Hi Erik, 

better late then never: 
you should use mri_convert --conform input output



Best, Martin 


> On 16. May 2018, at 12:19, Erik O'Hanlon <erikohan...@rcsi.ie> wrote:
> 
>         External Email - Use Caution        
> Thank Martin,
> 
> I've been looking into this and it appears that the slight changes in the 
> sequence may have occurred software updates to the scanner. So essentially 
> from what you say, this drastically impacts any longitudinal analyses as 
> there will be a systematic bias across the data. Is there any point in trying 
> to do longitudinal analyses with such data as it will be a factor in all 
> output? Is it worth resampling all three time points to 1mm and then rerun 
> the analysis as it will be difficult to say if any patterns of change arent 
> due to the acquistions as you said?
> 
> If I want to resample the data to a "standard 1mm3" voxel size, is there a FS 
> command for that or should I use something in FSL or AFNI tools and then feed 
> the resampled data back to the recon-all inistial step in FS.
> 
> Thanks for the help and guidance. Much appreciated
> 
> Erik  
> 
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
> <freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Martin Reuter 
> <mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>>
> Sent: 15 May 2018 23:39
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Longitudinal errors, Voxel size differs
>  
> Hi Erik, 
> 
> you should investigate why this is the case. Any difference in acquisition 
> will cause effects and it will be impossible to distinguish these from real 
> effects. 
> 
> Also you should never just resample one time point, as that will introduce 
> processing bias. I would advise to
> - find out why, and you need to report this in any analysis so that people 
> are aware of this potential bias
> - resample both time points to some 3rd space. Probably here simply conform 
> them to 1mm isotropic. 
> 
> Best, Martin
> 
>> 
>> Erik O'Hanlon 
>> Postdoctoral researcher
>> <rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png>
>> RCSI Psychiatry 
>> Royal College of Surgeons in Ireland 
>> Beaumont Road, Beaumont D9 Ireland
>> T: 8093740 
>> E: erikohan...@rcsi.ie <mailto:erikohan...@rcsi.ie> W: www.rcsi.com 
>> <http://www.rcsi.com/>
>> 
>> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
>> 2018-2022 <http://www.rcsi.ie/strategy2018>
>> 
>> RCSI DEVELOPING HEALTHCARE LEADERS
>> WHO MAKE A DIFFERENCE WORLDWIDE
>> 
>> 
>> <both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png>
>> 
>> On 15. May 2018, at 07:20, Erik O'Hanlon <erikohan...@rcsi.ie 
>> <mailto:erikohan...@rcsi.ie>> wrote:
>> 
>> Hi FS Experts,
>> 
>> I'm trying to run a longitudinal analysis across three timepoints and have 
>> run the cross steps for the data. I then ran the base step but found that my 
>> voxel dimensions are slightly different across the timepoints and I got the 
>> following error
>> 
>> ERROR: MultiRegistration::loadMovables: images have different voxel sizes.
>>   Currently not supported, maybe first make conform?
>>   Debug info: size(2) = 0.881117, 0.881117, 0.881117   size(0) = 0.884507, 
>> 0.884507, 0.884507
>> MultiRegistration::loadMovables: voxel size is different 
>> /projects/pi-vokeane/HPC_16_00925/MC_FS_testdata_EOH/freesurfer/subjects/abd025_tp3/mri/norm.mgz.
>> 
>> 
>> I assume I need to resample the data to the voxel size of the first time 
>> point and then rerun. Can you advise on what command to use to resample the 
>> images from time 2 and time 3 to those of time 1 before rerunning from 
>> scratch. I assume I can't avoid rerunning the initial reconall step once I 
>> resample my data.
>> 
>> Any guidance is much appreciated 
>> 
>> Best regards
>> 
>> Erik
>> 
>> Erik O'Hanlon 
>> Postdoctoral researcher
>> <rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png>
>> RCSI Psychiatry 
>> Royal College of Surgeons in Ireland 
>> Beaumont Road, Beaumont D9 Ireland
>> T: 8093740 
>> E: erikohan...@rcsi.ie <mailto:erikohan...@rcsi.ie> W: www.rcsi.com 
>> <http://www.rcsi.com/>
>> 
>> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
>> 2018-2022 <http://www.rcsi.ie/strategy2018>
>> 
>> RCSI DEVELOPING HEALTHCARE LEADERS
>> WHO MAKE A DIFFERENCE WORLDWIDE
>> 
>> 
>> <both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png>
>> 
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