Dear Freesurfer experts,
Based on this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033337... , I wrote a short script to extract the centroids from Desikan-Killiany atlas.
###### for hemi in lh rh; do mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels for label in ${labels}; do mri_surfcluster --in /usr/local/freesurfer/subjects/fsaverage/surf/${hemi}.thickness --clabel ./labels/${label}.label --sum ./labels/sum.${label} --centroid --thmin 0 --hemi ${hemi} --subject fsaverage tail -1 ./labels/sum.${label} | sed 's/ */ /g' | cut -d' ' -f6-8 >> ./labels/68parc.centroids.txt done done #######
However, 1) the value is not precise enough, it is only one digit after decimal point. And 2) I kept getting the same value for each hemisphere. Eg,. 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0
I would appreciate if you have any suggestions regarding extracting centroids and the aforementioned issues! Thank you for your time!
Best, Foucault
Hi Foucault,
In the snippet you added you don’t define the labels variable (which you subsequently loop over in for label in ${labels}).
There are two possible mistakes that are easy to fix. One may be that you forgot to read in the labels! And the other is that to get all the values in an array you need ${labels[@]}.
I don’t think you need greater precision than you have. The regions are pretty far apart in mm terms :)
Kirstie
Sent from my iPhone, please excuse any typos or excessive brevity
On 21 Feb 2018, at 03:44, zuxfoucault Wong zuxfoucault@gmail.com wrote:
Dear Freesurfer experts,
Based on this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033337... , I wrote a short script to extract the centroids from Desikan-Killiany atlas.
###### for hemi in lh rh; do mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels for label in ${labels}; do mri_surfcluster --in /usr/local/freesurfer/subjects/fsaverage/surf/${hemi}.thickness --clabel ./labels/${label}.label --sum ./labels/sum.${label} --centroid --thmin 0 --hemi ${hemi} --subject fsaverage tail -1 ./labels/sum.${label} | sed 's/ */ /g' | cut -d' ' -f6-8 >> ./labels/68parc.centroids.txt done done #######
However, 1) the value is not precise enough, it is only one digit after decimal point. And 2) I kept getting the same value for each hemisphere. Eg,. 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0
I would appreciate if you have any suggestions regarding extracting centroids and the aforementioned issues! Thank you for your time!
Best, Foucault
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.
Hi Kirstie,
Thank you very much for the suggestions! I modified my snippet to prevent it from looping the same value and still got the same results?
###### input=($(cat ./names_68parc.txt)) labels=() hemis=() j=0 for i in "${input[@]}"; do if [[ $i == lh_* ]]; then hemis[j]="lh" i=$(echo $i | sed 's/^lh_//g') labels[j]="$i" (( j++ )) elif [[ $i == rh_* ]]; then hemis[j]="rh" i=$(echo $i | sed 's/^rh_//g') labels[j]="$i" (( j++ )) fi done
nlabel=68 if [[ ${#labels[@]} != $nlabel ]] && [[ ${#hemi[@]} != $nlabel ]]; then echo " number of label not match " fi
for hemi in lh rh; do mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels done
for ((i=0;i<${#labels[@]};i++)); do mri_surfcluster --in /usr/local/freesurfer_orig/subjects/fsaverage/surf/${hemis[i]}.thickness --clabel ./labels/${hemis[i]}.${labels[i]}.label --sum ./labels/sum.${hemis[i]}.${labels[i]} --centroid --thmin 0 --hemi ${hemis[i]} --subject fsaverage tail -1 ./labels/sum.${hemis[i]}.${labels[i]} | sed 's/ */ /g' | cut -d' ' -f6-8 >> ./labels/68parc.centroids.txt done ######
The output message of mri_surfcluster: ###### thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $ hemi = rh srcid = /usr/local/freesurfer_orig/subjects/fsaverage/surf/rh.thickness srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = abs thmin = 0 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm clabelfile = ./labels/rh.lateraloccipital.label clabelinv = 0 nth = -1 sumfile = ./labels/sum.rh.lateraloccipital subjectsdir = /usr/local/freesurfer_orig/subjects FixMNI = 1 Loading clabel ./labels/rh.lateraloccipital.label. Found 5963 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /usr/local/freesurfer_orig/subjects/fsaverage/mri/transforms/talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; ---------------------------------------------------- Reading source surface /usr/local/freesurfer_orig/subjects/fsaverage/surf/rh.white Done reading source surface Computing metric properties Loading source values number of voxels in search space = 5963 Done loading source values (nvtxs = 163842) overall max = 3.19752 at vertex 122846 overall min = 0 at vertex 0 surface nvertices 163842 metric props tot surface area 65020.839844 group_avg_vtxarea_loaded 1 masked surface area 4459.747559 NOT Adjusting threshold for 1-tailed test thminadj = 0 Searching for Clusters ... thmin=0.000000 (0.000000), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000 Found 1 clusters Max cluster size 82167.000000 INFO: fixing MNI talairach coordinates
On Wed, Feb 21, 2018 at 3:15 PM, Kirstie Whitaker kw401@cam.ac.uk wrote:
Hi Foucault,
In the snippet you added you don’t define the labels variable (which you subsequently loop over in for label in ${labels}).
