Segmentation fault (core dumped)

[ImmanuelSamuel]

Authored by K.A. Eklund 
fMRI data size: 64 x 64 x 13586 x 1 
fMRI voxel size: 3.500000 x 3.500000 x 3.500000 mm 
fMRI TR: 1.980000 s 
fMRI slice order: Seqential increasing 
T1 data size: 155 x 208 x 190 
T1 voxel size: 1.000000 x 1.000000 x 1.000000 mm 
MNI data size: 182 x 218 x 182 
MNI voxel size: 1.000000 x 1.000000 x 1.000000 mm 
Number of original GLM regressors: 1 
Number of total GLM regressors: 5 
Number of contrasts: 1 

Performing registration between T1 and MNI
Performing registration between fMRI and T1
Segmentation fault (core dumped)

[wanderine]

There is something strange with your fMRI data, it has 13586 slices but only one time point?

What do you get if you run fslinfo (FSL) or 3dinfo (AFNI) for the fMRI dataset?

2015-08-16 18:58 GMT+02:00 ImmanuelSamuel notifications@github.com:

Authored by K.A. Eklund fMRI data size: 64 x 64 x 13586 x 1 fMRI voxel size: 3.500000 x 3.500000 x 3.500000 mm fMRI TR: 1.980000 s fMRI slice order: Seqential increasing T1 data size: 155 x 208 x 190 T1 voxel size: 1.000000 x 1.000000 x 1.000000 mm MNI data size: 182 x 218 x 182 MNI voxel size: 1.000000 x 1.000000 x 1.000000 mm Number of original GLM regressors: 1 Number of total GLM regressors: 5 Number of contrasts: 1

Performing registration between T1 and MNI Performing registration between fMRI and T1 Segmentation fault (core dumped)

— Reply to this email directly or view it on GitHub https://github.com/wanderine/BROCCOLI/issues/20.

Anders Eklund, PhD

[ImmanuelSamuel]

I used dcm2nii converter from mricron. Yeah I saw that I am check it now.

[wanderine]

OK I haven't used it but for some reason it puts all the fMRI data into a single volume, instead of several volumes. I think your dataset should be something like

64 x 64 x 34 x 400

Is there any option that you can change?

2015-08-16 19:02 GMT+02:00 ImmanuelSamuel notifications@github.com:

I used dcm2nii converter from mricron

— Reply to this email directly or view it on GitHub https://github.com/wanderine/BROCCOLI/issues/20#issuecomment-131583561.

Anders Eklund, PhD

[ImmanuelSamuel]

fslinfo shows

data_type      INT16
dim1           64
dim2           64
dim3           13586
dim4           1
datatype       4
pixdim1        3.500000
pixdim2        3.500000
pixdim3        3.500000
pixdim4        1.980000
cal_max        0.0000
cal_min        0.0000
file_type      NIFTI-1+

I am reconverting them after some changes and checking if dim4>1. It is taking time for conversion will update after it is done.

what do you use?

[ImmanuelSamuel]

So I tried to use fslhd to look at the header to see if there is number of slices per volume tag. But I am getting this error saying couldn't open file. My linux inexperience is really showing now.

Using sudo gets me the permission but now I can read the libraries associated with fsl just like what happened yesterday.

Tried chown -R immanuel:immanuel /path to directory but didnt work.

[wanderine]

Try

chmod +x filename

2015-08-16 21:12 GMT+02:00 ImmanuelSamuel notifications@github.com:

So I tried to use fslhd to look at the header to see if there is number of slices per volume tag. But I am getting this error saying couldn't open file. My linux inexperience is really showing now.

Using sudo gets me the permission but now I can read the libraries associated with fsl just like what happened yesterday.

Tried chown -R immanuel:immanuel /path to directory but didnt work.

— Reply to this email directly or view it on GitHub https://github.com/wanderine/BROCCOLI/issues/20#issuecomment-131605324.

Anders Eklund, PhD

[ImmanuelSamuel]

3dinfo also shows 64 x 64 x 13586 ... I used other converters and they said cannot find slice per volume info in the header. I used dicom_hdr to look at header information no slice per volume information. So wierd.

[wanderine]

Did you try to3d in afni?

to3d -epan -prefix mynifti.nii -time:zt nz nt TR *.dcm

nz is the number of slices nt is the number of time points TR is the repetition time, in milliseconds, i.e. 2000 for 2 seconds

2015-08-16 21:27 GMT+02:00 ImmanuelSamuel notifications@github.com:

yeah it worked 3dinfo also shows 64 x 64 x 13586 ... I used other converters and they said cannot find slice per volume info in the header. So wierd.

— Reply to this email directly or view it on GitHub https://github.com/wanderine/BROCCOLI/issues/20#issuecomment-131611577.

Anders Eklund, PhD

[wanderine]

Sorry should be

to3d -epan -prefix mynifti.nii -time:zt nz nt TR timepattern *.dcm

tpattern = Code word that identifies how the slices (z-direction)

           were gathered in time.  The values that can be used:

   alt+z = altplus    = alternating in the plus direction

   alt+z2             = alternating, starting at slice #1

   alt-z = altminus   = alternating in the minus direction

   alt-z2             = alternating, starting at slice #nz-2

   seq+z = seqplus    = sequential in the plus direction

   seq-z = seqminus   = sequential in the minus direction

   zero  = simult     = simultaneous acquisition

   FROM_IMAGE         = (try to) read offsets from input images

   @filename          = read temporal offsets from 'filename'

2015-08-16 21:38 GMT+02:00 Anders Eklund andek034@gmail.com:

Did you try to3d in afni?

to3d -epan -prefix mynifti.nii -time:zt nz nt TR *.dcm

nz is the number of slices nt is the number of time points TR is the repetition time, in milliseconds, i.e. 2000 for 2 seconds

2015-08-16 21:27 GMT+02:00 ImmanuelSamuel notifications@github.com:

yeah it worked 3dinfo also shows 64 x 64 x 13586 ... I used other converters and they said cannot find slice per volume info in the header. So wierd.

— Reply to this email directly or view it on GitHub https://github.com/wanderine/BROCCOLI/issues/20#issuecomment-131611577.

Anders Eklund, PhD

Anders Eklund, PhD

[ImmanuelSamuel]

Ok found the problem. I usually use SPM so I just reject the last two images that are usually incomplete images. This occurs due to partial acquisition. I just might have to try other converters that gives better control of conversion parameters.