External Email - Use Caution
Hello,
I'm new to infant freesurfer. I was initially relieved when a first run of a test patient went through after I created mprage.nii.gz using mri_convert.
1. Today I wanted to rerun it, but it gives me an error message although the "original" file mprage.nii.gz is sitting unchanged right there in the directory (ERROR: must have the input file in home/inga/Inga/Daten/test/pmd2-0/mprage.nii.gz!). Could you help me find my error? I've copied the output on my screen below.
2. I wanted to look at the results using freeview and following along the lines of FS tutorial on FS output. However there is no T1.mgz in /mri and brainmask.mgz is referred to norm.mgz which is empty. Does this indicate the analysis went through but didn't work?
3. Is there a tutorial for infant freesurfer which I've missed and which might answer (some of) my questions?
Best, Inga.
-- Inga Harting private email: inga.harting@gmx.de
Dpt. Neuroradiology Heidelberg University Medical Center INF400, 69120 Heidelberg inga.harting@med.uni-heidelberg.de
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error for infant_revon_all--
inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0$ pwd /home/inga/Inga/Daten/test/pmd2-0 inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0$ ls -la insgesamt 33808 drwxrwxrwx 11 inga inga 4096 Oct 19 12:10 . drwxrwxr-x 10 inga inga 4096 Oct 19 12:10 .. drwxrwxrwx 2 inga inga 4096 Apr 6 2019 1.2.840.113619.2.322.2807.4236267.23758.1434086473.218 drwxrwxrwx 2 inga inga 36864 Apr 6 2019 1.2.840.113619.2.322.2807.4236267.23758.1434086473.219 drwxrwxrwx 2 inga inga 12288 Apr 6 2019 1.2.840.113619.2.322.2807.4236267.23758.1434086473.223 drwxrwxrwx 2 inga inga 16384 Apr 6 2019 1.2.840.113619.2.322.2807.4236267.23758.1434086473.224 drwxrwxrwx 2 inga inga 12288 Apr 6 2019 1.2.840.113619.2.5.181722182500.1102.1434102017.91 drwxrwxrwx 2 inga inga 32768 Apr 6 2019 1.2.840.113619.2.80.4248871915.7044.1434101403.1.4.2 drwxrwxrwx 2 inga inga 40960 Apr 6 2019 1.2.840.113619.2.80.4248871915.7044.1434101419.123.4.2 drwxrwxrwx 2 inga inga 36864 Apr 6 2019 1.2.840.113619.2.80.4248871915.8240.1434101490.1.4.2 drwxrwxr-x 7 inga inga 4096 Oct 19 11:44 iFS_output_2022-10-05 -rw-rw-r-- 1 inga inga 34372241 Oct 5 14:36 mprage.nii.gz -rw-rw-r-- 1 inga inga 1350 Oct 5 10:39 scan.log inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0$ infant_recon_all --s pmd2-0 --age 4 InfantReconAll scripts DIR /usr/local/freesurfer/bin PWD /home/inga/Inga/Daten/test/pmd2-0 ERROR: must have the input file in home/inga/Inga/Daten/test/pmd2-0/mprage.nii.gz! inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0$ --
output from infant freesurfer /mri (result of first run)
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inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0/iFS_output_2022-10-05/mri$ ls -la insgesamt 4824 drwxrwxr-x 3 inga inga 4096 Oct 5 15:44 . drwxrwxr-x 7 inga inga 4096 Oct 19 11:44 .. -rw-rw-r-- 1 inga inga 232837 Oct 5 15:44 aparc+aseg.mgz -rw-rw-r-- 1 inga inga 39 Oct 5 15:44 aseg.count.txt -rw-rw-r-- 1 inga inga 186355 Oct 5 15:44 aseg.mgz -rw-rw-r-- 1 inga inga 186080 Oct 5 15:44 aseg.nii.gz -rw-rw-r-- 1 inga inga 186355 Oct 5 15:44 aseg.presurf.mgz -rw-rw-r-- 1 inga inga 606165 Oct 5 15:44 brain.finalsurfs.mgz lrwxrwxrwx 1 inga inga 8 Oct 5 15:44 brainmask.mgz -> norm.mgz lrwxrwxrwx 1 inga inga 11 Oct 5 15:44 brainmask.nii.gz -> norm.nii.gz lrwxrwxrwx 1 inga inga 8 Oct 5 15:44 brain.mgz -> norm.mgz lrwxrwxrwx 1 inga inga 11 Oct 5 15:44 brain.nii.gz -> norm.nii.gz -rw-rw-r-- 1 inga inga 102107 Oct 5 15:44 filled.mgz -rw-rw-r-- 1 inga inga 1000069 Oct 5 15:44 lh.dpial.ribbon.mgz -rw-rw-r-- 1 inga inga 598075 Oct 5 15:44 lh.dwhite.ribbon.mgz -rw-rw-r-- 1 inga inga 53037 Oct 5 15:44 lh.ribbon.mgz -rw-rw-r-- 1 inga inga 0 Oct 18 19:08 norm.mgz -rw-rw-r-- 1 inga inga 0 Oct 18 19:08 norm.nii.gz -rw-rw-r-- 1 inga inga 1011650 Oct 5 15:44 rh.dpial.ribbon.mgz -rw-rw-r-- 1 inga inga 372114 Oct 5 15:44 rh.dwhite.ribbon.mgz -rw-rw-r-- 1 inga inga 54091 Oct 5 15:44 rh.ribbon.mgz -rw-rw-r-- 1 inga inga 93026 Oct 5 15:44 ribbon.mgz drwxrwxr-x 2 inga inga 4096 Oct 5 15:44 transforms -rw-rw-r-- 1 inga inga 62243 Oct 5 15:44 wm.mgz --