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 <fis...@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 <tud...@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 <fis...@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 <tud...@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 > > > > > > > > > > _______________________________________________ > > 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 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. > > > > > > > >_______________________________________________ > 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 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. >
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