There are two possible mistakes that are easy to fix. One may be that you forgot to read in the labels! And the other is that to get all the values in an array you need ${labels[@]}.
I don’t think you need greater precision than you have. The regions are pretty far apart in mm terms :)
Kirstie
Sent from my iPhone, please excuse any typos or excessive brevity
On 21 Feb 2018, at 03:44, zuxfoucault Wong zuxfoucault@gmail.com wrote:
Dear Freesurfer experts,
Based on this https://mail.nmr.mgh.harvard.edu/pipermail// freesurfer/2013-September/033337.html , I wrote a short script to extract the centroids from Desikan-Killiany atlas.
###### for hemi in lh rh; do mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels for label in ${labels}; do mri_surfcluster --in /usr/local/freesurfer/subjects/fsaverage/surf/${hemi}.thickness --clabel ./labels/${label}.label --sum ./labels/sum.${label} --centroid --thmin 0 --hemi ${hemi} --subject fsaverage tail -1 ./labels/sum.${label} | sed 's/ */ /g' | cut -d' ' -f6-8 >> ./labels/68parc.centroids.txt done done #######
However, 1) the value is not precise enough, it is only one digit after decimal point. And 2) I kept getting the same value for each hemisphere. Eg,. 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0
I would appreciate if you have any suggestions regarding extracting centroids and the aforementioned issues! Thank you for your time!
Best, Foucault
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
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.
Attach name file and result file.
Thank you for your time!
Best, Foucault
On Wed, Feb 21, 2018 at 5:24 PM, zuxfoucault Wong zuxfoucault@gmail.com wrote:
Hi Kirstie,
Thank you very much for the suggestions! I modified my snippet to prevent it from looping the same value and still got the same results?
###### input=($(cat ./names_68parc.txt)) labels=() hemis=() j=0 for i in "${input[@]}"; do if [[ $i == lh_* ]]; then hemis[j]="lh" i=$(echo $i | sed 's/^lh_//g') labels[j]="$i" (( j++ )) elif [[ $i == rh_* ]]; then hemis[j]="rh" i=$(echo $i | sed 's/^rh_//g') labels[j]="$i" (( j++ )) fi done
nlabel=68 if [[ ${#labels[@]} != $nlabel ]] && [[ ${#hemi[@]} != $nlabel ]]; then echo " number of label not match " fi
for hemi in lh rh; do mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels done
for ((i=0;i<${#labels[@]};i++)); do mri_surfcluster --in /usr/local/freesurfer_orig/subjects/fsaverage/surf/${hemis[i]}.thickness --clabel ./labels/${hemis[i]}.${labels[i]}.label --sum ./labels/sum.${hemis[i]}.${labels[i]} --centroid --thmin 0 --hemi ${hemis[i]} --subject fsaverage tail -1 ./labels/sum.${hemis[i]}.${labels[i]} | sed 's/ */ /g' | cut -d' ' -f6-8 >> ./labels/68parc.centroids.txt done ######
The output message of mri_surfcluster: ###### thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $ hemi = rh srcid = /usr/local/freesurfer_orig/subjects/fsaverage/surf/rh. thickness srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = abs thmin = 0 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm clabelfile = ./labels/rh.lateraloccipital.label clabelinv = 0 nth = -1 sumfile = ./labels/sum.rh.lateraloccipital subjectsdir = /usr/local/freesurfer_orig/subjects FixMNI = 1 Loading clabel ./labels/rh.lateraloccipital.label. Found 5963 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /usr/local/freesurfer_orig/subjects/fsaverage/mri/transforms/talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000;
