External Email - Use Caution
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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