 01_1 -all
            recon-all -subjid 01_2 -all
            ..
         3. recon-all -base 01 -tp 01_1 -tp 01_2 -all
            ..
         4. recon-all -long 01_1 01 -all
            recon-all -long 01_2 01 -all
            ..
        However, the base step has led to warnings of the type: "WARNING:
        Image geometries differ across time, maybe
        due to aquisition changes?  This can potentially bias a longitudinal
        study! ", and consequently to an empty
        /stats folder -- even though my pre and post images are aligned and
        have similar acquisition parameters.

        Have I done something wrong, and how can I fix this warning/error?
        Many thanks in advance for any help.

        Best wishes,
        Tudor




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Hi Tudor,

5.3 had some difficulties reporting image geometry differences even when they were tiny. That was fixed in 6.0. However Bruce’s recommendation (to reslice the second time point exactly as the first) should do the trick. Alternatively (in order to avoid processing bias) you could also simply conform both inputs first

mri_convert - - conform in out (I think)

The other problems that you report are strange and could be caused by partially processing things and maybe incorrect ways to call recon-all. You would need to completely remove (or move to backup) existing cross runs, base runs and long runs.

Then re-run the cross sectionals first (and make sure the norm.mgz exists). If it does not, this has nothing to do with the longitudinal stream but some other problem. It also has nothing to do with the geometries. Once you have completed cross runs, do the base run. Since both time points were conformed in the pre-processing step, there should be no error message due to geometry differences and it should work

Best, Martin

On 13. Jun 2018, at 16:34, Tudor Popescu tudor3@gmail.com wrote:

Hi Bruce,

I am guessing that Martin might be unavailable for now, judging by the date of his last input to the list.

However, my intuition is that there is something really trivial that's causing this chain of (circular!) errors...

For any more ideas of what I could try, I'd remain really indebted!

Cheers, Tudor

On Mon, 11 Jun 2018 at 16:03, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Tudor

I think Martin is probably better able to sort this out than I am.

Bruce

On Mon, 11 Jun 2018, Tudor Popescu wrote:

...

    External Email - Use Caution        

Hi Bruce, I assumed a subject-specific target for the mri_convert, so I used this command to realign subject1's post to his pre: mri_convert -rl 01_1.nii.gz 01_2.nii.gz 01_2resampled.nii.gz

(and renamed the resampled file to 01_2). However, then the base step recon-all -base 01 -tp 01_1 -tp 01_2 -all

still gives the same warning about geometries differing across time; and also in addition, this error message (which might have been there earlier too but had gone unnoticed): 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: 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

..has 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 <templateid> -tp <tpNid> ... '

..and 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

Not sure what to do at this stage!.. Thanks again for any pointers!

Cheers, Tudor

On Thu, 7 Jun 2018 at 18:16, Tudor Popescu <tudor3@gmail.com mailto:tudor3@gmail.com> wrote: Hi Bruce, Thanks for your answer! Before seeing this warning (rather: error, as no output is produced), I'd not have thought the pre-post images have different geometries, as I'm pretty sure their acquisition parameters were the same. The pre and post of any one subject, as well as the different subjects' images, all seem to have identical voxel size (1x1x1) and image size (176x224x160). Furthemore, the (0,0,0) point seems to always overlap well-enough on the anterior commissure...

This all suggests to me the geometry differences are trivial, so the resampling is worth a try. However, I'm unsure whether, in the call to mri_convert -rl, the target would have to be subject-specific (e.g. resample each 'post' to the 'pre' baseline), or if I should use a single target for all the pre&post images in the study, a bit like the study-specific template used by VBM?

Cheers, Tudor

On 6 June 2018 at 16:37, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Tudor

  if you are sure that the differences are trivial you can resample the images to
  all have exactly the same geometries and rerun (I think mri_convert -rl <target
  vol> <source vol> <source vol resampled>

  should do it (-rl is "reslice like"). If they are not trivial though you may find
  effects that only reflect the acquisition differences.

  cheers
  Bruce

  On Wed, 6 Jun 2018, Tudor Popescu wrote:


                External Email - Use Caution        

        Hello,
        If any more information is needed to address my question, please do
        let me know. I hope to hear back and once again
        thanks a lot for any assistance with this.

        Best wishes,
        Tudor

        On 1 June 2018 at 16:07, Tudor Popescu <tudor3@gmail.com <mailto:tudor3@gmail.com>> wrote:
              Dear all,
        I have pre and post-intervention data for a single group of subjects,
        and I'd like to extract the cortical
        thickness pre and post, for all standard regions in the atlas, and use
        those in subsequent analyses.

        Following the standard approach for longitudinal studies, I used the
        following types of commands:
         1. recon-all -i 01_1.nii.gz -subjid 01_1
            recon-all -i 01_2.nii.gz -subjid 01_2
            recon-all -i 02_1.nii.gz -subjid 02_1
            ..
            where e.g. 01 is the subj code, and _1 and _2 represent pre and
        post scans
         2. recon-all -subjid 01_1 -all
            recon-all -subjid 01_2 -all
            ..
         3. recon-all -base 01 -tp 01_1 -tp 01_2 -all
            ..
         4. recon-all -long 01_1 01 -all
            recon-all -long 01_2 01 -all
            ..
        However, the base step has led to warnings of the type: "WARNING:
        Image geometries differ across time, maybe
        due to aquisition changes?  This can potentially bias a longitudinal
        study! ", and consequently to an empty
        /stats folder -- even though my pre and post images are aligned and
        have similar acquisition parameters.

        Have I done something wrong, and how can I fix this warning/error?
        Many thanks in advance for any help.

        Best wishes,
        Tudor




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