Thanks Martin, I deleted the older runs for base run and started a new run with -use–mritotal flag in the command line: Following is my script for base run for the subjects ( AA543 and AA550) that were giving me errors other than AA510.T1
#!/bin/bash
SUBJECTS_DIR=~/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/FreeSurfer export SUBJECTS_DIR
recon-all -base AA543.long1 -tp AA543.T0 -tp AA543.T2 -tp AA543.T3 -use-mritotal -all </dev/null&> FSAA543.long1 & recon-all -base AA550.long1 -tp AA550.T1 -tp AA550.T2 -tp AA550.T3 -use-mritotal -all </dev/null&> FSAA550.long1 &
The base runs for AA453, AA550 and AA510 completed without error, So I ran the long run for each time point. My script for that was
#!/bin/bash
SUBJECTS_DIR=~/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/FreeSurfer export SUBJECTS_DIR
recon-all -long AA543.T0 AA543.long1 -use-mritotal -all </dev/null&> FSAA543.T0long & recon-all -long AA543.T2 AA543.long1 -use-mritotal -all </dev/null&> FSAA543.T2long & recon-all -long AA543.T3 AA543.long1 -use-mritotal -all </dev/null&> FSAA543.T3long & recon-all -long AA550.T1 AA550.long1 -use-mritotal -all </dev/null&> FSAA550.T1long & recon-all -long AA550.T2 AA550.long1 -use-mritotal -all </dev/null&> FSAA550.T2long & recon-all -long AA550.T3 AA550.long1 -use-mritotal -all </dev/null&> FSAA550.T3long & recon-all -long AA510.T1 AA510.long1 -use-mritotal -all </dev/null&> FSAA550.T1long & recon-all -long AA510.T2 AA510.long1 -use-mritotal -all </dev/null&> FSAA550.T2long & recon-all -long AA510.T7 AA510.long1 -use-mritotal -all </dev/null&> FSAA550.T1long &
The long run for All AA510 time points and AA543.T2 and AA550.T1 and .T3 were completed without error, however surprisingly AA550.T2, AA543.T1 and AA543.T3 exited with error, the srcipt log didn't define any error other than suggesting the error to be reported. All incomplete runs exited at the same point. Attached are the script log of the runs that exited with error. I am also atatching the log file for AA543.T2 which completed the long run
Message: 7 Date: Thu, 24 May 2012 18:42:17 -0400 From: Martin Reuter <mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] error longitudinal processing To: Rashmi Singh <rsingh@laureateinstitute.orgmailto:rsingh@laureateinstitute.org> Cc: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <1337899337.19912.95.camel@riemann.nmr.mgh.harvard.edumailto:1337899337.19912.95.camel@riemann.nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8
Hi Rashmi,
the command line for running the base (subject-template) should be: recon-all -base AA510 -tp AA510.T1 -tp AA510.T2 -tp AA510.T7 -all we usually don't put the '.long' after the base.
I don't think this is causing your problem however. In your case for some reason the talairach transform fails. It could be that something earlier fails.
You should
- check the .....AA510.long/mri/norm_template.mgz if it looks OK (it is the average of your time points). also the .....AA510.long/mri/orig.mgz should look good.
if they are OK, you need to find out why the talairach reg is failing .....AA510.long/mri/transforms/talairach.xfm
forgot the command for it, but it is the same as in cross sectional processing.
What is weird is your log says this: "INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm"
So probably you have an old talairach.xfm there. I think deleting the AA510.long and rerunning the base from scratch may fix everything. So maybe you want to try that first.
Best, Martin
On Tue, 2012-05-22 at 15:00 +0000, Rashmi Singh wrote: Hello, I ran longitudinal processing which exited with errors. I am attaching the output file. Please advise why this error occurred. The recon ?all run ran perfectly for all the time points for this subject. My command was as follows: recon-all -base AA510.long -tp AA510.T1 -tp AA510.T2 -tp AA510.T7 -all </dev/null&> FSAA510.long & My all other subjects longitudinal run completed without error. Thanks, Rashmi
________________________________
This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.