Hi experts,
I am having trouble performing a Monte Carlo correction using mri_glmfit-sim.
My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. I then ran mri_glmfit on the data.
I want to do my analysis/correction only in auditory cortex (AC) so I did my own simulation in AC of each hemisphere using mri_mcsim (as per http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
So far, so good.
But when I try to run:
mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it didn't help.
Any thoughts? Also, can you clarify which comparison neg vs pos will give me?
Thank you,
Susan McLaughlin, PhD Research Scientist Laboratory for Auditory Brain Sciences & Neuroengineering Institute for Learning & Brain Sciences (I-LABS) Portage Bay Bldg. Room 204 University of Washington, Box 357988 Seattle, WA 98195-7988
Ph: (206) 616-0102 Fx: (206) 221-6472 Cell: 206-850-8638 E-mail: smcl@uw.edu
Can you run
mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log
and send me doug.log?
On 11/02/2015 05:08 PM, smcl@u.washington.edu wrote:
Hi experts,
I am having trouble performing a Monte Carlo correction using mri_glmfit-sim.
My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. I then ran mri_glmfit on the data.
I want to do my analysis/correction only in auditory cortex (AC) so I did my own simulation in AC of each hemisphere using mri_mcsim (as per http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
So far, so good.
But when I try to run:
mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it didn't help.
Any thoughts? Also, can you clarify which comparison neg vs pos will give me?
Thank you,
Susan McLaughlin, PhD Research Scientist Laboratory for Auditory Brain Sciences & Neuroengineering Institute for Learning & Brain Sciences (I-LABS) Portage Bay Bldg. Room 204 University of Washington, Box 357988 Seattle, WA 98195-7988
Ph: (206) 616-0102 Fx: (206) 221-6472 Cell: 206-850-8638 E-mail: smcl@uw.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Do you mean:
mri_glmfit-sim --debug --glmdir /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee doug.log?
When I tried running the same code with |& tee doug.log at the end, I kept getting:
syntax error near unexpected token `&'
Thanks, Susan
On Tue, 3 Nov 2015, Douglas N Greve wrote:
Can you run
mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log
and send me doug.log?
On 11/02/2015 05:08 PM, smcl@u.washington.edu wrote:
Hi experts,
I am having trouble performing a Monte Carlo correction using mri_glmfit-sim.
My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. I then ran mri_glmfit on the data.
I want to do my analysis/correction only in auditory cortex (AC) so I did my own simulation in AC of each hemisphere using mri_mcsim (as per http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
So far, so good.
But when I try to run:
mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it didn't help.
Any thoughts? Also, can you clarify which comparison neg vs pos will give me?
Thank you,
Susan McLaughlin, PhD Research Scientist Laboratory for Auditory Brain Sciences & Neuroengineering Institute for Learning & Brain Sciences (I-LABS) Portage Bay Bldg. Room 204 University of Washington, Box 357988 Seattle, WA 98195-7988
Ph: (206) 616-0102 Fx: (206) 221-6472 Cell: 206-850-8638 E-mail: smcl@uw.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
I meant &. The & works for tcsh (or csh). Are you using bash? I'm not sure what the bash equivalent is. Maybe |2 instead of |& perhaps some bash experts can weigh in
On 11/03/2015 01:41 PM, smcl@u.washington.edu wrote:
Hi Doug,
Do you mean:
mri_glmfit-sim --debug --glmdir /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee doug.log?
When I tried running the same code with |& tee doug.log at the end, I kept getting:
syntax error near unexpected token `&'
Thanks, Susan
On Tue, 3 Nov 2015, Douglas N Greve wrote:
Can you run
mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log
and send me doug.log?
On 11/02/2015 05:08 PM, smcl@u.washington.edu wrote:
Hi experts,
I am having trouble performing a Monte Carlo correction using mri_glmfit-sim.
My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. I then ran mri_glmfit on the data.
I want to do my analysis/correction only in auditory cortex (AC) so I did my own simulation in AC of each hemisphere using mri_mcsim (as per http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
So far, so good.
But when I try to run:
mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it didn't help.
Any thoughts? Also, can you clarify which comparison neg vs pos will give me?
Thank you,
Susan McLaughlin, PhD Research Scientist Laboratory for Auditory Brain Sciences & Neuroengineering Institute for Learning & Brain Sciences (I-LABS) Portage Bay Bldg. Room 204 University of Washington, Box 357988 Seattle, WA 98195-7988
Ph: (206) 616-0102 Fx: (206) 221-6472 Cell: 206-850-8638 E-mail: smcl@uw.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I am using bash. I am trying to google the bash equivalent of tcsh |&, but if anybody knows it, please let me know.
thanks, Susan
On Tue, 3 Nov 2015, Douglas N Greve wrote:
I meant &. The & works for tcsh (or csh). Are you using bash? I'm not sure what the bash equivalent is. Maybe |2 instead of |& perhaps some bash experts can weigh in
On 11/03/2015 01:41 PM, smcl@u.washington.edu wrote:
Hi Doug,
Do you mean:
mri_glmfit-sim --debug --glmdir /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee doug.log?
