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?

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer