Hi Anton,

Has a solution to this problem been identified? I have this when thresholding. Here is the execution log:  

Best wishes,
Brandon

IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...

Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [txt] = [foobin] * [E:/THC]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [E:/THC] = clusters from [foomul] with size >= 10
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [txt] = [foobin] * [E:/THC]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [foomul2] = [foomul] * -1
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [E:/THC] = clusters from [foomul2] with size >= 10
WARNING: File 'foomul2' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
Home dir C:\Users\k1754869\sdm.conf
aPerforming imgcalc calls
oPerforming imgcalc calls
aCalling web browser to display the report
Prior open browser
After open browser
o
aCalling MRICron to display 3D results
Mricron call: "C:/Users/k1754869/Downloads/win/mricron/mricron.exe" C:\Users\k1754869\Downloads\SdmPsiGui-win64-v6.11\SdmPsiGui-win64-v6.11\bin\windows64\..\..\/share/sdm_template.nii.gz -o E:/THC txt folder/analysis_THC_Mean/THC_Mean_z_p_0.05000_10.nii.gz -o E:/THC txt folder/analysis_THC_Mean/THC_Mean_z_p_0.05000_10_neg