When I tried running the same code with |& tee doug.log at the end, I kept getting:
syntax error near unexpected token `&'
Thanks, Susan
On Tue, 3 Nov 2015, Douglas N Greve wrote:
Can you run
mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log
and send me doug.log?
On 11/02/2015 05:08 PM, smcl@u.washington.edu wrote:
Hi experts,
I am having trouble performing a Monte Carlo correction using mri_glmfit-sim.
My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. I then ran mri_glmfit on the data.
I want to do my analysis/correction only in auditory cortex (AC) so I did my own simulation in AC of each hemisphere using mri_mcsim (as per http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
So far, so good.
But when I try to run:
mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it didn't help.
Any thoughts? Also, can you clarify which comparison neg vs pos will give me?
Thank you,
Susan McLaughlin, PhD Research Scientist Laboratory for Auditory Brain Sciences & Neuroengineering Institute for Learning & Brain Sciences (I-LABS) Portage Bay Bldg. Room 204 University of Washington, Box 357988 Seattle, WA 98195-7988
Ph: (206) 616-0102 Fx: (206) 221-6472 Cell: 206-850-8638 E-mail: smcl@uw.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi DOug,
doug.log is attached
the bash equivalent for |& is 2>&1 |
thanks, Susan
On Tue, 3 Nov 2015, Douglas N Greve wrote:
I meant &. The & works for tcsh (or csh). Are you using bash? I'm not sure what the bash equivalent is. Maybe |2 instead of |& perhaps some bash experts can weigh in
On 11/03/2015 01:41 PM, smcl@u.washington.edu wrote:
Hi Doug,
Do you mean:
mri_glmfit-sim --debug --glmdir /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee doug.log?
When I tried running the same code with |& tee doug.log at the end, I kept getting:
syntax error near unexpected token `&'
Thanks, Susan
On Tue, 3 Nov 2015, Douglas N Greve wrote:
Can you run
mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log
and send me doug.log?
On 11/02/2015 05:08 PM, smcl@u.washington.edu wrote:
Hi experts,
I am having trouble performing a Monte Carlo correction using mri_glmfit-sim.
My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. I then ran mri_glmfit on the data.
I want to do my analysis/correction only in auditory cortex (AC) so I did my own simulation in AC of each hemisphere using mri_mcsim (as per http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
So far, so good.
But when I try to run:
mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it didn't help.
Any thoughts? Also, can you clarify which comparison neg vs pos will give me?
Thank you,
Susan McLaughlin, PhD Research Scientist Laboratory for Auditory Brain Sciences & Neuroengineering Institute for Learning & Brain Sciences (I-LABS) Portage Bay Bldg. Room 204 University of Washington, Box 357988 Seattle, WA 98195-7988
Ph: (206) 616-0102 Fx: (206) 221-6472 Cell: 206-850-8638 E-mail: smcl@uw.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
it cannot find this file
/Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat
which should have been created by mri_glmfit. What is your mri_glmfit command line?
Also, don't use --grf, that is for volumes only
On 11/03/2015 02:27 PM, smcl@u.washington.edu wrote:
Hi DOug,
doug.log is attached
the bash equivalent for |& is 2>&1 |
thanks, Susan
On Tue, 3 Nov 2015, Douglas N Greve wrote:
I meant &. The & works for tcsh (or csh). Are you using bash? I'm not sure what the bash equivalent is. Maybe |2 instead of |& perhaps some bash experts can weigh in
On 11/03/2015 01:41 PM, smcl@u.washington.edu wrote:
Hi Doug,
Do you mean:
mri_glmfit-sim --debug --glmdir /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee doug.log?
When I tried running the same code with |& tee doug.log at the end, I kept getting:
syntax error near unexpected token `&'
Thanks, Susan
On Tue, 3 Nov 2015, Douglas N Greve wrote:
Can you run
mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log
and send me doug.log?
On 11/02/2015 05:08 PM, smcl@u.washington.edu wrote:
Hi experts,
I am having trouble performing a Monte Carlo correction using mri_glmfit-sim.
My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. I then ran mri_glmfit on the data.
I want to do my analysis/correction only in auditory cortex (AC) so I did my own simulation in AC of each hemisphere using mri_mcsim (as per http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
So far, so good.
But when I try to run:
mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it didn't help.
Any thoughts? Also, can you clarify which comparison neg vs pos will give me?
Thank you,
Susan McLaughlin, PhD Research Scientist Laboratory for Auditory Brain Sciences & Neuroengineering Institute for Learning & Brain Sciences (I-LABS) Portage Bay Bldg. Room 204 University of Washington, Box 357988 Seattle, WA 98195-7988
Ph: (206) 616-0102 Fx: (206) 221-6472 Cell: 206-850-8638 E-mail: smcl@uw.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It's:
mri_glmfit --y /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh --osgm --glmdir /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx --surf fsaverage lh --label /Applications/freesurfer/subjects/fsaverage/label/lh.AC.label
fwhm.dat is actually in [MyData]/cope7ACroi_rh.osgm.rfx rather than [MyData]/cope7ACroi_rh.osgm.rfx/osgm. I think that actually also happened for some other files needed and I moved them. Is the problem something in my mri_glmfit command?
