Hi Inga,

Did you infant_recon_all run through without any errors? If you see the regular FS directory structure in your subejct directory that woudl mean the infant_recon_all successfull completed. If there is only a "work" directory there, that means the process quit in the middle of the processing.

Lilla
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Inga Harting <inga.harting@gmx.de>
Sent: Wednesday, October 19, 2022 8:03 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Inga_klinik <inga.harting@med.uni-heidelberg.de>
Subject: Re: [Freesurfer] infant freesurfer - input and output questions
 
        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.harting@gmx.de

Dpt. Neuroradiology
Heidelberg University Medical Center
INF400, 69120 Heidelberg
inga.harting@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.harting@gmx.de
>
> Dpt. Neuroradiology
> Heidelberg University Medical Center
> INF400, 69120 Heidelberg
> inga.harting@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
> --
>

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