Hi Anastasia, yes, I have check the SUBJECTS_DIR. I do not understand why all previous configuration file start normally and this no.Do you note some line that might be wrong additionally to setenv SUBJECTS_DIR line.
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 5-giu-2013 16.09 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: Tracula
Is the "setenv SUBJECTS_DIR" line really commented out? You must set SUBJECTS_DIR, see the example configuration file on the wiki and under $FREESURFER_HOME/bin/dmrirc.example.
On Wed, 5 Jun 2013, stdp82@virgilio.it wrote:
Hi list and Anastasia, I'm performing a set of data with tracula version 3.0. I have change my dmrirc file respect to previous analyses and now I have one problem
"set: Variable name must begin with a letter. ERROR: must specify as many DWI dicoms as subjects".
I do not find the line that is wrong. I think to have approximately used the same lines of previous and correct analysis.
I have attached the configuration file. Note that I'm using nii.gz.
Thanks and best regards.
Stefano
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
What do you get when you run "echo $SUBJECTS_DIR"?
On Thu, 6 Jun 2013, stdp82@virgilio.it wrote:
Hi Anastasia,
yes, I have check the SUBJECTS_DIR. I do not understand why all previous configuration file start normally and this no. Do you note some line that might be wrong additionally to setenv SUBJECTS_DIR line.
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 5-giu-2013 16.09 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: Tracula
Is the "setenv SUBJECTS_DIR" line really commented out? You must set SUBJECTS_DIR, see the example configuration file on the wiki and under $FREESURFER_HOME/bin/dmrirc.example.
On Wed, 5 Jun 2013, stdp82@virgilio.it wrote:
Hi list and Anastasia, I'm performing a set of data with tracula version 3.0. I have change my dmrirc file respect to previous analyses and now I have one problem
"set: Variable name must begin with a letter. ERROR: must specify as many DWI dicoms as subjects".
I do not find the line that is wrong. I think to have approximately used
the
same lines of previous and correct analysis.
I have attached the configuration file. Note that I'm using nii.gz.
Thanks and best regards.
Stefano
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Experts!
I am trying to montage snapshots from tkmedit. the output of my tcl scripts are tiff. to save ink i am trying to change the background to white before concatenating them into larger images.
the following works fine with tksurfer but does NOT work with tkmedit generated tiffs -- i am guess i may have to add flags ? but not sure which:
convert -fill white -opaque black file.tif file.jpg
if convert is not the right executable for the tkmedit *tif images please let me know - was under the impression there is no special masking in any tcl generated tiffs with either tksurfer or tkmedit so not sure why this is not workink on the solid black areas
best regards polly
Hi Polly
I don't know why convert wouldn't work properly with tkmedit. I guess you could try freeview
cheers Bruce On Wed, 5 Jun 2013, Polly Dhond wrote:
Hi Experts!
I am trying to montage snapshots from tkmedit. the output of my tcl scripts are tiff. to save ink i am trying to change the background to white before concatenating them into larger images.
the following works fine with tksurfer but does NOT work with tkmedit generated tiffs -- i am guess i may have to add flags ? but not sure which:
convert -fill white -opaque black file.tif file.jpg
if convert is not the right executable for the tkmedit *tif images please let me know - was under the impression there is no special masking in any tcl generated tiffs with either tksurfer or tkmedit so not sure why this is not workink on the solid black areas
best regards polly
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Polly Dhond -
stdp82＠virgilio.it