i have
Sent from my iPhone
> On 2 Sep 2019, at 01:43, Noam Schneck <[log in to unmask]> wrote:
>
> Did you try fslreorient2std?
>
> Sent from my iPhone
>
>> On Sep 1, 2019, at 7:00 PM, FSL automatic digest system <[log in to unmask]> wrote:
>>
>> There is 1 message totaling 654 lines in this issue.
>>
>> Topics of the day:
>>
>> 1. VBM: Inconsistent orientations for individual images when attempting to
>> merge... Error in size-match along non-concatenated dimension for input
>> file:
>>
>> ########################################################################
>>
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>> ----------------------------------------------------------------------
>>
>> Date: Sun, 1 Sep 2019 13:05:33 +0200
>> From: Renew Andrade <[log in to unmask]>
>> Subject: VBM: Inconsistent orientations for individual images when attempting to merge... Error in size-match along non-concatenated dimension for input file:
>>
>> Dear FSL experts:
>> I am a medicine student with some background in programming trying to learn how to process in FSL for VBM studies that being said I am a beginner with no experience in FSL only SPM. I have 6 controls and 6 patients but I cannot pass from fslmerge because there is a problem with an error. I put terminal output for all I have done:
>>
>> sh-3.2# ls
>> ._IXI016-Guys-0697-T1.nii.gz IXI016-Guys-0697-T1.nii.gz
>> ._IXI017-Guys-0698-T1.nii.gz IXI017-Guys-0698-T1.nii.gz
>> ._IXI020-Guys-0700-T1.nii.gz IXI020-Guys-0700-T1.nii.gz
>> ._IXI021-Guys-0703-T1.nii.gz IXI021-Guys-0703-T1.nii.gz
>> ._IXI022-Guys-0701-T1.nii.gz IXI022-Guys-0701-T1.nii.gz
>> ._IXI023-Guys-0699-T1.nii.gz IXI023-Guys-0699-T1.nii.gz
>> ._SS_084_MR_anat.nii.gz SS_084_MR_anat.nii.gz
>> ._SS_085_MR_anat.nii.gz SS_085_MR_anat.nii.gz
>> ._SS_086_MR_anat.nii.gz SS_086_MR_anat.nii.gz
>> ._SS_087_MR_anat.nii.gz SS_087_MR_anat.nii.gz
>> ._SS_088_MR_anat.nii.gz SS_088_MR_anat.nii.gz
>> ._SS_089_MR_anat.nii.gz SS_089_MR_anat.nii.gz
>>
>>
>> sh-3.2# slicesdir `imglob *`
>> CON_IXI016_Guys_0697_T1
>> CON_IXI017_Guys_0698_T1
>> CON_IXI020_Guys_0700_T1
>> CON_IXI021_Guys_0703_T1
>> CON_IXI022_Guys_0701_T1
>> CON_IXI023_Guys_0699_T1
>> PAT_SS_084_MR_anat
>> PAT_SS_085_MR_anat
>> PAT_SS_086_MR_anat
>> PAT_SS_087_MR_anat
>> PAT_SS_088_MR_anat
>> PAT_SS_089_MR_anat
>>
>> Finished. To view, point your web browser at
>> file:/Volumes/FREESURFER/FSL/my_fsl_vbm/slicesdir/index.html
>>
>>
>> fslmerge -t avgsubj CON_* PAT_*
>>
>> WARNING:: Inconsistent orientations for individual images when attempting to merge.
>> Merge will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
>>
>>
>> WARNING:: Inconsistent orientations for individual images when attempting to merge.
>> Merge will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
>>
>> Error in size-match along non-concatenated dimension for input file: CON_IXI020_Guys_0700_T1.nii.gz
>>
>>
>> sh-3.2# fslreorient2std CON_IXI020_Guys_0700_T1.nii.gz CON_IXI020_Guys_0700_T1_reoriented.nii.gz
>> sh-3.2# fslmerge -t avgsubj CON_* PAT_*
>>
>> WARNING:: Inconsistent orientations for individual images when attempting to merge.
>> Merge will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
>>
>>
>> WARNING:: Inconsistent orientations for individual images when attempting to merge.