Susan
On Tue, 3 Nov 2015, Douglas N Greve wrote:
it cannot find this file
/Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat
which should have been created by mri_glmfit. What is your mri_glmfit command line?
Also, don't use --grf, that is for volumes only
On 11/03/2015 02:27 PM, smcl@u.washington.edu wrote:
Hi DOug,
doug.log is attached
the bash equivalent for |& is 2>&1 |
thanks, Susan
On Tue, 3 Nov 2015, Douglas N Greve wrote:
I meant &. The & works for tcsh (or csh). Are you using bash? I'm not sure what the bash equivalent is. Maybe |2 instead of |& perhaps some bash experts can weigh in
On 11/03/2015 01:41 PM, smcl@u.washington.edu wrote:
Hi Doug,
Do you mean:
mri_glmfit-sim --debug --glmdir /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee doug.log?
When I tried running the same code with |& tee doug.log at the end, I kept getting:
syntax error near unexpected token `&'
Thanks, Susan
On Tue, 3 Nov 2015, Douglas N Greve wrote:
Can you run
mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log
and send me doug.log?
On 11/02/2015 05:08 PM, smcl@u.washington.edu wrote:
Hi experts,
I am having trouble performing a Monte Carlo correction using mri_glmfit-sim.
My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. I then ran mri_glmfit on the data.
I want to do my analysis/correction only in auditory cortex (AC) so I did my own simulation in AC of each hemisphere using mri_mcsim (as per http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
So far, so good.
But when I try to run:
mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it didn't help.
Any thoughts? Also, can you clarify which comparison neg vs pos will give me?
Thank you,
Susan McLaughlin, PhD Research Scientist Laboratory for Auditory Brain Sciences & Neuroengineering Institute for Learning & Brain Sciences (I-LABS) Portage Bay Bldg. Room 204 University of Washington, Box 357988 Seattle, WA 98195-7988
Ph: (206) 616-0102 Fx: (206) 221-6472 Cell: 206-850-8638 E-mail: smcl@uw.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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The fwhm.dat file was in the right place. You passed the wrong folder to mri_glmfit-sim. You should pass it
cope7ACroi_rh.osgm.rfx
doug
On 11/03/2015 02:40 PM, smcl@u.washington.edu wrote:
It's:
mri_glmfit --y /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh --osgm --glmdir /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx --surf fsaverage lh --label /Applications/freesurfer/subjects/fsaverage/label/lh.AC.label
fwhm.dat is actually in [MyData]/cope7ACroi_rh.osgm.rfx rather than [MyData]/cope7ACroi_rh.osgm.rfx/osgm. I think that actually also happened for some other files needed and I moved them. Is the problem something in my mri_glmfit command?
Susan
On Tue, 3 Nov 2015, Douglas N Greve wrote:
it cannot find this file
/Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat
which should have been created by mri_glmfit. What is your mri_glmfit command line?
Also, don't use --grf, that is for volumes only
On 11/03/2015 02:27 PM, smcl@u.washington.edu wrote:
Hi DOug,
doug.log is attached
the bash equivalent for |& is 2>&1 |
thanks, Susan
On Tue, 3 Nov 2015, Douglas N Greve wrote:
I meant &. The & works for tcsh (or csh). Are you using bash? I'm not sure what the bash equivalent is. Maybe |2 instead of |& perhaps some bash experts can weigh in
On 11/03/2015 01:41 PM, smcl@u.washington.edu wrote:
Hi Doug,
Do you mean:
mri_glmfit-sim --debug --glmdir/Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee doug.log?
When I tried running the same code with |& tee doug.log at the end, I kept getting:
syntax error near unexpected token `&'
Thanks, Susan
On Tue, 3 Nov 2015, Douglas N Greve wrote:
Can you run
mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log
and send me doug.log?
On 11/02/2015 05:08 PM, smcl@u.washington.edu wrote: > Hi experts, > > I am having trouble performing a Monte Carlo correction using > mri_glmfit-sim. > > My data were sampled to fsaverage and smoothed at fwhm 5, using > mris_preproc. I then ran mri_glmfit on the data. > > I want to do my analysis/correction only in auditory cortex (AC) > so I did my own simulation in AC of each hemisphere using > mri_mcsim (as per > http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo). > > So far, so good. > > But when I try to run: > > mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm > --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space > > I get "fwhm: Undefined variable." I tried adding --fwhm-override > 5, but it didn't help. > > Any thoughts? Also, can you clarify which comparison neg vs pos > will give me? > > Thank you, > > Susan McLaughlin, PhD > Research Scientist > Laboratory for Auditory Brain Sciences & Neuroengineering > Institute for Learning & Brain Sciences (I-LABS) > Portage Bay Bldg. Room 204 > University of Washington, Box 357988 > Seattle, WA 98195-7988 > > Ph: (206) 616-0102 Fx: (206) 221-6472 > Cell: 206-850-8638 > E-mail: smcl@uw.edu > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
>
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
smcl＠u.washington.edu