External Email - Use Caution
Hello,
I'm trying to run freesurfer v5.3 recon-all and running into an error I'm not sure how to troubleshoot. I'm using essentially the same commands that i've successfully used to run version 6.0 recently, and that i've also successfully run 5.3 with in the past.
On my first pass, I attempted to run this full recon-all command:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -i /cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file
Lots of lh surf files were produced as well as 3 of the lh stats files (aparc, curv, w-g), but nothing for rh, and I could not find the rh.white file. I then tried running rh using:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -hemi rh
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/rh.EC_average/surf/rh.sphere.reg): could not open file
One thing that seems weird about the second error is that it is looking in $SUBJECTS_DIR instead of $SUBJECTS_DIR/<subject> for the rh.sphere file, when the file does exist in $SUBJECTS_DIR/<subject>/surf (but not the top dir where it's looking)
Also wanted to note that i'm running this a slightly tweaked version to remove symlinks which aren't allowed on the cluster i'm working on (which is running CentOS 8):
$ diff /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all 3447c3447 < cp $subj1 ${diffsubj}_tmp ---
ln -s $subj1 ${diffsubj}_tmp
3753c3753 < cp $subj1 ${diffsubj}_tmp ---
ln -s $subj1 ${diffsubj}_tmp
3911c3911 < set cmd=(cp $FREESURFER_HOME/subjects/fsaverage) ---
set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4028c4028 < set cmd=(cp $FREESURFER_HOME/subjects/fsaverage) ---
set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4157c4157 < set cmd=(cp $FREESURFER_HOME/subjects/${hemi}.EC_average) ---
set cmd=(ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average)
Any tips on how I can troubleshoot this? Attaching recon-all.log file. Thanks!!
Annchen
External Email - Use Caution
Hi Annchen,
Your cp commands are missing destination file operands, see the errors in recon-all.log.
ln -s $FREESURFER_HOME/subjects/fsaverage and ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average create symbolic links to directory. You will have to copy those two directories for your subject. I think if you copy them before recon-all, it won’t go through the codes to create the link.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Annchen Knodt Sent: Thursday, June 1, 2023 2:10 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution Hello,
I'm trying to run freesurfer v5.3 recon-all and running into an error I'm not sure how to troubleshoot. I'm using essentially the same commands that i've successfully used to run version 6.0 recently, and that i've also successfully run 5.3 with in the past.
On my first pass, I attempted to run this full recon-all command:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -i /cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file
Lots of lh surf files were produced as well as 3 of the lh stats files (aparc, curv, w-g), but nothing for rh, and I could not find the rh.white file. I then tried running rh using:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -hemi rh
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/rh.EC_average/surf/rh.sphere.reg): could not open file
One thing that seems weird about the second error is that it is looking in $SUBJECTS_DIR instead of $SUBJECTS_DIR/<subject> for the rh.sphere file, when the file does exist in $SUBJECTS_DIR/<subject>/surf (but not the top dir where it's looking)
Also wanted to note that i'm running this a slightly tweaked version to remove symlinks which aren't allowed on the cluster i'm working on (which is running CentOS 8):
$ diff /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all 3447c3447 < cp $subj1 ${diffsubj}_tmp ---
ln -s $subj1 ${diffsubj}_tmp
3753c3753 < cp $subj1 ${diffsubj}_tmp ---
ln -s $subj1 ${diffsubj}_tmp
3911c3911 < set cmd=(cp $FREESURFER_HOME/subjects/fsaverage) ---
set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4028c4028 < set cmd=(cp $FREESURFER_HOME/subjects/fsaverage) ---
set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4157c4157 < set cmd=(cp $FREESURFER_HOME/subjects/${hemi}.EC_average) ---
set cmd=(ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average)
Any tips on how I can troubleshoot this? Attaching recon-all.log file. Thanks!!
Annchen
External Email - Use Caution
Hi Yujing,
Thanks so much for your response! I tried copying $FREESURFER_HOME/subjects/fsaverage and $FREESURFER_HOME/subjects/${hemi}.EC_average to $SUBJECTS dir before running, and this time I ran with the original recon-all instead of the one that had been edited to remove links (recon-all_noLink). I was sure this would solve the problem, but I ended up getting the same error:
Command:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all -all -s sub-0223_mprage -openmp 1 -i /cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz
Error:
MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file
Did I need to copy them somewhere besides $SUBJECTS_DIR ? I’m not seeing any “failed to create symbolic link” messages which I interpret as the script having found the files and not need to run the ‘ln -s’ commands.
