External Email - Use Caution
Dear FreeSurfer experts,
I am trying to compute local lGI in FreeSurfer 6 for a subject that has undergone longitudinal processing.
In this example, the longitudinal base subject folder (with the long template recon-all output for that subject) is called "111002" and the folder with the data for timepoint 1, for which I would like to compute lGI now, is called "111002_MR1.long.111002". So I run the following command:
recon-all -long 111002_MR1.long.111002 111002 -localGI
The only output, after less than a second, is:
Unmatched '"'.
Then the script terminates and I am back at the shell. Any thoughts on this or ideas?
I have successfully computed local lGI for the cross subjects on the same computer, it finished this morning (using the command 'recon-all -s $CROSS_SUBJECT -localGI'). So the recon-all command in general seems to work, the error is specific to the lgi long command it seems.
Here is some system info:
cat $FREESURFER_HOME/build-stamp.txt
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
uname -a
Linux lxsrv2 5.8.0-59-generic #66~20.04.1-Ubuntu SMP Thu Jun 17 11:14:10 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
All the best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
External Email - Use Caution
I should maybe add some more info to the last email:
* The error is not subject-specific. I tried for all my subjects, and the error is identical for all of them. * I am aware of the face that one needs Matlab to run lGI, and it is on the PATH (otherwise the lGI computation for the cross subjects would also fail). * I know that the error message, on first glance, seems to suggest that there is a syntax error in the recon-all shell script, and that this may suggest that someone messed with it. I strongly believe that this is not the case though, because: 1) FreeSurfer is installed in a directory where only root has write access. 2) The cross subject lGI computation finished successfully this morning. 3) Running 'stat' on the recon-all file shows that it has not been modified after the installation data, more than a year ago.
If you want me to upload subject data, please let me know.
Best,
Tim
On 07/22/2021 9:43 AM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use Caution
Dear FreeSurfer experts,
I am trying to compute local lGI in FreeSurfer 6 for a subject that has undergone longitudinal processing.
In this example, the longitudinal base subject folder (with the long template recon-all output for that subject) is called "111002" and the folder with the data for timepoint 1, for which I would like to compute lGI now, is called "111002_MR1.long.111002". So I run the following command:
recon-all -long 111002_MR1.long.111002 111002 -localGIThe only output, after less than a second, is:
Unmatched '"'.Then the script terminates and I am back at the shell. Any thoughts on this or ideas?
I have successfully computed local lGI for the cross subjects on the same computer, it finished this morning (using the command 'recon-all -s $CROSS_SUBJECT -localGI'). So the recon-all command in general seems to work, the error is specific to the lgi long command it seems.
Here is some system info:
cat $FREESURFER_HOME/build-stamp.txt
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
uname -a
Linux lxsrv2 5.8.0-59-generic #66~20.04.1-Ubuntu SMP Thu Jun 17 11:14:10 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
All the best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1-WUV2Ug0jhZw_z4dV-IQQiAPApnIaPSiC-0atT-7zi_og4...
External Email - Use Caution
Hi Tim,
I don't think you need to use the `-long` flag when using the `-localGI` flag since that just invokes `mris_compute_lgi` on the lh/rh.pial files.
So after running the longitudinal pipeline to generate lh/rh.pial files, I think you can simply run recon-all -s 111002_MR1.long.111002 -localGI
Here, `111002_MR1.long.111002` is assumed to be the dir with the longitudinal outputs.
Alternatively, you could try running `mris_compute_lgi` directly on the pial surfaces of interest.
-Paul
On Thu, Jul 22, 2021 at 3:55 AM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionI should maybe add some more info to the last email:
- The error is not subject-specific. I tried for all my subjects, and the
error is identical for all of them.
- I am aware of the face that one needs Matlab to run lGI, and it is on
the PATH (otherwise the lGI computation for the cross subjects would also fail).
- I know that the error message, on first glance, seems to suggest that
there is a syntax error in the recon-all shell script, and that this may suggest that someone messed with it. I strongly believe that this is not the case though, because:
- FreeSurfer is installed in a directory where only root has write access.
