External Email - Use Caution
Dear FreeSurfer developers,
Hi,
Prior to the FreeSurfer-based longitudinal analysis, it's inevitable that the scanner will change over time in a long follow-up study. We had multiple follow-up data for the same subjects [e.g., baseline and 1st follow-up (scanner 1), 2nd follow-up (scanner 2)]. I applied the longitudinal pipeline of FreeSurfer to the data as follows:
1. Cross-sectional process for each time point 2. Create template (recon-all -base long_base -tp long_tp1 -tp long_tp2 -tp long_tp3 -all -parallel -openmp 4) 3. Longitudinal process
In process 2, I encountered the following warning, but completed the entire process without errors. ******************************************************************************* WARNING: Image parameters differ across time, maybe due to aquisition changes? Consistent changes in, e.g., resolution can potentially bias a longitudinal study! You can check image parameters by running mri_info on each input image. Will continue in 10 seconds ... ******************************************************************************* There are resolutions of our data for each time point:
- Baseline (scanner1, 512 x 512 x 244 or 512 x 512 x 180) - 1st follow-up (scanner1, 512 x 512 x 180) - 2nd follow-up (scanner2, 448 x 448 x 192 or 448 x 448 x 208)
Can I ignore the warning? Or is there anything I need to fix before doing process 3 (longitudinal process)? Also, could you please give me any suggestions on longitudinal analyses?
Thank you very much
Sincerely, Yoonho
External Email - Use Caution
Hi,
Thank you for raising this issue. I am having exactly the same error for an MS study and couldn’t find a solution yet. Any help would be appreciated.
Best, Ahmet
On Wed, 24 Jul 2024 at 4:55 AM Yoonho Hwang ken.lmstar11@gmail.com wrote:
External Email - Use CautionDear FreeSurfer developers,
Hi,
Prior to the FreeSurfer-based longitudinal analysis, it's inevitable that the scanner will change over time in a long follow-up study. We had multiple follow-up data for the same subjects [e.g., baseline and 1st follow-up (scanner 1), 2nd follow-up (scanner 2)]. I applied the longitudinal pipeline of FreeSurfer to the data as follows:
- Cross-sectional process for each time point
- Create template (recon-all -base long_base -tp long_tp1 -tp
long_tp2 -tp long_tp3 -all -parallel -openmp 4) 3. Longitudinal process
In process 2, I encountered the following warning, but completed the entire process without errors.
WARNING: Image parameters differ across time, maybe due to aquisition changes? Consistent changes in, e.g., resolution can potentially bias a longitudinal study! You can check image parameters by running mri_info on each input image. Will continue in 10 seconds ...
There are resolutions of our data for each time point:
- Baseline (scanner1, 512 x 512 x 244 or 512 x 512 x 180)
- 1st follow-up (scanner1, 512 x 512 x 180)
- 2nd follow-up (scanner2, 448 x 448 x 192 or 448 x 448 x 208)
Can I ignore the warning? Or is there anything I need to fix before doing process 3 (longitudinal process)? Also, could you please give me any suggestions on longitudinal analyses?
Thank you very much
Sincerely, Yoonho
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freesurfer@nmr.mgh.harvard.edu
-
Ahmet Kaya -
Yoonho Hwang