Attaching the log file from this latest run.
Thanks!
Annchen
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@mgh.harvard.edu Date: Thursday, June 1, 2023 at 3:06 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution Hi Annchen,
Your cp commands are missing destination file operands, see the errors in recon-all.log.
ln -s $FREESURFER_HOME/subjects/fsaverage and ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average create symbolic links to directory. You will have to copy those two directories for your subject. I think if you copy them before recon-all, it won’t go through the codes to create the link.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Annchen Knodt Sent: Thursday, June 1, 2023 2:10 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution Hello,
I'm trying to run freesurfer v5.3 recon-all and running into an error I'm not sure how to troubleshoot. I'm using essentially the same commands that i've successfully used to run version 6.0 recently, and that i've also successfully run 5.3 with in the past.
On my first pass, I attempted to run this full recon-all command:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -i /cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file
Lots of lh surf files were produced as well as 3 of the lh stats files (aparc, curv, w-g), but nothing for rh, and I could not find the rh.white file. I then tried running rh using:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -hemi rh
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/rh.EC_average/surf/rh.sphere.reg): could not open file
One thing that seems weird about the second error is that it is looking in $SUBJECTS_DIR instead of $SUBJECTS_DIR/<subject> for the rh.sphere file, when the file does exist in $SUBJECTS_DIR/<subject>/surf (but not the top dir where it's looking)
Also wanted to note that i'm running this a slightly tweaked version to remove symlinks which aren't allowed on the cluster i'm working on (which is running CentOS 8):
$ diff /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all 3447c3447 < cp $subj1 ${diffsubj}_tmp ---
ln -s $subj1 ${diffsubj}_tmp
3753c3753 < cp $subj1 ${diffsubj}_tmp ---
ln -s $subj1 ${diffsubj}_tmp
3911c3911 < set cmd=(cp $FREESURFER_HOME/subjects/fsaverage) ---
set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4028c4028 < set cmd=(cp $FREESURFER_HOME/subjects/fsaverage) ---
set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4157c4157 < set cmd=(cp $FREESURFER_HOME/subjects/${hemi}.EC_average) ---
set cmd=(ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average)
Any tips on how I can troubleshoot this? Attaching recon-all.log file. Thanks!!
Annchen
External Email - Use Caution
Hi Annchen,
It seems that recon-all only processed lh. By default, it should process both lh and rh. Original recon-all have this line ‘set hemilist = (lh rh);’ at the beginning of the script. Can you make sure the one you are running is the original?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Annchen Knodt Sent: Friday, June 2, 2023 2:53 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution Hi Yujing,
Thanks so much for your response! I tried copying $FREESURFER_HOME/subjects/fsaverage and $FREESURFER_HOME/subjects/${hemi}.EC_average to $SUBJECTS dir before running, and this time I ran with the original recon-all instead of the one that had been edited to remove links (recon-all_noLink). I was sure this would solve the problem, but I ended up getting the same error:
Command:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all -all -s sub-0223_mprage -openmp 1 -i /cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz
Error:
MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file
Did I need to copy them somewhere besides $SUBJECTS_DIR ? I’m not seeing any “failed to create symbolic link” messages which I interpret as the script having found the files and not need to run the ‘ln -s’ commands.
Attaching the log file from this latest run.
Thanks!
Annchen
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Thursday, June 1, 2023 at 3:06 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution Hi Annchen,
Your cp commands are missing destination file operands, see the errors in recon-all.log.
ln -s $FREESURFER_HOME/subjects/fsaverage and ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average create symbolic links to directory. You will have to copy those two directories for your subject. I think if you copy them before recon-all, it won’t go through the codes to create the link.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Annchen Knodt Sent: Thursday, June 1, 2023 2:10 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution Hello,
I'm trying to run freesurfer v5.3 recon-all and running into an error I'm not sure how to troubleshoot. I'm using essentially the same commands that i've successfully used to run version 6.0 recently, and that i've also successfully run 5.3 with in the past.
