Hi,
Just adding a word about the e-mail of ma colleague Josue. What he meant is that he extracted volumes for exactly the same ROI (a merging of destrieux labels of Hechl’s gyrus, Heschl's sulcus and planum temporale) using 1- a .curv file of this ROI, mri_binarize and mri_segstats or 2- a .label file of this ROI and mris_anatomical_stats.
We get a different volume output (ratio of difference between the 2 methods = approx. 2.5, similar to mean thickness I would say…), so we would like to understand what is happening exactly.
Using the method 1, it’s actually a surface measurement we get no?
Would that be possible to convert a .cuvr file to a .label file ?
Thank you and best, Damien
Josue Luiz Dalboni Da Rocha Wed, 12 Oct 2016 07:26:32 -0700 Dear Doug,
Thank you very much for your advice! We get to extract results for the volumes from a ".curv file encoded ROI" using your recommended command lines (mri_binarize and mri_segstats ), but unfortunately the results are much smaller (around 3 times) than when we extract total gray matter volumes from a respective ".label file encoded ROI" using mris_anatomical_stats . Example: Volumes from a ".curv file encoded ROI" using your recommended command lines (mri_binarize and mri_segstats): Subject1 = 1090 Subject2 = 1181 Subject3 = 713 Subject4 = 1230 Volumes from a respective ".label file encoded ROI" (mris_anatomical_stats): Subject1 = 3497 Subject2 = 3786 Subject3 = 2268 Subject4 = 3491
Are the volumes extracted from a ".curv file encoded ROI" (using mri_binarize and mri_segstats) an estimation of the total gray matter volumes? Why these values are differing that much?
Thank you very much, Josue Dalboni ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve gr...@nmr.mgh.harvard.edu Sent: Wednesday, October 5, 2016 5:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes
I would binarize the curv file with
mri_binarize --i lh.yourcurvfile --abs --min .0000001 --o lh.yourcurvfilebin.mgh
Then compute the volume with
mri_segstats --seg lh.yourcurvfilebin.mgh --id 1 --i lh.volume --accumulate --sum lh.vol.yourcurv.sum
On 10/05/2016 09:09 AM, Josue Luiz Dalboni Da Rocha wrote:
Dear Douglas,
I have a ".curv" file that contains the curvature information inside an automatically delineated ROI and 0 everywhere else. I would like to calculate the volume of this ROI,
Can I extract statistics directly from the ".curv" file?
Best regards, Josue ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve gr...@nmr.mgh.harvard.edu Sent: Tuesday, October 4, 2016 9:41 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes
What is the nature of the segmentation? Is it just a binary (1=in, 0=out) segmentation? And what file format? In general we don't use .w anymore, but it can be converted into something else.
doug
On 10/03/2016 12:35 PM, Josue Luiz Dalboni Da Rocha wrote:
Dear Douglas,
I have a segmented gyrus curvature file (.curv or .w) and I would like to calculate the volume (and other statistics) of this gyrus.
I currently only know mris_anatomical_stats to perform that, but requiring a '.label' file.
Can I extract statistics directly from the ".curv" file?
Or can I convert directly from .curv to .label in order to extract these statistics?
As another option, is it feasible to convert the '.curv' file to nifti volume (mri_surf2vol), binarize it (mri_binarize), and then convert to label (mri_cor2label)?
What does the output nifti file from 'mri_surf2vol' contain? Does it contain the complete volume behind the surface? Or does it only contain the surface over the 3D space?
Thank you very much in advance for your help!
Best regards,
Josue
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 gr...@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
please send command lines
On 10/14/16 6:36 AM, Damien MARIE wrote:
Hi,
Just adding a word about the e-mail of ma colleague Josue. What he meant is that he extracted volumes for exactly the same ROI (a merging of destrieux labels of Hechl’s gyrus, Heschl's sulcus and planum temporale) using 1- a .curv file of this ROI, mri_binarize and mri_segstats or 2- a .label file of this ROI and mris_anatomical_stats.
We get a different volume output (ratio of difference between the 2 methods = approx. 2.5, similar to mean thickness I would say…), so we would like to understand what is happening exactly.
Using the method 1, it’s actually a surface measurement we get no?
Would that be possible to convert a .cuvr file to a .label file ?
