External Email - Use Caution Hello again.
Please forget about my first question. I just realised I had moved my Inga/local directory (new after installing freesurfer) before data backup. Just moved it back and now iFS is running again. But, I'm still new to infant freesufer, trying to find my way, am stumbling and glad for some help: Looking at the results using freeview and following along the lines of FS tutorial on FS output, 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? Is there a tutorial for infant freesurfer which I've missed and which might answer (some of) my (current and future) questions? Best, Inga --output copy from my screen for the directory /mri 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 -- -- Inga Harting private email: inga.hart...@gmx.de Dpt. Neuroradiology Heidelberg University Medical Center INF400, 69120 Heidelberg inga.hart...@med.uni-heidelberg.de Am 19/10/2022 um 12:53 schrieb Inga Harting: > 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.hart...@gmx.de > > Dpt. Neuroradiology > Heidelberg University Medical Center > INF400, 69120 Heidelberg > inga.hart...@med.uni-heidelberg.de > > -- > > 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) > > -- > > 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 > -- > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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