On my first pass, I attempted to run this full recon-all command:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -i /cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file
Lots of lh surf files were produced as well as 3 of the lh stats files (aparc, curv, w-g), but nothing for rh, and I could not find the rh.white file. I then tried running rh using:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -hemi rh
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/rh.EC_average/surf/rh.sphere.reg): could not open file
One thing that seems weird about the second error is that it is looking in $SUBJECTS_DIR instead of $SUBJECTS_DIR/<subject> for the rh.sphere file, when the file does exist in $SUBJECTS_DIR/<subject>/surf (but not the top dir where it's looking)
Also wanted to note that i'm running this a slightly tweaked version to remove symlinks which aren't allowed on the cluster i'm working on (which is running CentOS 8):
$ diff /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all 3447c3447 < cp $subj1 ${diffsubj}_tmp ---
ln -s $subj1 ${diffsubj}_tmp
3753c3753 < cp $subj1 ${diffsubj}_tmp ---
ln -s $subj1 ${diffsubj}_tmp
3911c3911 < set cmd=(cp $FREESURFER_HOME/subjects/fsaverage) ---
set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4028c4028 < set cmd=(cp $FREESURFER_HOME/subjects/fsaverage) ---
set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4157c4157 < set cmd=(cp $FREESURFER_HOME/subjects/${hemi}.EC_average) ---
set cmd=(ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average)
Any tips on how I can troubleshoot this? Attaching recon-all.log file. Thanks!!
Annchen
External Email - Use Caution
I followed 5.3 recon-all a little bit. rh will be processed after lh. Your recon-all stopped while it was still processing lh.
The error ‘MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file’ happened when recon-all was doing Parcellation Stats lh:
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-0223_mprage lh white
I don’t understand why it tried to read rh.white while it was doing lh white.
I’m wondering maybe it was actually complaining about ../stats/lh.aparc.stats. Can you do ‘ls -l’ of your stats directory?
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: Friday, June 2, 2023 3:31 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution Hi Annchen,
It seems that recon-all only processed lh. By default, it should process both lh and rh. Original recon-all have this line ‘set hemilist = (lh rh);’ at the beginning of the script. Can you make sure the one you are running is the original?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Annchen Knodt Sent: Friday, June 2, 2023 2:53 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution Hi Yujing,
Thanks so much for your response! I tried copying $FREESURFER_HOME/subjects/fsaverage and $FREESURFER_HOME/subjects/${hemi}.EC_average to $SUBJECTS dir before running, and this time I ran with the original recon-all instead of the one that had been edited to remove links (recon-all_noLink). I was sure this would solve the problem, but I ended up getting the same error:
Command:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all -all -s sub-0223_mprage -openmp 1 -i /cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz
Error:
MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file
Did I need to copy them somewhere besides $SUBJECTS_DIR ? I’m not seeing any “failed to create symbolic link” messages which I interpret as the script having found the files and not need to run the ‘ln -s’ commands.
Attaching the log file from this latest run.
Thanks!
Annchen
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Thursday, June 1, 2023 at 3:06 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution Hi Annchen,
Your cp commands are missing destination file operands, see the errors in recon-all.log.
ln -s $FREESURFER_HOME/subjects/fsaverage and ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average create symbolic links to directory. You will have to copy those two directories for your subject. I think if you copy them before recon-all, it won’t go through the codes to create the link.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Annchen Knodt Sent: Thursday, June 1, 2023 2:10 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution Hello,
I'm trying to run freesurfer v5.3 recon-all and running into an error I'm not sure how to troubleshoot. I'm using essentially the same commands that i've successfully used to run version 6.0 recently, and that i've also successfully run 5.3 with in the past.
