Hi Theresa,

first, if you use the -hires flag in version 5.3 the processing pipeline will 
not start to downsample your data at some point (if I remember correctly during 
the normalization stage). As you stated that you were expecting the automatic 
downsampling you should either omit the hires flag or you could follow the 
HiResRecon (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon) to process 
your data in your native resolution. You may need to change or add a few flags 
to process your data with hippocampal subfield segmentation and changes to 
version 5.3 (compared to 5.1). In case you want your data to be downsampled you 
should at least use the -3T flag additionally to correct for inhomogeneities in 
regards to your 7T data.

Second, the hippocampal subfield segmentation was, as far I read in the mailing 
list, vastly improved in version 6. As is it still in development, data 
processing should be done for testing only and not publication. Version 6 
additionally has full support for high resolution data (using the -hires flag 
should avoid downsampling to 1 mm). It can be downloaded as a developmental 

Lastly, in regards to your issue, this usually happened to me if the resolution 
is not exactly 0.7 mm, but something like 0.69998. This results in a rounding 
conflict between conversion with mri_convert and mri_nu_intensity.mni. To 
resolve the issue you have two options: You can either use mri_convert -cs 
<size in mm> on your dataset prior to feeding it to the recon-all script, this 
will result in resampling your dataset (using the size of actual voxel size 
should avoid interpolation). Otherwise you can use mri_convert --cropsize 
<x,y,z> to remove one voxel in every dimension prior to the inhomogeneity 
correction stage.


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Köbe, Theresa
Gesendet: Mittwoch, 21. September 2016 13:51
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Recon hires 7T {Disarmed}

Dear FreeSurfer Developers,

I am attempting to run recon-all on 7T MP2RAGE images (resolution 
0.7x0.7x0.7mm³) with hippocampus subfield segmentation. I use the freesurfer 
version 5.3 so that I expect an automatic down-sampling to 1x1x1mm³.

I used the data directly from the scanner (without reorientation to standard 
etc.) and used the following command:

recon-all -s $subject.freesurfer -hires -i $subject.mp2rage.nii -expert 
/media/NeuroMet_Project/scripts/expert.opts -all -hippo-subfields"

As expert option I used only: mris_inflate -n 15

The processing starts fine but ends with the following error:

 ERROR: dimension mismatch between input volume and seg
  input 321 321 321
  seg   322 322 322
Could you please help me dealing with this problem?
I attached also the log-file

Thank you so much.

Best Theresa

Charité - Universitätsmedizin Berlin
NeuroCure Clinical Research Center NCRC
Dipl.-Biol. Theresa Köbe
AG Kognitive Neurologie
Wiss. Mitarbeiter
Charitéplatz 1, D-10117 Berlin
Tel  +49 30 450 560 185
Fax +49 30 450 7 560 280
Interne Besuchsadresse: CCM, Sauerbruchweg 5, E2
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