# Monkey 5ttgen

**URL:** https://community.mrtrix.org/t/monkey-5ttgen/7438
**Category:** Uncategorized
**Tags:** preprocessing
**Created:** [March 14, 2024, 1:30am UTC](https://community.mrtrix.org/t/monkey-5ttgen/7438 "2024-03-14T01:30:07Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![minjik0923](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/m/3e96dc/32.png) [@minjik0923](https://community.mrtrix.org/u/minjik0923)
#### Post date: [March 14, 2024, 1:30am UTC](https://community.mrtrix.org/t/monkey-5ttgen/7438/1 "2024-03-14T01:30:08Z")

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I am trying to run 5ttgen with monkey data.

this was my code: (anat.mif is T1 file)

5ttgen fsl anat.mif 5tt\_nocoreg.mif

cp 5tt\_nocoreg.mif …/dwi/5tt\_nocoreg.mif

cd …/dwi

and i got this warning sign, 5ttgen fsl anat.mif 5tt\_nocoreg.mif

cp 5tt\_nocoreg.mif …/dwi/5tt\_nocoreg.mif

cd …/dwi

5ttgen:

5ttgen: _Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information._

5ttgen:

5ttgen: _Generated scratch directory: /Users/MINJIKIM/R1006\_2/5ttgen-tmp-P7C2QH/_

_Command:_ mrconvert /Users/MINJIKIM/R1006\_2/anat.mif /Users/MINJIKIM/R1006\_2/5ttgen-tmp-P7C2QH/input.mif

5ttgen: _Changing to scratch directory (/Users/MINJIKIM/R1006\_2/5ttgen-tmp-P7C2QH/)_

_Command:_ mrconvert input.mif T1.nii -strides -1,+2,+3

_Command:_ maskfilter /Users/MINJIKIM/fsl/data/standard/MNI152\_T1\_1mm\_brain\_mask\_dil.nii.gz dilate mni\_mask.nii -npass 4

_Command:_ standard\_space\_roi T1.nii T1\_preBET.nii.gz -maskMASK mni\_mask.nii -roiFOV

_Command:_ bet T1\_preBET.nii.gz T1\_BET.nii.gz -f 0.15 -R

_Command:_ fast T1\_BET.nii.gz

_Command:_ run\_first\_all -m none -s L\_Accu,R\_Accu,L\_Caud,R\_Caud,L\_Pall,R\_Pall,L\_Puta,R\_Puta,L\_Thal,R\_Thal -i T1.nii -o first

5ttgen: **[ERROR] FSL FIRST has failed; only 6 of 10 structures were segmented successfully (check /Users/MINJIKIM/R1006\_2/5ttgen-tmp-P7C2QH/first.logs)**

5ttgen: _Scratch directory retained; location: /Users/MINJIKIM/R1006\_2/5ttgen-tmp-P7C2QH/_

cp: 5tt\_nocoreg.mif: No such file or directory

cd: no such file or directory: …/dwi

how can i solve this problem is it because my data is not human but monkey data?