On my first pass, I attempted to run this full recon-all command:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -i /cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file
Lots of lh surf files were produced as well as 3 of the lh stats files (aparc, curv, w-g), but nothing for rh, and I could not find the rh.white file. I then tried running rh using:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -hemi rh
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/rh.EC_average/surf/rh.sphere.reg): could not open file
One thing that seems weird about the second error is that it is looking in $SUBJECTS_DIR instead of $SUBJECTS_DIR/<subject> for the rh.sphere file, when the file does exist in $SUBJECTS_DIR/<subject>/surf (but not the top dir where it's looking)
Also wanted to note that i'm running this a slightly tweaked version to remove symlinks which aren't allowed on the cluster i'm working on (which is running CentOS 8):
$ diff /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all 3447c3447 < cp $subj1 ${diffsubj}_tmp ---
ln -s $subj1 ${diffsubj}_tmp
3753c3753 < cp $subj1 ${diffsubj}_tmp ---
ln -s $subj1 ${diffsubj}_tmp
3911c3911 < set cmd=(cp $FREESURFER_HOME/subjects/fsaverage) ---
set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4028c4028 < set cmd=(cp $FREESURFER_HOME/subjects/fsaverage) ---
set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4157c4157 < set cmd=(cp $FREESURFER_HOME/subjects/${hemi}.EC_average) ---
set cmd=(ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average)
Any tips on how I can troubleshoot this? Attaching recon-all.log file. Thanks!!
Annchen
External Email - Use Caution
Thank you for looking into this, Yujing! here's my stats dir:
$ ls -l /work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/stats total 77 -rwxrwxrwx. 1 ark19 root 972 Jun 3 17:03 lh.aparc.stats -rwxrwxrwx. 1 ark19 root 49236 Jun 3 16:22 lh.curv.stats -rw-rw-r--. 1 ark19 root 6606 Jun 3 17:03 lh.w-g.pct.stats
FWIW I confirmed that I'm running the original version of recon-all (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 from 2013) ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@mgh.harvard.edu Sent: Friday, June 2, 2023 4:23 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
I followed 5.3 recon-all a little bit. rh will be processed after lh. Your recon-all stopped while it was still processing lh.
The error ‘MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file’ happened when recon-all was doing Parcellation Stats lh:
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-0223_mprage lh white
I don’t understand why it tried to read rh.white while it was doing lh white.
I’m wondering maybe it was actually complaining about ../stats/lh.aparc.stats. Can you do ‘ls -l’ of your stats directory?
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: Friday, June 2, 2023 3:31 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
Hi Annchen,
It seems that recon-all only processed lh. By default, it should process both lh and rh. Original recon-all have this line ‘set hemilist = (lh rh);’ at the beginning of the script. Can you make sure the one you are running is the original?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Annchen Knodt Sent: Friday, June 2, 2023 2:53 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
Hi Yujing,
Thanks so much for your response! I tried copying $FREESURFER_HOME/subjects/fsaverage and $FREESURFER_HOME/subjects/${hemi}.EC_average to $SUBJECTS dir before running, and this time I ran with the original recon-all instead of the one that had been edited to remove links (recon-all_noLink). I was sure this would solve the problem, but I ended up getting the same error:
Command:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all -all -s sub-0223_mprage -openmp 1 -i /cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz
Error:
MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file
Did I need to copy them somewhere besides $SUBJECTS_DIR ? I’m not seeing any “failed to create symbolic link” messages which I interpret as the script having found the files and not need to run the ‘ln -s’ commands.
Attaching the log file from this latest run.
Thanks!
Annchen
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Thursday, June 1, 2023 at 3:06 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
Hi Annchen,
Your cp commands are missing destination file operands, see the errors in recon-all.log.
ln -s $FREESURFER_HOME/subjects/fsaverage and ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average create symbolic links to directory. You will have to copy those two directories for your subject. I think if you copy them before recon-all, it won’t go through the codes to create the link.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Annchen Knodt Sent: Thursday, June 1, 2023 2:10 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
Hello,
I'm trying to run freesurfer v5.3 recon-all and running into an error I'm not sure how to troubleshoot. I'm using essentially the same commands that i've successfully used to run version 6.0 recently, and that i've also successfully run 5.3 with in the past.