Reading source surface /usr/local/freesurfer_orig/ subjects/fsaverage/surf/rh.white Done reading source surface Computing metric properties Loading source values number of voxels in search space = 5963 Done loading source values (nvtxs = 163842) overall max = 3.19752 at vertex 122846 overall min = 0 at vertex 0 surface nvertices 163842 metric props tot surface area 65020.839844 group_avg_vtxarea_loaded 1 masked surface area 4459.747559 NOT Adjusting threshold for 1-tailed test thminadj = 0 Searching for Clusters ... thmin=0.000000 (0.000000), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000 Found 1 clusters Max cluster size 82167.000000 INFO: fixing MNI talairach coordinates
On Wed, Feb 21, 2018 at 3:15 PM, Kirstie Whitaker kw401@cam.ac.uk wrote:
Hi Foucault,
In the snippet you added you don’t define the labels variable (which you subsequently loop over in for label in ${labels}).
There are two possible mistakes that are easy to fix. One may be that you forgot to read in the labels! And the other is that to get all the values in an array you need ${labels[@]}.
I don’t think you need greater precision than you have. The regions are pretty far apart in mm terms :)
Kirstie
Sent from my iPhone, please excuse any typos or excessive brevity
On 21 Feb 2018, at 03:44, zuxfoucault Wong zuxfoucault@gmail.com wrote:
Dear Freesurfer experts,
Based on this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/ 2013-September/033337.html , I wrote a short script to extract the centroids from Desikan-Killiany atlas.
###### for hemi in lh rh; do mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels for label in ${labels}; do mri_surfcluster --in /usr/local/freesurfer/subjects /fsaverage/surf/${hemi}.thickness --clabel ./labels/${label}.label --sum ./labels/sum.${label} --centroid --thmin 0 --hemi ${hemi} --subject fsaverage tail -1 ./labels/sum.${label} | sed 's/ */ /g' | cut -d' ' -f6-8 >> ./labels/68parc.centroids.txt done done #######
However, 1) the value is not precise enough, it is only one digit after decimal point. And 2) I kept getting the same value for each hemisphere. Eg,. 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0
I would appreciate if you have any suggestions regarding extracting centroids and the aforementioned issues! Thank you for your time!
Best, Foucault
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
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.
Hi Foucalt,
I think you need to set the threshold to slightly larger than 0 otherwise you're taking the center of mass of the whole image (including the 0s) when really you want to exclude the 0s and only look at the individual regions.
I changed --thmin 0 to --thmin 0.1 and the results looked good.
Kx
On 21 February 2018 at 09:28, zuxfoucault Wong zuxfoucault@gmail.com wrote:
Attach name file and result file.
Thank you for your time!
Best, Foucault
On Wed, Feb 21, 2018 at 5:24 PM, zuxfoucault Wong zuxfoucault@gmail.com wrote:
Hi Kirstie,
Thank you very much for the suggestions! I modified my snippet to prevent it from looping the same value and still got the same results?
