can you send the terminal output?
On 7/31/17 5:00 PM, Linda Eva Heidinger wrote: > Hello Dr. Greve, > I ran the program below and got the following errors. Can you help??? I > really would appreciate it. -Linda > > Loading source LTA boldregister003.dat > INFO: This REGISTER_DAT transform is valid only for volumes between COR > types with c_(r,a,s) = 0. > Loading GCAM Subject06/cvs_CVS35MNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z > setting orig areas to linear transform determinant scaled 1.00 > Loading destination LTA > /pkg64/brainmap/freesurfer-v6.0.0_x86_64/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta > MRIvol2volGCAM(): VSM not used > MRIvol2volGCAM(): interpolation type is 0 nearest > MRIvol2volGCAM(): Chaning Source LTA type to vox2vox > > The initial command that was run: > mri_vol2vol --gcam run_003regraijNIFTI.nii boldregister003.dat > Subject06/cvs_CVS35MNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z > $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 0 > subject003matrix.nii > ________________________________________ > From: [email protected] > <[email protected]> on behalf of Douglas N Greve > <[email protected]> > Sent: Tuesday, July 25, 2017 2:27 PM > To: [email protected] > Subject: Re: [Freesurfer] reducing a matrix > > Add another 0 after the register.lta > > > On 07/25/2017 02:46 PM, Linda Eva Heidinger wrote: >> The -gcam command requires 7 arguments. What would the seventh be? Please >> let me know. I really appreciate all your help! >> ________________________________________ >> From: [email protected] >> <[email protected]> on behalf of Douglas N Greve >> <[email protected]> >> Sent: Tuesday, July 18, 2017 3:31 PM >> To: [email protected] >> Subject: Re: [Freesurfer] reducing a matrix >> >> try >> >> >> mri_vol2vol --gcam 005.mc.nii boldregister.dat >> $SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z >> $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 >> output.nii.gz >> >> >> This will sample it down to a 2mm space within the CVS atlas (should >> overlap pretty well with the MNI152 2mm space) >> >> >> >> On 07/18/2017 03:48 PM, Linda Eva Heidinger wrote: >>> Dear experts in freesurfer, >>> >>> I myself am a very beginner in freesurfer but I come with a difficult >>> question to answer. As you can see from the script below, I am trying >>> to obtain the Bold in CVS35MNI152 template space which hopefully has >>> better properties for accuracy and determination of location of a >>> voxel for targeting in use with TMS. One can see that bbregister and >>> mri_cvs_register were used followed by mri_vol2vol to register the >>> Bold and transform it from subject space to the above template. >>> Unfortunately, the template space is in freesurfer space (1mm^3,256^3) >>> . When we try to run the result that we obtain after transformation in >>> our AFNI programs, they couldn't run on our computers because of the >>> size of the Bold matrix being too large. I am wondering if it is >>> possible for mri_cvs_register to use a template that is of the same >>> size as the T1? or really we should just somehow reformulate the >>> transformation matrix resulting from mri_cvs_register which I believe >>> is: final_CVSmorph_tocvs_avg35_MNI152.m3z to allow for a reduced final >>> Bold matrix from mri_vol2vol which will have the same dimensions as >>> the subject space which the original Bold had? >>> >>> I appreciate the time and attention you give this question. >>> >>> Thanks, >>> >>> -Linda >>> >>> >>> >>> # FreeSurfer commands >>> >>> nmr-std-env >>> >>> setenv SUBJECTS_DIR <path to the directory where all MRI data for this >>> study reside> >>> >>> setenv SUBJECT <my subject code> >>> >>> cd $SUBJECTS_DIR >>> >>> # First, run FS recon-all on the T1 (MEMPRAGE) anatomical as usual. >>> >>> recon-all -subjid $SUBJECT -i temp_${SUBJECT}/001.mgz -all -openmp 4 >>> >>> # Second, do co-registration at the individual level between the hires >>> anatomical and the bold (functional) image. >>> # In the below example the already motion corrected (and otherwise >>> preprocessed) bold data for run 005 are in >>> # $SUBJECTS_DIR/$SUBJECT/bold/005/005.mc.nii >>> # Use boundary-based registration (bbregister) - this by far the most >>> accurate tool. >>> # Note: