External Email - Use Caution
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 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 CautionHi 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 fileMultiRegistration::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 01however 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 resamplethe images to
all have exactly the same geometries and rerun (I thinkmri_convert -rl <target
vol> <source vol> <source vol resampled> should do it (-rl is "reslice like"). If they are not trivialthough 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 ofsubjects,
and I'd like to extract the cortical thickness pre and post, for all standard regions in theatlas, and use
those in subsequent analyses. Following the standard approach for longitudinal studies, Iused 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 representpre 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 alongitudinal
study! ", and consequently to an empty /stats folder -- even though my pre and post images arealigned and
have similar acquisition parameters. Have I done something wrong, and how can I fix thiswarning/error?
Many thanks in advance for any help. Best wishes, Tudor _______________________________________________ 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 towhom it is
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