>> Merge will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
>>
>> Error in size-match along non-concatenated dimension for input file: CON_IXI020_Guys_0700_T1.nii.gz
>>
>> sh-3.2# for i in CON_* PAT_*; do fslorient -getorient $i; done
>> RADIOLOGICAL
>> RADIOLOGICAL
>> RADIOLOGICAL
>> RADIOLOGICAL
>> RADIOLOGICAL
>> RADIOLOGICAL
>> RADIOLOGICAL
>> RADIOLOGICAL
>> RADIOLOGICAL
>> RADIOLOGICAL
>> RADIOLOGICAL
>> RADIOLOGICAL
>> RADIOLOGICAL
>>
>>
>>
>> sh-3.2# for i in CON_* PAT_*; do fslorient -getsform $i; done
>> 0.0507977 0.0415984 1.19705 -99.4976 -0.910725 -0.214486 0.0755313 136.383 -0.216578 0.911686 -0.0368493 -81.9329 0 0 0 1
>> -1.19705 -0.0507977 0.0415984 91.8166 -0.0755313 0.910725 -0.214486 -84.5976 0.0368493 0.216578 0.911686 -142.651 0 0 0 1
>> -1.19755 0.024535 0.0546792 76.1407 0.0144908 0.912291 -0.215647 -99.7943 0.0753313 0.214546 0.910721 -148.072 0 0 0 1
>> -0.024535 0.0546792 1.19755 -84.062 -0.912291 -0.215647 -0.0144908 134.854 -0.214546 0.910721 -0.0753313 -82.8919 0 0 0 1
>> -0.00841715 -0.0218239 1.19962 -86.2912 -0.912521 -0.214562 -0.0168854 144.585 -0.214802 0.912356 0.0247244 -87.3808 0 0 0 1
>> 0.055452 0.0271163 1.19739 -95.8247 -0.910874 -0.213522 0.077035 147.851 -0.2148 0.912458 -0.0175572 -66.3337 0 0 0 1
>> 0.0325847 0.00594133 1.19925 -84.9204 -0.911966 -0.214778 0.0423411 121.584 -0.214854 0.912547 0.00215749 -86.1624 0 0 0 1
>> -0.9375 0 0 120 0 0 1.5 -96 0 -0.9375 0 120 0 0 0 1
>> -0.9375 0 0 120 0 0 1.5 -96 0 -0.9375 0 120 0 0 0 1
>> -0.9375 0 0 120 0 0 1.5 -118.5 0 -0.9375 0 120 0 0 0 1
>> -0.9375 0 0 120 0 0 1.5 -118.5 0 -0.9375 0 120 0 0 0 1
>> -0.9375 0 0 120 0 0 1.5 -96 0 -0.9375 0 120 0 0 0 1
>> -0.9375 0 0 120 0 0 1.5 -118.5 0 -0.9375 0 120 0 0 0 1
>> sh-3.2# for i in CON_* PAT_*; do fslorient -getqform $i; done
>> 0.0507977 0.0415984 1.19705 -99.4976 -0.910725 -0.214486 0.0755313 136.383 -0.216578 0.911686 -0.0368494 -81.9329 0 0 0 1
>> -1.19705 -0.0507979 0.041597 91.8166 -0.0755311 0.910725 -0.214486 -84.5976 0.0368476 0.216577 0.911686 -142.651 0 0 0 1
>> -1.19755 0.0245348 0.0546773 76.1407 0.0144911 0.912291 -0.215647 -99.7943 0.0753289 0.214546 0.910721 -148.072 0 0 0 1
>> -0.024535 0.0546792 1.19755 -84.062 -0.912291 -0.215647 -0.0144908 134.854 -0.214546 0.910721 -0.0753314 -82.8919 0 0 0 1
>> -0.00841713 -0.0218239 1.19962 -86.2912 -0.912521 -0.214562 -0.0168854 144.585 -0.214802 0.912356 0.0247245 -87.3808 0 0 0 1
>> 0.055452 0.0271163 1.19739 -95.8247 -0.910874 -0.213522 0.0770351 147.851 -0.2148 0.912457 -0.0175572 -66.3337 0 0 0 1
>> 0.0325846 0.00594134 1.19925 -84.9204 -0.911966 -0.214779 0.042341 121.584 -0.214854 0.912546 0.00215748 -86.1624 0 0 0 1
>> -0.9375 0 -0 120 0 0 1.5 -96 -0 -0.9375 -0 120 0 0 0 1
>> -0.9375 0 -0 120 0 0 1.5 -96 -0 -0.9375 -0 120 0 0 0 1
>> -0.9375 0 -0 120 0 0 1.5 -118.5 -0 -0.9375 -0 120 0 0 0 1
>> -0.9375 0 -0 120 0 0 1.5 -118.5 -0 -0.9375 -0 120 0 0 0 1
>> -0.9375 0 -0 120 0 0 1.5 -96 -0 -0.9375 -0 120 0 0 0 1
>> -0.9375 0 -0 120 0 0 1.5 -118.5 -0 -0.9375 -0 120 0 0 0 1
>>
>>
>>
>>
>> sh-3.2# for i in CON_* PAT_*; do fslswapdim $i RL PA IS swapdim_$i; done
>> sh-3.2# fslmerge -t avgsubj swapdim_*
>>
>> WARNING:: Inconsistent orientations for individual images when attempting to merge.
>> Merge will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
>>
>> Error in size-match along non-concatenated dimension for input file: swapdim_CON_IXI020_Guys_0700_T1.nii.gz
>>
>>
>> Im running out of tutorial options. Some help would be appreciated!
>>
>> Thanks!
>> Sincerely,
>> Andrade.
>>
>>
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>>
>> ------------------------------
>>
>> End of FSL Digest - 30 Aug 2019 to 1 Sep 2019 (#2019-251)
>> *********************************************************
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