This is rigid 6 DOF. It is almost always best to use rigid DOF >>> 6 for within-subject registration. >>> >>> bbregister >>> --mov $SUBJECT/bold/005/005.mc.nii >>> --frame 0 >>> --bold >>> --s $SUBJECT >>> --init-fsl >>> --reg boldregister.dat >>> --fslmat ${SUBJECT}_anat2bold.mat >>> >>> # Just in case, let us make FSL type coregistration matrices as well. >>> >>> convert_xfm >>> -omat ${SUBJECT}_bold2anat.mat >>> -inverse ${SUBJECT}_anat2bold.mat >>> >>> >>> # Now, we will compute a group-level coregistration from the >>> individual brain to a template brain for both volumetric non-linear >>> morphing. >>> # We will use the standard brain cvs_avg35_inMNI152 as the >>> target/template. >>> >>> mri_cvs_register --mov $SUBJECT --mni --outdir >>> $SUBJECT/cvs_CVS35MNI152 --openmp 8 >>> >>> # Finally, we can move the bold image from the individual spac into >>> the standard space: >>> >>> mri_vol2vol \ >>> --mov $SUBJECT/bold/005/005.mc.nii \ >>> --targ $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/norm.mgz \ >>> --o Grand_Average/${SUBJECT}_CVS35MNI152_005.mc.nii \ >>> --m3z $SUBJECT/cvs_CVS35MNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z \ >>> --noDefM3zPath \ >>> --interp nearest \ >>> --reg $SUBJECT/bold/boldregister.dat \ >>> --no-save-reg \ >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=GKqetTp2xTIvLtRg3X4KoRv99hJX9SmTpU_XT1IjyuA&m=F4vpLZROq5u7kq8YbZVopqrYx7Jslz07HbbISgZfszY&s=1lVk1OkzVqlOUNNoWqTFzLK4e9pW4aOdftXwolSPlss&e= >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> [email protected] >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: >> https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=DwIGaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=GKqetTp2xTIvLtRg3X4KoRv99hJX9SmTpU_XT1IjyuA&m=F4vpLZROq5u7kq8YbZVopqrYx7Jslz07HbbISgZfszY&s=4zYCc1b9UkUaDFyiR42inwna9C5wumHuQiLmGGrpXX0&e= >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=DwIGaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=GKqetTp2xTIvLtRg3X4KoRv99hJX9SmTpU_XT1IjyuA&m=F4vpLZROq5u7kq8YbZVopqrYx7Jslz07HbbISgZfszY&s=LM9fj0PgyZlV7hgiAUSHlhRLH111nMCZX-uMKXCl8f0&e= >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=GKqetTp2xTIvLtRg3X4KoRv99hJX9SmTpU_XT1IjyuA&m=F4vpLZROq5u7kq8YbZVopqrYx7Jslz07HbbISgZfszY&s=1lVk1OkzVqlOUNNoWqTFzLK4e9pW4aOdftXwolSPlss&e= >> >> >> 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 >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIGaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=GKqetTp2xTIvLtRg3X4KoRv99hJX9SmTpU_XT1IjyuA&m=F4vpLZROq5u7kq8YbZVopqrYx7Jslz07HbbISgZfszY&s=xLTC0J3GCxhg-ML_CjDaNZ7oFiWqreaIKbIt8TmT83E&e= >> . 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 >> [email protected] >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICJg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=GKqetTp2xTIvLtRg3X4KoRv99hJX9SmTpU_XT1IjyuA&m=BwvuPcL_GwlXte75Q7JwV6TVJGsYDUBNP4DpXf1qvGM&s=FCQZVwn1U_UHZLqMAWOqVofw-VdFBWCc-jkyCxfqeRk&e= >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: > https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=DwICJg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=GKqetTp2xTIvLtRg3X4KoRv99hJX9SmTpU_XT1IjyuA&m=BwvuPcL_GwlXte75Q7JwV6TVJGsYDUBNP4DpXf1qvGM&s=gaZIm86T9LzCRJrfTVwIxena9oL3KIWdvzbwnIIrRk0&e= > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=DwICJg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=GKqetTp2xTIvLtRg3X4KoRv99hJX9SmTpU_XT1IjyuA&m=BwvuPcL_GwlXte75Q7JwV6TVJGsYDUBNP4DpXf1qvGM&s=2d0ZW5P4iS4XtE5MYxsl-LmCvv3qoQXUijix6B0_GmQ&e= > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICJg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=GKqetTp2xTIvLtRg3X4KoRv99hJX9SmTpU_XT1IjyuA&m=BwvuPcL_GwlXte75Q7JwV6TVJGsYDUBNP4DpXf1qvGM&s=FCQZVwn1U_UHZLqMAWOqVofw-VdFBWCc-jkyCxfqeRk&e= > > > 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 > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwICJg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=GKqetTp2xTIvLtRg3X4KoRv99hJX9SmTpU_XT1IjyuA&m=BwvuPcL_GwlXte75Q7JwV6TVJGsYDUBNP4DpXf1qvGM&s=Z3wA07dHdk_PHNfQZpZhVKC9F-2Uuin_yF7DFyUoPSs&e= > . 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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list [email protected] 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.