###### input=($(cat ./names_68parc.txt)) labels=() hemis=() j=0 for i in "${input[@]}"; do if [[ $i == lh_* ]]; then hemis[j]="lh" i=$(echo $i | sed 's/^lh_//g') labels[j]="$i" (( j++ )) elif [[ $i == rh_* ]]; then hemis[j]="rh" i=$(echo $i | sed 's/^rh_//g') labels[j]="$i" (( j++ )) fi done
nlabel=68 if [[ ${#labels[@]} != $nlabel ]] && [[ ${#hemi[@]} != $nlabel ]]; then echo " number of label not match " fi
for hemi in lh rh; do mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels done
for ((i=0;i<${#labels[@]};i++)); do mri_surfcluster --in /usr/local/freesurfer_orig/sub jects/fsaverage/surf/${hemis[i]}.thickness --clabel ./labels/${hemis[i]}.${labels[i]}.label --sum ./labels/sum.${hemis[i]}.${labels[i]} --centroid --thmin 0 --hemi ${hemis[i]} --subject fsaverage tail -1 ./labels/sum.${hemis[i]}.${labels[i]} | sed 's/ */ /g' | cut -d' ' -f6-8 >> ./labels/68parc.centroids.txt done ######
The output message of mri_surfcluster: ###### thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $ hemi = rh srcid = /usr/local/freesurfer_orig/sub jects/fsaverage/surf/rh.thickness srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = abs thmin = 0 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm clabelfile = ./labels/rh.lateraloccipital.label clabelinv = 0 nth = -1 sumfile = ./labels/sum.rh.lateraloccipital subjectsdir = /usr/local/freesurfer_orig/subjects FixMNI = 1 Loading clabel ./labels/rh.lateraloccipital.label. Found 5963 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /usr/local/freesurfer_orig/subjects/fsaverage/mri/transforms /talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000;
Reading source surface /usr/local/freesurfer_orig/sub jects/fsaverage/surf/rh.white Done reading source surface Computing metric properties Loading source values number of voxels in search space = 5963 Done loading source values (nvtxs = 163842) overall max = 3.19752 at vertex 122846 overall min = 0 at vertex 0 surface nvertices 163842 metric props tot surface area 65020.839844 group_avg_vtxarea_loaded 1 masked surface area 4459.747559 NOT Adjusting threshold for 1-tailed test thminadj = 0 Searching for Clusters ... thmin=0.000000 (0.000000), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000 Found 1 clusters Max cluster size 82167.000000 INFO: fixing MNI talairach coordinates
On Wed, Feb 21, 2018 at 3:15 PM, Kirstie Whitaker kw401@cam.ac.uk wrote:
Hi Foucault,
In the snippet you added you don’t define the labels variable (which you subsequently loop over in for label in ${labels}).
There are two possible mistakes that are easy to fix. One may be that you forgot to read in the labels! And the other is that to get all the values in an array you need ${labels[@]}.
I don’t think you need greater precision than you have. The regions are pretty far apart in mm terms :)
Kirstie
Sent from my iPhone, please excuse any typos or excessive brevity
On 21 Feb 2018, at 03:44, zuxfoucault Wong zuxfoucault@gmail.com wrote:
Dear Freesurfer experts,
Based on this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/ 2013-September/033337.html , I wrote a short script to extract the centroids from Desikan-Killiany atlas.
###### for hemi in lh rh; do mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels for label in ${labels}; do mri_surfcluster --in /usr/local/freesurfer/subjects /fsaverage/surf/${hemi}.thickness --clabel ./labels/${label}.label --sum ./labels/sum.${label} --centroid --thmin 0 --hemi ${hemi} --subject fsaverage tail -1 ./labels/sum.${label} | sed 's/ */ /g' | cut -d' ' -f6-8 >> ./labels/68parc.centroids.txt done done #######
However, 1) the value is not precise enough, it is only one digit after decimal point. And 2) I kept getting the same value for each hemisphere. Eg,. 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0
I would appreciate if you have any suggestions regarding extracting centroids and the aforementioned issues! Thank you for your time!
Best, Foucault
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
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
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.
Yes! I got better results now! Thanks!!
On Thu, Feb 22, 2018 at 12:57 AM Kirstie Whitaker kw401@cam.ac.uk wrote:
Hi Foucalt,
I think you need to set the threshold to slightly larger than 0 otherwise you're taking the center of mass of the whole image (including the 0s) when really you want to exclude the 0s and only look at the individual regions.
I changed --thmin 0 to --thmin 0.1 and the results looked good.
Kx
On 21 February 2018 at 09:28, zuxfoucault Wong zuxfoucault@gmail.com wrote:
Attach name file and result file.
Thank you for your time!
Best, Foucault
On Wed, Feb 21, 2018 at 5:24 PM, zuxfoucault Wong zuxfoucault@gmail.com wrote:
Hi Kirstie,
Thank you very much for the suggestions! I modified my snippet to prevent it from looping the same value and still got the same results?