On my first pass, I attempted to run this full recon-all command:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -i /cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file
Lots of lh surf files were produced as well as 3 of the lh stats files (aparc, curv, w-g), but nothing for rh, and I could not find the rh.white file. I then tried running rh using:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -hemi rh
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/rh.EC_average/surf/rh.sphere.reg): could not open file
One thing that seems weird about the second error is that it is looking in $SUBJECTS_DIR instead of $SUBJECTS_DIR/<subject> for the rh.sphere file, when the file does exist in $SUBJECTS_DIR/<subject>/surf (but not the top dir where it's looking)
Also wanted to note that i'm running this a slightly tweaked version to remove symlinks which aren't allowed on the cluster i'm working on (which is running CentOS 8):
$ diff /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all
3447c3447
< cp $subj1 ${diffsubj}_tmp
---
ln -s $subj1 ${diffsubj}_tmp
3753c3753
< cp $subj1 ${diffsubj}_tmp
---
ln -s $subj1 ${diffsubj}_tmp
3911c3911
< set cmd=(cp $FREESURFER_HOME/subjects/fsaverage)
---
set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4028c4028
< set cmd=(cp $FREESURFER_HOME/subjects/fsaverage)
---
set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4157c4157
< set cmd=(cp $FREESURFER_HOME/subjects/${hemi}.EC_average)
---
set cmd=(ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average)
Any tips on how I can troubleshoot this? Attaching recon-all.log file. Thanks!!
Annchen
External Email - Use Caution
Hi Annchen,
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 has a release date of May 2013. All your individual programs reported BuildTimeStamp: Dec 19 2017 00:02:05.
Here is the information for mris_anatomical_stats. It also shows the program was built from ‘mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34’. It is newer than the release date. I think the correct version should be ‘mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26’.
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2023/06/02-13:56:44-GMT BuildTimeStamp: Dec 19 2017 00:02:05 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: ark19 Machine: dcc-youlab-01 Platform: Linux PlatformVersion: 4.18.0-408.el8.x86_64 CompilerName: GCC CompilerVersion: 40800
There seems to be a mismatch between your recon-all and all the programs.
Can you try the following: 1. exit your current terminal, restart a new one 2. source correct Freesurfer environment 3. run ‘which recon-all’ to check the environment has been sourced correctly 4. resubmit recon-all (you don’t need the full path to recon-all if Freesurfer environment is set up correctly)
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Annchen Knodt Sent: Sunday, June 4, 2023 9:22 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution Thank you for looking into this, Yujing! here's my stats dir:
$ ls -l /work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/stats total 77 -rwxrwxrwx. 1 ark19 root 972 Jun 3 17:03 lh.aparc.stats -rwxrwxrwx. 1 ark19 root 49236 Jun 3 16:22 lh.curv.stats -rw-rw-r--. 1 ark19 root 6606 Jun 3 17:03 lh.w-g.pct.stats
FWIW I confirmed that I'm running the original version of recon-all (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 from 2013) ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Friday, June 2, 2023 4:23 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
I followed 5.3 recon-all a little bit. rh will be processed after lh. Your recon-all stopped while it was still processing lh.
The error ‘MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file’ happened when recon-all was doing Parcellation Stats lh:
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-0223_mprage lh white
I don’t understand why it tried to read rh.white while it was doing lh white.
I’m wondering maybe it was actually complaining about ../stats/lh.aparc.stats. Can you do ‘ls -l’ of your stats directory?
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Huang, Yujing Sent: Friday, June 2, 2023 3:31 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
Hi Annchen,
It seems that recon-all only processed lh. By default, it should process both lh and rh. Original recon-all have this line ‘set hemilist = (lh rh);’ at the beginning of the script. Can you make sure the one you are running is the original?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Annchen Knodt Sent: Friday, June 2, 2023 2:53 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
Hi Yujing,
Thanks so much for your response! I tried copying $FREESURFER_HOME/subjects/fsaverage and $FREESURFER_HOME/subjects/${hemi}.EC_average to $SUBJECTS dir before running, and this time I ran with the original recon-all instead of the one that had been edited to remove links (recon-all_noLink). I was sure this would solve the problem, but I ended up getting the same error:
Command:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all -all -s sub-0223_mprage -openmp 1 -i /cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz
Error:
MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file
Did I need to copy them somewhere besides $SUBJECTS_DIR ? I’m not seeing any “failed to create symbolic link” messages which I interpret as the script having found the files and not need to run the ‘ln -s’ commands.
Attaching the log file from this latest run.
Thanks!
