Hello Ziad,

I ran the following commands and I still end up with an EPI dataset filled with 0's.

@auto_tlrc \
-base MNI_avg152T1+tlrc \
-input gz15_MP+orig

@Align_Centers \
-base /home/pbedard/Pat/abin/TT_EPI+tlrc \
-dset gz15_MP_at_TT+tlrc \
-child run1_EP+orig

@auto_tlrc \
-base /home/pbedard/Pat/abin/TT_EPI+tlrc \
-apar gz15_MP_at_TT+tlrc \
-input run1_EP_shft+orig \ ## output of @Align_Centers
-dxyz 3 \
-suffix _TT


I used the @Align_Centers because when I tried to align the EPI with the EPI_TT+tlrc in @auto_tlrc I received this message:


*********** Warning *************
Dataset centers are 182.753428 mm
apart. If registration fails, or if
parts of the original anatomy gets
cropped, try recentering all the
input data using this command:
@Align_Centers -base /home/pbedard/Pat/abin/TT_EPI+tlrc \
-dset run1_EP+orig \
-child ./*.HEAD\

Then rerun @auto_tlrc using the _shft
version of your datasets.

*********************************
Hit Enter to proceed.


Padding ...
++ Program 3dZeropad: AFNI version=AFNI_2006_12_22_0933 [32-bit]
++ output dataset: ./__ats_tmp__ref_TT_EPI_40pad+tlrc.BRIK
Skull Stripping ...
Error SUMA_LoadPrepInVol (SUMA_BrainWrap.c:89):
98 percentile is 0!
What kind of dataset is this?
Error 3dSkullStrip (SUMA_3dSkullStrip.c:1438):
Failed to load/prep volume
Error: Failed to create skull stripped brain


Is there anything I should have done with to3d to avoid that problem?

Thank you for your help,