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
check if the directory 005_IHD_1_base exists. Also check if this file exits: /usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm
Best, Martin
On 04/04/2017 05:55 PM, Brad Matushewski wrote:
*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 https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongProcessing
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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