Hi Brad,

the base commands needs a space before -tp

recon-all -base 005_IHD_1_base -tp 005_IHD_1 -tp 005_IHD_1_post -all

 

 

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Brad Matushewski
Sent: March 30, 2017 2:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Trying to compare 2 scans from same person, 6 months apart.

 

 

First scan is 005_IHD_1

 

Second scan is 005_IHD_1_post

 

These were in $SUBJECTS / ihd

 

I moved them into $SUBJECTS

(i.e. no subfolder within $SUBJECTS folder).

 

I am following this;

 

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongProcessing

FsTutorial/LongProcessing - Free Surfer Wiki surfer.nmr.mgh.harvard.edu Processing your data consists of three steps: First, run all your data independently (we also say cross sectionally) using "recon-all -all" (i.e. all time points for ...

I ran a normal recon all on both scans first.

 

I then ran this command:

 

recon-all -base 005_IHD_1_base-tp 005_IHD_1 -tp 005_IHD_1_post -all

 

and all seemed well.

 

I then tried to run this command.

recon-all -long <tpNid> <templateID> -all

This is how I entered the command:

 

recon-all -long 005_IHD_1 005_IHD_1_base -all

 

 

It resulted in errors...here is the last bit of the error log:

 

Applying LTAtransformInterp (resample_type 5)
MRItoBSpline degree 3
writing to /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/rawavg.mgz...

 mri_add_xform_to_header -c /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/orig.mgz /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/orig.mgz

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Thu Mar 30 14:31:07 EDT 2017
/usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri

 cp /usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/transforms/talairach.auto.xfm

cp: cannot stat '/usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm': No such file or directory
Linux bjmatush-System-Product-Name 4.4.0-51-generic #72~14.04.1-Ubuntu SMP Thu Nov 24 19:22:30 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 005_IHD_1.long.005_IHD_1_base exited with ERRORS at Thu Mar 30 14:31:07 EDT 2017

 

 

 

What went wrong?

 

 

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