Hi All,
I am sorry to repost this message as I did not hear from you. I am wondering whether someone could tell me how I can do family wise error rate correction. I ran mri_glmfit with sim option and how I can perform the FWER correction using mri_surfcluster.
Thanks Venkatesh
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mri_glmfit-sim does the correction for you. It produces a file with the table of clusters. Run it with --help to get more info doug
On 9/13/13 4:48 PM, Venkatesh Rajagopalan wrote:
Hi All,
I am sorry to repost this message as I did not hear from you. I am wondering whether someone could tell me how I can do family wise error rate correction. I ran mri_glmfit with sim option and how I can perform the FWER correction using mri_surfcluster.
Thanks
Venkatesh
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The information in this transmission is intended for official use of the Kessler Foundation. It is intended for the exclusive use of the persons or entities to which it is addressed. If you are not an intended recipient or the employee or agent responsible for delivering this transmission to an intended recipient, be aware that any disclosure, dissemination, distribution or copying of this communication, or the use of its contents, is strictly prohibited. If you received this transmission in error, please notify the sender by return e-mail and delete the material from any computer.
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Hello Freesurfer experts,
We are trying to run func2roi-sess in stable 3 (this command still exists in stable 3). However, we get an error that says it can't find the analysis.info file, even though it is definitely there (not to mention that we previously ran this analysis for the same subjects using the same command lines and it worked).
Here is the exact series of commands used; for purposes of overwriting not being an issue, I deleted the directory that had been created when we ran this previously:
cd /cluster/ablood/1/AdjustedParadigmFiles
source /usr/local/freesurfer/nmr-stable3-env
setenv SUBJECTS_DIR /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
func2roi-sess -roidef M6_LH_t6_0_sm5_0thresh -analysis tap_lh_long_CD_R01BTX_ctrl1_sess1_sm5 -maskcontrast tap_lh_long_CD_R01BTX_ctrl1_sess1_sm5_contrast -labelfile /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_ctrl1_sess1_recon/label/M6_LH_CD_R01BTX_ctrl1_sess1.label
-maskthresh 6.0 -masktail pos -maskmap t -s CD_R01BTX_ctrl1_sess1 -df sessdirfile
And the readout is:
func2roi-sess logfile is /autofs/cluster/ablood/1/AdjustedParadigmFiles/log/func2roi-sess.log ---------------------------------------------------------- ERROR: cannot find tap_lh_long_CD_R01BTX_ctrl1_sess1_sm5/analysis.info
We get this error on multiple machines using multiple peoples' accounts, so I don't think there is a general error here somewhere... Please let us know if you can figure out what may be going on; is there anything about FSL settings that maybe needs to be specified since it's an old environment?
Thank you for the help! Jacob
Hello again,
It seems the issue was being caused by a change we had made to our director structure that did not account for a reference document to some of the outputs from earlier processing.
Thank you,
Jacob
Hello Freesurfer experts,
We are trying to run func2roi-sess in stable 3 (this command still exists in stable 3). However, we get an error that says it can't find the analysis.info file, even though it is definitely there (not to mention that we previously ran this analysis for the same subjects using the same command lines and it worked).
Here is the exact series of commands used; for purposes of overwriting not being an issue, I deleted the directory that had been created when we ran this previously:
cd /cluster/ablood/1/AdjustedParadigmFiles
source /usr/local/freesurfer/nmr-stable3-env
setenv SUBJECTS_DIR /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
func2roi-sess -roidef M6_LH_t6_0_sm5_0thresh -analysis tap_lh_long_CD_R01BTX_ctrl1_sess1_sm5 -maskcontrast tap_lh_long_CD_R01BTX_ctrl1_sess1_sm5_contrast -labelfile /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_ctrl1_sess1_recon/label/M6_LH_CD_R01BTX_ctrl1_sess1.label
-maskthresh 6.0 -masktail pos -maskmap t -s CD_R01BTX_ctrl1_sess1 -df sessdirfile
And the readout is:
func2roi-sess logfile is /autofs/cluster/ablood/1/AdjustedParadigmFiles/log/func2roi-sess.log
ERROR: cannot find tap_lh_long_CD_R01BTX_ctrl1_sess1_sm5/analysis.info
We get this error on multiple machines using multiple peoples' accounts, so I don't think there is a general error here somewhere... Please let us know if you can figure out what may be going on; is there anything about FSL settings that maybe needs to be specified since it's an old environment?
Thank you for the help! Jacob
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
JacobML＠nmr.mgh.harvard.edu -
Venkatesh Rajagopalan