- The cross subject lGI computation finished successfully this morning.
- Running 'stat' on the recon-all file shows that it has not been
modified after the installation data, more than a year ago.
If you want me to upload subject data, please let me know.
Best,
Tim
On 07/22/2021 9:43 AM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use Caution
Dear FreeSurfer experts,
I am trying to compute local lGI in FreeSurfer 6 for a subject that has
undergone longitudinal processing.
In this example, the longitudinal base subject folder (with the long
template recon-all output for that subject) is called "111002" and the folder with the data for timepoint 1, for which I would like to compute lGI now, is called "111002_MR1.long.111002". So I run the following command:
recon-all -long 111002_MR1.long.111002 111002 -localGIThe only output, after less than a second, is:
Unmatched '"'.Then the script terminates and I am back at the shell. Any thoughts on
this or ideas?
I have successfully computed local lGI for the cross subjects on the
same computer, it finished this morning (using the command 'recon-all -s $CROSS_SUBJECT -localGI'). So the recon-all command in general seems to work, the error is specific to the lgi long command it seems.
Here is some system info:
cat $FREESURFER_HOME/build-stamp.txt
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
uname -a
Linux lxsrv2 5.8.0-59-generic #66~20.04.1-Ubuntu SMP Thu Jun 17 11:14:10
UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
All the best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main,
Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1-WUV2Ug0jhZw_z4dV-IQQiAPApnIaPSiC-0atT-7zi_og4...
-- Tim Schäfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1-JjRy3gJKSThxfl_BXH1tHE9F7kEFW7ElW3p4qhUrfEWfB...
External Email - Use Caution
Hi Paul,
thanks for the suggestion. Leaving the -long part out like this:
recon-all -s 111002_MR1.long.111002 -localGI
...gives the following error instead:
ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters:
' -long <tpNid> <templateid> '
where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists.
I will try your second suggestion and run `mris_compute_lgi` directly.
Thanks,
Tim
On 07/22/2021 9:43 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use Caution
Hi Tim,
I don't think you need to use the `-long` flag when using the `-localGI` flag since that just invokes `mris_compute_lgi` on the lh/rh.pial files.
So after running the longitudinal pipeline to generate lh/rh.pial files, I think you can simply run recon-all -s 111002_MR1.long.111002 -localGI
Here, `111002_MR1.long.111002` is assumed to be the dir with the longitudinal outputs.
Alternatively, you could try running `mris_compute_lgi` directly on the pial surfaces of interest.
-Paul
On Thu, Jul 22, 2021 at 3:55 AM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionI should maybe add some more info to the last email:
- The error is not subject-specific. I tried for all my subjects, and the
error is identical for all of them.
- I am aware of the face that one needs Matlab to run lGI, and it is on
the PATH (otherwise the lGI computation for the cross subjects would also fail).
- I know that the error message, on first glance, seems to suggest that
there is a syntax error in the recon-all shell script, and that this may suggest that someone messed with it. I strongly believe that this is not the case though, because:
- FreeSurfer is installed in a directory where only root has write access.
- The cross subject lGI computation finished successfully this morning.
- Running 'stat' on the recon-all file shows that it has not been
modified after the installation data, more than a year ago.
If you want me to upload subject data, please let me know.
Best,
Tim
On 07/22/2021 9:43 AM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use Caution
Dear FreeSurfer experts,
I am trying to compute local lGI in FreeSurfer 6 for a subject that has
undergone longitudinal processing.
In this example, the longitudinal base subject folder (with the long
template recon-all output for that subject) is called "111002" and the folder with the data for timepoint 1, for which I would like to compute lGI now, is called "111002_MR1.long.111002". So I run the following command:
recon-all -long 111002_MR1.long.111002 111002 -localGIThe only output, after less than a second, is:
Unmatched '"'.Then the script terminates and I am back at the shell. Any thoughts on
this or ideas?