###### input=($(cat ./names_68parc.txt)) labels=() hemis=() j=0 for i in "${input[@]}"; do if [[ $i == lh_* ]]; then hemis[j]="lh" i=$(echo $i | sed 's/^lh_//g') labels[j]="$i" (( j++ )) elif [[ $i == rh_* ]]; then hemis[j]="rh" i=$(echo $i | sed 's/^rh_//g') labels[j]="$i" (( j++ )) fi done
nlabel=68 if [[ ${#labels[@]} != $nlabel ]] && [[ ${#hemi[@]} != $nlabel ]]; then echo " number of label not match " fi
for hemi in lh rh; do mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels done
for ((i=0;i<${#labels[@]};i++)); do mri_surfcluster --in /usr/local/freesurfer_orig/subjects/fsaverage/surf/${hemis[i]}.thickness --clabel ./labels/${hemis[i]}.${labels[i]}.label --sum ./labels/sum.${hemis[i]}.${labels[i]} --centroid --thmin 0 --hemi ${hemis[i]} --subject fsaverage tail -1 ./labels/sum.${hemis[i]}.${labels[i]} | sed 's/ */ /g' | cut -d' ' -f6-8 >> ./labels/68parc.centroids.txt done ######
The output message of mri_surfcluster: ###### thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $ hemi = rh srcid = /usr/local/freesurfer_orig/subjects/fsaverage/surf/rh.thickness srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = abs thmin = 0 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm clabelfile = ./labels/rh.lateraloccipital.label clabelinv = 0 nth = -1 sumfile = ./labels/sum.rh.lateraloccipital subjectsdir = /usr/local/freesurfer_orig/subjects FixMNI = 1 Loading clabel ./labels/rh.lateraloccipital.label. Found 5963 points in clabel. ------------- XFM matrix (RAS2RAS) ---------------
/usr/local/freesurfer_orig/subjects/fsaverage/mri/transforms/talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000;
Reading source surface /usr/local/freesurfer_orig/subjects/fsaverage/surf/rh.white Done reading source surface Computing metric properties Loading source values number of voxels in search space = 5963 Done loading source values (nvtxs = 163842) overall max = 3.19752 at vertex 122846 overall min = 0 at vertex 0 surface nvertices 163842 metric props tot surface area 65020.839844 group_avg_vtxarea_loaded 1 masked surface area 4459.747559 NOT Adjusting threshold for 1-tailed test thminadj = 0 Searching for Clusters ... thmin=0.000000 (0.000000), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000 Found 1 clusters Max cluster size 82167.000000 INFO: fixing MNI talairach coordinates
On Wed, Feb 21, 2018 at 3:15 PM, Kirstie Whitaker kw401@cam.ac.uk wrote:
Hi Foucault,
In the snippet you added you don’t define the labels variable (which you subsequently loop over in for label in ${labels}).
There are two possible mistakes that are easy to fix. One may be that you forgot to read in the labels! And the other is that to get all the values in an array you need ${labels[@]}.
I don’t think you need greater precision than you have. The regions are pretty far apart in mm terms :)
Kirstie
Sent from my iPhone, please excuse any typos or excessive brevity
On 21 Feb 2018, at 03:44, zuxfoucault Wong zuxfoucault@gmail.com wrote:
Dear Freesurfer experts,
Based on this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033337... , I wrote a short script to extract the centroids from Desikan-Killiany atlas.
###### for hemi in lh rh; do mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels for label in ${labels}; do mri_surfcluster --in /usr/local/freesurfer/subjects/fsaverage/surf/${hemi}.thickness --clabel ./labels/${label}.label --sum ./labels/sum.${label} --centroid --thmin 0 --hemi ${hemi} --subject fsaverage tail -1 ./labels/sum.${label} | sed 's/ */ /g' | cut -d' ' -f6-8 >> ./labels/68parc.centroids.txt done done #######
However, 1) the value is not precise enough, it is only one digit after decimal point. And 2) I kept getting the same value for each hemisphere. Eg,. 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0
I would appreciate if you have any suggestions regarding extracting centroids and the aforementioned issues! Thank you for your time!
Best, Foucault
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-- Kirstie Whitaker, PhD
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*Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB
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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.
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Kirstie Whitaker -
zuxfoucault Wong