Hi,
For anyone following this thread - we have found the solution, which is to edit the setup_masks script and replace the following line:
totcon=`echo ${out}.con.txt | wc -l`;
with
totcon=`cat ${out}.con.txt | wc -l`;
We will fix this in the next FSL patch.
All the best,
Mark
On 25 Jun 2013, at 17:20, Jeremy Strain <[log in to unmask]> wrote:
> Dear Dr. Webster,
> The files were transferred to a Mac with a virtual Windows machine but only just prior to uploading them to this forums. All the processing and computing was performed on the original Mac machine with no influence from a Windows operating system. I can resend the files from the original computer if that will help you but it could not be responsible for the original problem.
>
> Thanks,
> Jeremy
>
>
>> Hello,
>> Have your input files been modified by a Windows machine? It looks like there might be an issue with the CR/LF format?
>
>> Kind Regards
>
>> Matthew
>
>> Dear Mark,
>> Sorry for the confusion. I will only go through the process that got me the error. First, I ran the command:
>>
>> setup_masks test_with_age.mat test_with_age.con Con_Issue *.nii.gz
>>
>> All the Lesion masks were in the same template space and were the only nifti files in the folder. The output contained several Con_Issue_00## files listed from 4-63 which was correct plus the Con_Issue.con and Con_Issue.mat files. In the terminal I got the command to run randomise (I added in my variables and parameters):
>>
>> randomise -i all_FA_skeletonised.nii.gz -m mean_FA_skeleton_mask.nii.gz -d Contrasts/Con_Issue.mat -t Contrasts/Con_Issue.con -o Another_Test_fix/Work_maybe --vxl=4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63 --vxf=Another_Test/Con_Issue_0004,Another_Test/Con_Issue_0005,Another_Test/Con_Issue_0006,Another_Test/Con_Issue_0007,Another_Test/Con_Issue_0008,Another_Test/Con_Issue_0009,Another_Test/Con_Issue_0010,Another_Test/Con_Issue_0011,Another_Test/Con_Issue_0012,Another_Test/Con_Issue_0013,Another_Test/Con_Issue_0014,Another_Test/Con_Issue_0015,Another_Test/Con_Issue_0016,Another_Test/Con_Issue_0017,Another_Test/Con_Issue_0018,Another_Test/Con_Issue_0019,Another_Test/Con_Issue_0020,Another_Test/Con_Issue_0021,Another_Test/Con_Issue_0022,Another_Test/Con_Issue_0023,Another_Test/Con_Issue_0024,Another_Test/Con_Issue_0025,Another_Test/Con_Issue_0026,Another_Test/Con_Issue_0027,Another_Test/Con_Issue_0028,Another_Test/Con_Issue_0029,Another_Test/Con_Issue_0030,Another_Test/Con_Issue_0031,Another_Test/Con_Issue_0032,Another_Test/Con_Issue_0033,Another_Test/Con_Issue_0034,Another_Test/Con_Issue_0035,Another_Test/Con_Issue_0036,Another_Test/Con_Issue_0037,Another_Test/Con_Issue_0038,Another_Test/Con_Issue_0039,Another_Test/Con_Issue_0040,Another_Test/Con_Issue_0041,Another_Test/Con_Issue_0042,Another_Test/Con_Issue_0043,Another_Test/Con_Issue_0044,Another_Test/Con_Issue_0045,Another_Test/Con_Issue_0046,Another_Test/Con_Issue_0047,Another_Test/Con_Issue_0048,Another_Test/Con_Issue_0049,Another_Test/Con_Issue_0050,Another_Test/Con_Issue_0051,Another_Test/Con_Issue_0052,Another_Test/Con_Issue_0053,Another_Test/Con_Issue_0054,Another_Test/Con_Issue_0055,Another_Test/Con_Issue_0056,Another_Test/Con_Issue_0057,Another_Test/Con_Issue_0058,Another_Test/Con_Issue_0059,Another_Test/Con_Issue_0060,Another_Test/Con_Issue_0061,Another_Test/Con_Issue_0062,Another_Test/Con_Issue_0063 -n 5000 --T2 -V
>>
>> Soon after pressing enter I received the error that I described previously
>>
>> If you look at the Contrast file for Con_Issue I hope you will see the problems that I saw and attempted to correct in Con_Issue_fix.con. After changing the randomise command to use the Con_Issue_fix.mat and Con_Issue_fix.con it did not give me the error.
>>
>> Thanks,
>> Jeremy
>>
>> <Compressed_Con_and_Mat_Files.zip>