Annchen
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Thursday, June 1, 2023 at 3:06 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
Hi Annchen,
Your cp commands are missing destination file operands, see the errors in recon-all.log.
ln -s $FREESURFER_HOME/subjects/fsaverage and ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average create symbolic links to directory. You will have to copy those two directories for your subject. I think if you copy them before recon-all, it won’t go through the codes to create the link.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Annchen Knodt Sent: Thursday, June 1, 2023 2:10 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
Hello,
I'm trying to run freesurfer v5.3 recon-all and running into an error I'm not sure how to troubleshoot. I'm using essentially the same commands that i've successfully used to run version 6.0 recently, and that i've also successfully run 5.3 with in the past.
On my first pass, I attempted to run this full recon-all command:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -i /cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file
Lots of lh surf files were produced as well as 3 of the lh stats files (aparc, curv, w-g), but nothing for rh, and I could not find the rh.white file. I then tried running rh using:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -hemi rh
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/rh.EC_average/surf/rh.sphere.reg): could not open file
One thing that seems weird about the second error is that it is looking in $SUBJECTS_DIR instead of $SUBJECTS_DIR/<subject> for the rh.sphere file, when the file does exist in $SUBJECTS_DIR/<subject>/surf (but not the top dir where it's looking)
Also wanted to note that i'm running this a slightly tweaked version to remove symlinks which aren't allowed on the cluster i'm working on (which is running CentOS 8):
$ diff /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all
3447c3447
< cp $subj1 ${diffsubj}_tmp
---
ln -s $subj1 ${diffsubj}_tmp
3753c3753
< cp $subj1 ${diffsubj}_tmp
---
ln -s $subj1 ${diffsubj}_tmp
3911c3911
< set cmd=(cp $FREESURFER_HOME/subjects/fsaverage)
---
set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4028c4028
< set cmd=(cp $FREESURFER_HOME/subjects/fsaverage)
---
set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4157c4157
< set cmd=(cp $FREESURFER_HOME/subjects/${hemi}.EC_average)
---
set cmd=(ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average)
Any tips on how I can troubleshoot this? Attaching recon-all.log file. Thanks!!
Annchen
External Email - Use Caution
Hi Yujing,
Thanks so much for your help!! I followed your advice and started with a fresh version of freesurfer5.3 and observed that the timestamps were then correct. I ended up running into new errors that took me to these threads:
https://secure-web.cisco.com/1euQS-CcqSCSKsJXK7tWQHf6BlLZi8fEBxBeoPnOJicSL5d... https://secure-web.cisco.com/1-wBOmtQ41uwOS2A5hZP_Kfb6EfEa8jtILdSKD-v9SPaGRn...
where I learned that freesurfer v5.3 may not be compatible with newer linux versions (I’m on centOS8)
so instead I was able to do what I needed - I’m trying to run a specific brain-age algorithm that requires v5.3 - by using the bids app docker container for the algorithm (baracus). It’s got freesurfer 5.3 built in , and I was able to build a singularity/apptainer image from it and run it on my HPC just fine.
Thanks again!
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@mgh.harvard.edu Date: Monday, June 5, 2023 at 10:30 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution Hi Annchen,
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 has a release date of May 2013. All your individual programs reported BuildTimeStamp: Dec 19 2017 00:02:05.
Here is the information for mris_anatomical_stats. It also shows the program was built from ‘mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34’. It is newer than the release date. I think the correct version should be ‘mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26’.
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2023/06/02-13:56:44-GMT BuildTimeStamp: Dec 19 2017 00:02:05 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: ark19 Machine: dcc-youlab-01 Platform: Linux PlatformVersion: 4.18.0-408.el8.x86_64 CompilerName: GCC CompilerVersion: 40800
There seems to be a mismatch between your recon-all and all the programs.