Thank you and best, Damien
Josue Luiz Dalboni Da Rocha Wed, 12 Oct 2016 07:26:32 -0700 Dear Doug,
Thank you very much for your advice! We get to extract results for the volumes from a ".curv file encoded ROI" using your recommended command lines (mri_binarize and mri_segstats ), but unfortunately the results are much smaller (around 3 times) than when we extract total gray matter volumes from a respective ".label file encoded ROI" using mris_anatomical_stats . Example: Volumes from a ".curv file encoded ROI" using your recommended command lines (mri_binarize and mri_segstats): Subject1 = 1090 Subject2 = 1181 Subject3 = 713 Subject4 = 1230 Volumes from a respective ".label file encoded ROI" (mris_anatomical_stats): Subject1 = 3497 Subject2 = 3786 Subject3 = 2268 Subject4 = 3491
Are the volumes extracted from a ".curv file encoded ROI" (using mri_binarize and mri_segstats) an estimation of the total gray matter volumes? Why these values are differing that much?
Thank you very much, Josue Dalboni ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu> Sent: Wednesday, October 5, 2016 5:19 PM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes
I would binarize the curv file with
mri_binarize --i lh.yourcurvfile --abs --min .0000001 --o lh.yourcurvfilebin.mgh
Then compute the volume with
mri_segstats --seg lh.yourcurvfilebin.mgh --id 1 --i lh.volume --accumulate --sum lh.vol.yourcurv.sum
On 10/05/2016 09:09 AM, Josue Luiz Dalboni Da Rocha wrote:
Dear Douglas,
I have a ".curv" file that contains the curvature information inside an automatically delineated ROI and 0 everywhere else. I would like to calculate the volume of this ROI,
Can I extract statistics directly from the ".curv" file?
Best regards, Josue ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu
http://nmr.mgh.harvard.edu> on behalf of Douglas N Greve
<gr...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu> Sent: Tuesday, October 4, 2016 9:41 PM To: freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Quantifying volumes
What is the nature of the segmentation? Is it just a binary (1=in, 0=out) segmentation? And what file format? In general we don't use .w anymore, but it can be converted into something else.
doug
On 10/03/2016 12:35 PM, Josue Luiz Dalboni Da Rocha wrote:
Dear Douglas,
I have a segmented gyrus curvature file (.curv or .w) and I would like to calculate the volume (and other statistics) of this gyrus.
I currently only know mris_anatomical_stats to perform that, but requiring a '.label' file.
Can I extract statistics directly from the ".curv" file?
Or can I convert directly from .curv to .label in order to extract these statistics?
As another option, is it feasible to convert the '.curv' file to nifti volume (mri_surf2vol), binarize it (mri_binarize), and then convert to label (mri_cor2label)?
What does the output nifti file from 'mri_surf2vol' contain? Does it contain the complete volume behind the surface? Or does it only contain the surface over the 3D space?
Thank you very much in advance for your help!
Best regards,
Josue
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://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 mailto: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 mailto: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
Dear Doug,
From the curvature file of the ROI (selected portion of surface), we extract the volume using this 2 command lines:
mri_binarize --i $D_load/lh_masked_all.curv --max -.0000001 --o $D_load/lh_masked_all_bin.mgh mri_segstats --seg $D_load/lh_masked_all_bin.mgh --id 1 --i $SUBJECTS_DIR/$subj/surf/lh.volume --accumulate --sum $D_load/lh_masked_all_bin.txt
From the label file of the same ROI, we extract the volume using the following command line: mris_anatomical_stats -l $SUBJECTS_DIR/$subj/label/labelsAtlas2009/lh_masked_all.label -f $outD/lh_masked_all_Volume $subj lh
As the '.curv' file and the '.label' file represent the same ROI, we were expecting to get the same volume (total gray matter volume of the selected portion of surface). But the results using the first method are always about 3 time higher than using the second method.
We would like to understand what is going on, because for some selected portions of ROI we just have the '.curv' file to extract the volume from.
Thank you very much for your help!
Best regards, Josue
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu Sent: Friday, October 14, 2016 5:54 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes
please send command lines
On 10/14/16 6:36 AM, Damien MARIE wrote: Hi,
Just adding a word about the e-mail of ma colleague Josue. What he meant is that he extracted volumes for exactly the same ROI (a merging of destrieux labels of Hechl’s gyrus, Heschl's sulcus and planum temporale) using 1- a .curv file of this ROI, mri_binarize and mri_segstats or 2- a .label file of this ROI and mris_anatomical_stats.
