Opening a Slab in DSI Studio

[Gabriel Nasr]

Good day,

We have a couple of questions regarding opening human slab scans in DSI Studio.

We are trying to open scans of human brain slabs with anisotropic voxels of 0.75 x 1.5 x 0.75 and slice thickness of 1.5 in QSDR. However, we are receiving an error message "Poor R2 found in linear registration". 

(1) We think this might be due to the fact that the ICBM152_adult template is a whole brain, whereas our scans are slabs. Is this the case? and if so, is it possible to open these images in QSDR if we add a new template?

(2) When we open these images in GQI or DTI, the voxels appear as squares rather than rectangles, is DSI Studio compressing the data or is this only a visual effect that will not disrupt tractography and any data we draw from it? Note: We are declining resampling the data into 2mm isotropic resolution.

Thank you,

Gabriel

[Frank Yeh]

(1) We think this might be due to the fact that the ICBM152_adult template is a whole brain, whereas our scans are slabs. Is this the case? and if so, is it possible to open these images in QSDR if we add a new template?

You are right. DSI Studio support partial registration. You may search discussion forum to see if you may find previous posts about this. If no luck, I will help figure out the setting that works with your data (if possible, please send me the SRC file through the website private upload link).

(2) When we open these images in GQI or DTI, the voxels appear as squares rather than rectangles, is DSI Studio compressing the data or is this only a visual effect that will not disrupt tractography and any data we draw from it? Note: We are declining resampling the data into 2mm isotropic resolution.

The 3D visualization will consider the voxel distance, but the underlying data should be the original resolution. You may check the ROI window on the left to confirm.

Best,

Frank

Thank you,

Gabriel

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[Gabriel Nasr]

Hello Frank,

Thank you for your response. I went through the groups and I found this conversation Population-averaged template using GQI reconstructions (google.com). However, I am unsure as to what the specific settings/parameters should be to open the file. I've attempted to put in what I believe to be the proper MNI coordinates (-69 -9 -61 62 42 75) acquired from MRIcron, but I arrived at the same issue (Poor R2). I have sent the SRC file through the private link. Any assistance with finding the appropriate parameters would be greatly appreciated,

Thank you,

Gabriel