Can you try the following: 1. exit your current terminal, restart a new one 2. source correct Freesurfer environment 3. run ‘which recon-all’ to check the environment has been sourced correctly 4. resubmit recon-all (you don’t need the full path to recon-all if Freesurfer environment is set up correctly)
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Annchen Knodt Sent: Sunday, June 4, 2023 9:22 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution Thank you for looking into this, Yujing! here's my stats dir:
$ ls -l /work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/stats total 77 -rwxrwxrwx. 1 ark19 root 972 Jun 3 17:03 lh.aparc.stats -rwxrwxrwx. 1 ark19 root 49236 Jun 3 16:22 lh.curv.stats -rw-rw-r--. 1 ark19 root 6606 Jun 3 17:03 lh.w-g.pct.stats
FWIW I confirmed that I'm running the original version of recon-all (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 from 2013) ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Friday, June 2, 2023 4:23 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
I followed 5.3 recon-all a little bit. rh will be processed after lh. Your recon-all stopped while it was still processing lh.
The error ‘MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file’ happened when recon-all was doing Parcellation Stats lh:
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-0223_mprage lh white
I don’t understand why it tried to read rh.white while it was doing lh white.
I’m wondering maybe it was actually complaining about ../stats/lh.aparc.stats. Can you do ‘ls -l’ of your stats directory?
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Huang, Yujing Sent: Friday, June 2, 2023 3:31 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
Hi Annchen,
It seems that recon-all only processed lh. By default, it should process both lh and rh. Original recon-all have this line ‘set hemilist = (lh rh);’ at the beginning of the script. Can you make sure the one you are running is the original?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Annchen Knodt Sent: Friday, June 2, 2023 2:53 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
Hi Yujing,
Thanks so much for your response! I tried copying $FREESURFER_HOME/subjects/fsaverage and $FREESURFER_HOME/subjects/${hemi}.EC_average to $SUBJECTS dir before running, and this time I ran with the original recon-all instead of the one that had been edited to remove links (recon-all_noLink). I was sure this would solve the problem, but I ended up getting the same error:
Command:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all -all -s sub-0223_mprage -openmp 1 -i /cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz
Error:
MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file
Did I need to copy them somewhere besides $SUBJECTS_DIR ? I’m not seeing any “failed to create symbolic link” messages which I interpret as the script having found the files and not need to run the ‘ln -s’ commands.
Attaching the log file from this latest run.
Thanks!
Annchen
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Thursday, June 1, 2023 at 3:06 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
Hi Annchen,
Your cp commands are missing destination file operands, see the errors in recon-all.log.
ln -s $FREESURFER_HOME/subjects/fsaverage and ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average create symbolic links to directory. You will have to copy those two directories for your subject. I think if you copy them before recon-all, it won’t go through the codes to create the link.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Annchen Knodt Sent: Thursday, June 1, 2023 2:10 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
Hello,
I'm trying to run freesurfer v5.3 recon-all and running into an error I'm not sure how to troubleshoot. I'm using essentially the same commands that i've successfully used to run version 6.0 recently, and that i've also successfully run 5.3 with in the past.
On my first pass, I attempted to run this full recon-all command:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -i /cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file
Lots of lh surf files were produced as well as 3 of the lh stats files (aparc, curv, w-g), but nothing for rh, and I could not find the rh.white file. I then tried running rh using:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -hemi rh
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/rh.EC_average/surf/rh.sphere.reg): could not open file
One thing that seems weird about the second error is that it is looking in $SUBJECTS_DIR instead of $SUBJECTS_DIR/<subject> for the rh.sphere file, when the file does exist in $SUBJECTS_DIR/<subject>/surf (but not the top dir where it's looking)
Also wanted to note that i'm running this a slightly tweaked version to remove symlinks which aren't allowed on the cluster i'm working on (which is running CentOS 8):
$ diff /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all
3447c3447
< cp $subj1 ${diffsubj}_tmp
---
ln -s $subj1 ${diffsubj}_tmp
3753c3753
< cp $subj1 ${diffsubj}_tmp
---
ln -s $subj1 ${diffsubj}_tmp
3911c3911
< set cmd=(cp $FREESURFER_HOME/subjects/fsaverage)
---
set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4028c4028
< set cmd=(cp $FREESURFER_HOME/subjects/fsaverage)
---
set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4157c4157
< set cmd=(cp $FREESURFER_HOME/subjects/${hemi}.EC_average)
---
set cmd=(ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average)
Any tips on how I can troubleshoot this? Attaching recon-all.log file. Thanks!!
Annchen
freesurfer@nmr.mgh.harvard.edu
-
Annchen Knodt -
Huang, Yujing