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 \
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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The -gcam command requires 7 arguments. What would the seventh be? Please let me know. I really appreciate all your help! ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Tuesday, July 18, 2017 3:31 PM To: freesurfer@nmr.mgh.harvard.edu 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 Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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_complia... . 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.
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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Tuesday, July 18, 2017 3:31 PM To: freesurfer@nmr.mgh.harvard.edu 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 Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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_complia... . 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
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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Tuesday, July 25, 2017 2:27 PM To: freesurfer@nmr.mgh.harvard.edu 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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Tuesday, July 18, 2017 3:31 PM To: freesurfer@nmr.mgh.harvard.edu 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 Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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_complia... . 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://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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_complia... . 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.
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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Tuesday, July 25, 2017 2:27 PM To: freesurfer@nmr.mgh.harvard.edu 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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Tuesday, July 18, 2017 3:31 PM To: freesurfer@nmr.mgh.harvard.edu 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 \
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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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
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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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.
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Douglas Greve -
Douglas N Greve
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Linda Eva Heidinger