I have successfully computed local lGI for the cross subjects on the
same computer, it finished this morning (using the command 'recon-all -s $CROSS_SUBJECT -localGI'). So the recon-all command in general seems to work, the error is specific to the lgi long command it seems.
Here is some system info:
cat $FREESURFER_HOME/build-stamp.txt
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
uname -a
Linux lxsrv2 5.8.0-59-generic #66~20.04.1-Ubuntu SMP Thu Jun 17 11:14:10
UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
All the best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main,
Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1-WUV2Ug0jhZw_z4dV-IQQiAPApnIaPSiC-0atT-7zi_og4...
-- Tim Schäfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1-JjRy3gJKSThxfl_BXH1tHE9F7kEFW7ElW3p4qhUrfEWfB...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1OcbJVPQOmxVAYequdU_5aXNSHhsuyFAnnp5UCmt8d8pee3...
External Email - Use Caution
Running mris_compute_lgi directly works, thanks for the help!
Tim
On 07/23/2021 8:59 AM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use Caution
Hi Paul,
thanks for the suggestion. Leaving the -long part out like this:
recon-all -s 111002_MR1.long.111002 -localGI...gives the following error instead:
ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters:
\' -long <tpNid> <templateid> \' where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists.I will try your second suggestion and run `mris_compute_lgi` directly.
Thanks,
Tim
On 07/22/2021 9:43 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use Caution
Hi Tim,
I don't think you need to use the `-long` flag when using the `-localGI` flag since that just invokes `mris_compute_lgi` on the lh/rh.pial files.
So after running the longitudinal pipeline to generate lh/rh.pial files, I think you can simply run recon-all -s 111002_MR1.long.111002 -localGI
Here, `111002_MR1.long.111002` is assumed to be the dir with the longitudinal outputs.
Alternatively, you could try running `mris_compute_lgi` directly on the pial surfaces of interest.
-Paul
On Thu, Jul 22, 2021 at 3:55 AM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionI should maybe add some more info to the last email:
- The error is not subject-specific. I tried for all my subjects, and the
error is identical for all of them.
- I am aware of the face that one needs Matlab to run lGI, and it is on
the PATH (otherwise the lGI computation for the cross subjects would also fail).
- I know that the error message, on first glance, seems to suggest that
there is a syntax error in the recon-all shell script, and that this may suggest that someone messed with it. I strongly believe that this is not the case though, because:
- FreeSurfer is installed in a directory where only root has write access.
- The cross subject lGI computation finished successfully this morning.
- Running 'stat' on the recon-all file shows that it has not been
modified after the installation data, more than a year ago.
If you want me to upload subject data, please let me know.
Best,
Tim
On 07/22/2021 9:43 AM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use Caution
Dear FreeSurfer experts,
I am trying to compute local lGI in FreeSurfer 6 for a subject that has
undergone longitudinal processing.
In this example, the longitudinal base subject folder (with the long
template recon-all output for that subject) is called "111002" and the folder with the data for timepoint 1, for which I would like to compute lGI now, is called "111002_MR1.long.111002". So I run the following command:
recon-all -long 111002_MR1.long.111002 111002 -localGIThe only output, after less than a second, is:
Unmatched '"'.Then the script terminates and I am back at the shell. Any thoughts on
this or ideas?
I have successfully computed local lGI for the cross subjects on the
same computer, it finished this morning (using the command 'recon-all -s $CROSS_SUBJECT -localGI'). So the recon-all command in general seems to work, the error is specific to the lgi long command it seems.
Here is some system info:
cat $FREESURFER_HOME/build-stamp.txt
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
uname -a
Linux lxsrv2 5.8.0-59-generic #66~20.04.1-Ubuntu SMP Thu Jun 17 11:14:10
UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
All the best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main,
Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1-WUV2Ug0jhZw_z4dV-IQQiAPApnIaPSiC-0atT-7zi_og4...
-- Tim Schäfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1-JjRy3gJKSThxfl_BXH1tHE9F7kEFW7ElW3p4qhUrfEWfB...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1OcbJVPQOmxVAYequdU_5aXNSHhsuyFAnnp5UCmt8d8pee3...
