On 27 Sep 2011, at 03:25, Amandine Pelletier <
[log in to unmask]> wrote:
> Dear FSL experts,
>
> I'm working on a cohort of 154 subjects, two types of scans were acquired : anatomical MRI and DTI scans.
>
> In a first time, I have run segmentation of hippocampus using FIRST tool. Subsequently, I have used the mask of hippocampus in my MD images registered to the 3D T1 for each subject, in order to extracted MD values using the command line called fslmeants.
>
> In a second time, I have created a "skeletonised ROI" using following commands lines:
> fslmaths /.../JHU/JHU-WhiteMatter-labels-1mm.nii.gz -thr 38 -uthr 38 -mas mean_FA_skeleton_mask mask_Left_Cingulum_hippocampus
> fslmeants -i all_skeletonised.nii.gz -m mask_Left_Cingulum_hippocampus -o meants.txt
>
> Now, I would like to study the correlations between MD values in hippocampus and MD (or FA) values in the Cingulum_hippocampus (ROI created in JHU atlas). The problem is that the ROI created in the JHU Atlas is in normalized space while the mask of hippocampus, created with FIRST tool, is in native space for each subject. I would like to know if is it possible to deproject the ROI, created in the JHU Atlas, into the subject's native space. I have run tbss_deproject, using the following command line:
> tbss_deproject mask_Left_Cingulum_hippocampus 2 -n
>
> The result contains the following error :
>
> de-projecting <skeleton-space-image> into all_FA (nonlinearly aligned) subject space
> output from stage 1 deprojection will be mask_Left_Cingulum_Hippocampus_to_all_FA
> Image Exception : #99 :: Out of memory
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/tbss_deproject: line 94: 11363 Abandon $FSLDIR/bin/tbss_skeleton -i mean_FA -p `cat thresh.txt` mean_FA_skeleton_mask_dst $FSLDIR/data/standard/LowerCingulum_1mm all_FA ${IN}_tmp -D $IN
> de-projection done
> now creating inverse warp fields...
> ** ERROR (nifti_image_read): failed to find header file for 'mask_Left_Cingulum_Hippocampus_to_all_FA'
> ** ERROR: nifti_image_open(mask_Left_Cingulum_Hippocampus_to_all_FA): bad header info
> ERROR: failed to open file mask_Left_Cingulum_Hippocampus_to_all_FA
> Cannot open volume mask_Left_Cingulum_Hippocampus_to_all_FA for reading!
> list of original images = lis_9009006-0770_FA lis_9009008-0918_FA lis_9009011-0993_FA …..
> original target = target
> processing lis_9009006-0770_FA:
> dc: stack empty
> dc: stack empty
> dc: stack empty
> dc: dc: stack empty
> dc: stack empty
> dc: dc: input base must be a number between 2 and 16 (inclusive)
> dc: register 'l' (0154) is empty
> dc: stack empty
> dc: stack empty
> dc: stack empty
> dc: dc: dc: stack empty
> dc: dc: stack empty
> dc: stack empty
> dc: stack empty
> dc: dc: dc: stack empty
> dc: dc: stack empty
> dc: stack empty
> dc: stack empty
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> dc: stack empty
> dc: stack empty
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> dc: stack empty
> dc: stack empty
> dc: stack empty
> dc: stack empty
> dc: dc: input base must be a number between 2 and 16 (inclusive)
> dc: stack empty
> dc: stack empty
> dc: stack empty
> dc: stack empty
> dc: dc: input base must be a number between 2 and 16 (inclusive)
> dc: stack empty
> dc: stack empty
> dc: stack empty
> dc: stack empty
> max label value = 't' (0164) unimplemented
> 0
> 0
> 'w' (0167) unimplemented
> 0
> 0
> 0
> 't' (0164) unimplemented
> 'h' (0150) unimplemented
> 'e' (0145) unimplemented
> 0
> 't' (0164) unimplemented
> 'h' (0150) unimplemented
> 'e' (0145) unimplemented
> 0
> 0
> 0
> 0
> 0
> 0
> 0
> 0
> 0
> 0
> 0
> 0
> 0
> 0
> 0
> 0
> 0
> 0
> 0
> 0
> 0
> 'b' (0142) unimplemented
> 0
> 'b' (0142) unimplemented
> 0
> 0
> 0
> /usr/local/fsl/bin/tbss_deproject: line 130: [: 't' : nombre entier attendu comme expression
> combining across label values
>
> Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds]
> -t : concatenate images in time
> -x : concatenate images in the x direction
> -y : concatenate images in the y direction
> -z : concatenate images in the z direction
> -a : auto-choose: single slices -> volume, volumes -> 4D (time series)
> -tr : concatenate images in time and set the output image tr to the final option value
> ** ERROR (nifti_image_read): failed to find header file for 'lis_9009006-0770_FA_mask_Left_Cingulum_Hippocampus'
> ** ERROR: nifti_image_open(lis_9009006-0770_FA_mask_Left_Cingulum_Hippocampus): bad header info
> ERROR: failed to open file lis_9009006-0770_FA_mask_Left_Cingulum_Hippocampus
> Cannot open volume lis_9009006-0770_FA_mask_Left_Cingulum_Hippocampus for reading!
> ** ERROR (nifti_image_read): failed to find header file for 'lis_9009006-0770_FA_mask_Left_Cingulum_Hippocampus'
> ** ERROR: nifti_image_open(lis_9009006-0770_FA_mask_Left_Cingulum_Hippocampus): bad header info
> ERROR: failed to open file lis_9009006-0770_FA_mask_Left_Cingulum_Hippocampus
> Cannot open volume lis_9009006-0770_FA_mask_Left_Cingulum_Hippocampus for reading!
>
> I don’t know if it’s a problem of memory or a problem of command line ?
>
> Thank for your time and your help,
>
> Amandine
>