Sorry for all the troubles.

‘-sd /home/lirh717c/Desktop/V5LGN/’ needs to be added to your recon-all command line. I see you only have ‘-sd’ added.

Can you attach recon-all.log if you continue to have problems?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Livia Ruehr
Sent: Friday, January 13, 2023 9:43 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

External Email - Use Caution

Hello,

I've tried the echo command, which didn't work. Afterwards I tried -sd:

recon-all -s sub-04 -i -sd /home/lirh717c/Desktop/V5LGN/sub-04-ses-01_T1w.nii.gz -all ; recon-all -s sub-08 -i -sd /home/lirh717c/Desktop/V5LGN/sub-08-ses-01_T1w.nii.gz -all ; recon-all -s sub-19 -i -sd /home/lirh717c/Desktop/V5LGN/sub-19-ses-01_T1w.nii.gz -all

It created the following:

ERROR: cannot find -sd
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-04 exited with ERRORS at Fri Jan 13 15:38:54 CET 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

ERROR: cannot find -sd
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-08 exited with ERRORS at Fri Jan 13 15:38:54 CET 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

ERROR: cannot find -sd
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-19 exited with ERRORS at Fri Jan 13 15:38:54 CET 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

As I've said, I've tried everything now. Normally, it always worked after setting

FREESURFER_HOME=/path
SUBJECTS_DIR=/Subjectdirectorypath
souce FREESURFER_HOME=SetUpFreeSurfer.sh

and then I've ran recon-all with just the subject names.. Now, even if adding the path, it does not find my subjects dir. anymore.

Best wishes

Livia

Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von Huang, Yujing <YHUANG43@MGH.HARVARD.EDU>
Gesendet: Freitag, 13. Januar 2023 15:30:51
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

Hi Livia,

I’m not sure why your $SUBJECTS_DIR is not recognized.

In the same terminal window,

1. echo $SUBJECTS_DIR

2. submit your recon-all

If this doesn’t work, you can use -sd flag as suggested. In you case, add ‘-sd /home/lirh717c/Desktop/V5LGN/’ to your recon-all.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Livia Ruehr
Sent: Friday, January 13, 2023 7:40 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

External Email - Use Caution

Hi,

I've tried it today with the path in the command line:

recon-all -s sub-04 -i /home/lirh717c/Desktop/V5LGN/sub-04-ses-01_T1w.nii.gz -all ; recon-all -s sub-08 -i /home/lirh717c/Desktop/V5LGN/sub-08-ses-01_T1w.nii.gz -all ; recon-all -s sub-19 -i /home/lirh717c/Desktop/V5LGN/sub-19-ses-01_T1w.nii.gz -all

However, it returns the following error (again):

ERROR: environment variable SUBJECTS_DIR not set
this can be done by setting it in the shell before
executing recon-all or by using the -sd flag
ERROR: environment variable SUBJECTS_DIR not set
this can be done by setting it in the shell before
executing recon-all or by using the -sd flag
ERROR: environment variable SUBJECTS_DIR not set
this can be done by setting it in the shell before
executing recon-all or by using the -sd flag

I asked for showing up my subjects directory, which returns the following (correctly):

lirh717c@bam7-mint-chel:/freesurfer$ $SUBJECTS_DIR
bash: /home/lirh717c/Desktop/V5LGN: Is a directory

I do not understand what could still cause the problems...

Thank you so much in advance!

Best

Livia

Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von Huang, Yujing <YHUANG43@MGH.HARVARD.EDU>
Gesendet: Donnerstag, 12. Januar 2023 18:25:58
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

Hi Livia,

Yes, put /home/lirh717c/Desktop/V5LGN/ in front of .nii.gz in the command.

SUBJECTS_DIR is not used to find images specified in recon-all command line.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Livia Ruehr
Sent: Thursday, January 12, 2023 12:06 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

External Email - Use Caution

Dear Yujing,

Thank your for your fast reply. So you mean that I need to paste the whole path (home/../../..) before the name of the .nii.gz file in the command ?

It is weird, because I have always used it as sent and it worked until today. My subjects directory (called V5LGN, see mail below) contains all compressed nifti files of my subjects and additional output directories of the successfully processed subjects. This is why I thought that with the specification of SUBJECTS _DIR freesurfer knows where the subjects called are since they are there on this level without any subdirectories...?

Best
Livia

Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von Huang, Yujing <YHUANG43@MGH.HARVARD.EDU>
Gesendet: Donnerstag, 12. Januar 2023 17:53:41
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

Hi Livia,

SUBJECTS_DIR is the root directory for recon-all processed data. Each individual subject will have a separate subdirectory under SUBJECTS_DIR.

You need to specify full path to your images in recon-all command line.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Livia Ruehr
Sent: Thursday, January 12, 2023 11:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] WG: Problem with recon-all --> nii.gz file not found

External Email - Use Caution

Von: Rühr, Livia
Gesendet: Donnerstag, 12. Januar 2023 17:25
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Problem with recon-all --> nii.gz file not found

Dear Sir or Madame,

for my thesis I am running recon-all on my subjects' nii.gz T1-weighted scans. I use Freesurfer 7.0 on a Linux Mint 21"Vanessa".

I am using the following layout:

recon-all -s sub-03 -i sub-03-ses-01_T1w.nii.gz -all

This worked for me in december, whereby all my subjects were processed successfully and freesurfer created the directories. However, today I wanted to continue my work, but now it says that the file "sub-03-ses-01_T1w.nii.gz" ist not found (error message):

ERROR: cannot find sub-03-ses-01_T1w.nii.gz
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-03 exited with ERRORS at Thu Jan 12 16:59:42 CET 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

This applies not only to one file, but for all of them. I have also tried to rerun recon-all of another file that had been successful in december, I have also copied and renamed it to not overwrite it.. but none of the data sets were found!

For Setup, I have defined my $FREESURFER_HOME, my $SUBJECTS_DIR and also the source (SetUpFreeSurfer.sh).

After typing the following: source $FREESURFER_HOME/SetUpFreeSurfer.sh

... I can now clearly see, that I am in the correct SUBJECTS_DIR

-------- freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /freesurfer
FSFAST_HOME       /freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /home/lirh717c/Desktop/V5LGN
MNI_DIR           /freesurfer/mni

After navigating to this directory (cd $SUBJECTS_DIR) I can also see all my files. Additionally, I can open freesurfer now and open

the scans within freeview, so that the following appears to me:

- my data are okay and I can open them

- freesurfer is generally running (only thing is one warning: (process:3965): Gtk-WARNING **: 17:07:37.677: Locale not supported by C library.

    Using the fallback 'C' locale.)

- even if setting subjects directory to another directory, it is not working, the problem is neither the data nor the directory

- the subjects directory has correctly been set and I can access it --> my files are seen here


To this reason, I have no ideas anymore.

I am looking forward to your reply!

Kind regards

Livia Rühr