-- Tim Schäfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/149i5otHc3Vfz-SNjbXb2XIt9OuzZiN3D-ubuQpYP9pXJMd...
External Email - Use Caution
Ok good to hear! Thanks for the update.
-Paul
On Fri, Jul 23, 2021 at 3:22 AM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionRunning mris_compute_lgi directly works, thanks for the help!
Tim
On 07/23/2021 8:59 AM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use Caution
Hi Paul,
thanks for the suggestion. Leaving the -long part out like this:
recon-all -s 111002_MR1.long.111002 -localGI...gives the following error instead:
ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters:
\' -long <tpNid> <templateid> \' where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists.I will try your second suggestion and run `mris_compute_lgi` directly.
Thanks,
Tim
On 07/22/2021 9:43 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use Caution
Hi Tim,
I don't think you need to use the `-long` flag when using the
`-localGI`
flag since that just invokes `mris_compute_lgi` on the lh/rh.pial
files.
So after running the longitudinal pipeline to generate lh/rh.pial
files, I
think you can simply run recon-all -s 111002_MR1.long.111002 -localGI
Here, `111002_MR1.long.111002` is assumed to be the dir with the longitudinal outputs.
Alternatively, you could try running `mris_compute_lgi` directly on the pial surfaces of interest.
-Paul
On Thu, Jul 22, 2021 at 3:55 AM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionI should maybe add some more info to the last email:
- The error is not subject-specific. I tried for all my subjects,
and the
error is identical for all of them.
- I am aware of the face that one needs Matlab to run lGI, and it is
on
the PATH (otherwise the lGI computation for the cross subjects would
also
fail).
- I know that the error message, on first glance, seems to suggest
that
there is a syntax error in the recon-all shell script, and that this
may
suggest that someone messed with it. I strongly believe that this is
not
the case though, because:
- FreeSurfer is installed in a directory where only root has write
access.
- The cross subject lGI computation finished successfully this
morning.
- Running 'stat' on the recon-all file shows that it has not been
modified after the installation data, more than a year ago.
If you want me to upload subject data, please let me know.
Best,
Tim
On 07/22/2021 9:43 AM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use Caution
Dear FreeSurfer experts,
I am trying to compute local lGI in FreeSurfer 6 for a subject
that has
undergone longitudinal processing.
In this example, the longitudinal base subject folder (with the
long
template recon-all output for that subject) is called "111002" and
the
folder with the data for timepoint 1, for which I would like to
compute lGI
now, is called "111002_MR1.long.111002". So I run the following
command:
recon-all -long 111002_MR1.long.111002 111002 -localGIThe only output, after less than a second, is:
Unmatched '"'.Then the script terminates and I am back at the shell. Any
thoughts on
this or ideas?
I have successfully computed local lGI for the cross subjects on
the
same computer, it finished this morning (using the command
'recon-all -s
$CROSS_SUBJECT -localGI'). So the recon-all command in general seems
to
work, the error is specific to the lgi long command it seems.
Here is some system info:
cat $FREESURFER_HOME/build-stamp.txt
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
uname -a
Linux lxsrv2 5.8.0-59-generic #66~20.04.1-Ubuntu SMP Thu Jun 17
11:14:10
UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
All the best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main,
Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1-WUV2Ug0jhZw_z4dV-IQQiAPApnIaPSiC-0atT-7zi_og4...
-- Tim Schäfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1-JjRy3gJKSThxfl_BXH1tHE9F7kEFW7ElW3p4qhUrfEWfB...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1OcbJVPQOmxVAYequdU_5aXNSHhsuyFAnnp5UCmt8d8pee3...
-- Tim Schäfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/149i5otHc3Vfz-SNjbXb2XIt9OuzZiN3D-ubuQpYP9pXJMd...
-- Tim Schäfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1J4PagdiKrruT5yiW5d_y1ce0eWt7RTg-b8dt7fO-pfLeRt...
freesurfer@nmr.mgh.harvard.edu
-
Paul Wighton -
Tim Schäfer