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Hi Everyone

I've managed to fix my problem. In case anyone else has the same problem, the problem was that the subject name was repeated twice in the subjectname file within the subject_ID (in my case 20_1) folder.

Best wishes, Keri

On Thu, Jan 10, 2019 at 11:57 AM Keri Woods keri.woods@gmail.com wrote:

Hi

I’m having a problem that I’m hoping someone could help me with.

I’m trying to check the quality of the alignment of structural and functional data, using the command:

tkregister-sess -s 20_1 -fsd bold -per-run

where 20_1 is the subject ID. Nothing opens, and I get the following error:

---

tkregister-sess logfile is /home/keri/audio2/log/tkregister-sess.log

---

Session: 20_1 ----------------

if: Expression Syntax.

I’ve opened the log file, which doesn’t shed much light on the problem. Its contents are:

tkregister-sess log file

$Id: tkregister-sess,v 1.42 2015/12/10 22:51:31 zkaufman Exp $

setenv SUBJECTS_DIR /home/keri/recon_all/subjects

cd /home/keri/audio

/usr/local/freesurfer/fsfast/bin/tkregister-sess -s 20_1 -fsd bold -per-run

buddha

/usr/local/freesurfer/bin/tkregister2

Session: 20_1 ----------------

The SUBJECTS_DIR show here is correct.

I’ve been looking through the archives, and someone suggested checking whether tkmedit works when having problems with tkregister. I’ve done this, and it works fine.

On a side note, when checking the quality of registration using the command in the format of:

tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum

I get very poor results for many of the subjects (some of them are even > 1, which I didn’t think was possible). Could this be part of the problem? The subject 20_1 I used as a example did have a fairly good result (eg 0.5090 for one run).

Thanks in advance.

Best wishes,

Keri