We get a different volume output (ratio of difference between the 2 methods = approx. 2.5, similar to mean thickness I would say…), so we would like to understand what is happening exactly.
Using the method 1, it’s actually a surface measurement we get no?
Would that be possible to convert a .cuvr file to a .label file ?
Thank you and best, Damien
Josue Luiz Dalboni Da Rocha Wed, 12 Oct 2016 07:26:32 -0700 Dear Doug,
Thank you very much for your advice! We get to extract results for the volumes from a ".curv file encoded ROI" using your recommended command lines (mri_binarize and mri_segstats ), but unfortunately the results are much smaller (around 3 times) than when we extract total gray matter volumes from a respective ".label file encoded ROI" using mris_anatomical_stats . Example: Volumes from a ".curv file encoded ROI" using your recommended command lines (mri_binarize and mri_segstats): Subject1 = 1090 Subject2 = 1181 Subject3 = 713 Subject4 = 1230 Volumes from a respective ".label file encoded ROI" (mris_anatomical_stats): Subject1 = 3497 Subject2 = 3786 Subject3 = 2268 Subject4 = 3491
Are the volumes extracted from a ".curv file encoded ROI" (using mri_binarize and mri_segstats) an estimation of the total gray matter volumes? Why these values are differing that much?
Thank you very much, Josue Dalboni ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu> Sent: Wednesday, October 5, 2016 5:19 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes
I would binarize the curv file with
mri_binarize --i lh.yourcurvfile --abs --min .0000001 --o lh.yourcurvfilebin.mgh
Then compute the volume with
mri_segstats --seg lh.yourcurvfilebin.mgh --id 1 --i lh.volume --accumulate --sum lh.vol.yourcurv.sum
On 10/05/2016 09:09 AM, Josue Luiz Dalboni Da Rocha wrote:
Dear Douglas,
I have a ".curv" file that contains the curvature information inside an automatically delineated ROI and 0 everywhere else. I would like to calculate the volume of this ROI,
Can I extract statistics directly from the ".curv" file?
Best regards, Josue ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu> Sent: Tuesday, October 4, 2016 9:41 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes
What is the nature of the segmentation? Is it just a binary (1=in, 0=out) segmentation? And what file format? In general we don't use .w anymore, but it can be converted into something else.
doug
On 10/03/2016 12:35 PM, Josue Luiz Dalboni Da Rocha wrote:
Dear Douglas,
I have a segmented gyrus curvature file (.curv or .w) and I would like to calculate the volume (and other statistics) of this gyrus.
I currently only know mris_anatomical_stats to perform that, but requiring a '.label' file.
Can I extract statistics directly from the ".curv" file?
Or can I convert directly from .curv to .label in order to extract these statistics?
As another option, is it feasible to convert the '.curv' file to nifti volume (mri_surf2vol), binarize it (mri_binarize), and then convert to label (mri_cor2label)?
What does the output nifti file from 'mri_surf2vol' contain? Does it contain the complete volume behind the surface? Or does it only contain the surface over the 3D space?
Thank you very much in advance for your help!
Best regards,
Josue
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
How did you create the label ?
On 10/14/16 12:43 PM, Josue Luiz Dalboni Da Rocha wrote:
Dear Doug,
From the curvature file of the ROI (selected portion of surface), we extract the volume using this 2 command lines:
mri_binarize --i $D_load/lh_masked_all.curv --max -.0000001 --o $D_load/lh_masked_all_bin.mgh mri_segstats --seg $D_load/lh_masked_all_bin.mgh --id 1 --i $SUBJECTS_DIR/$subj/surf/lh.volume --accumulate --sum $D_load/lh_masked_all_bin.txt
From the label file of the same ROI, we extract the volume using the following command line: mris_anatomical_stats -l $SUBJECTS_DIR/$subj/label/labelsAtlas2009/lh_masked_all.label -f $outD/lh_masked_all_Volume $subj lh
As the '.curv' file and the '.label' file represent the same ROI, we were expecting to get the same volume (total gray matter volume of the selected portion of surface). But the results using the first method are always about 3 time higher than using the second method.
We would like to understand what is going on, because for some selected portions of ROI we just have the '.curv' file to extract the volume from.
Thank you very much for your help!
Best regards, Josue
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Friday, October 14, 2016 5:54 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Quantifying volumes
please send command lines
On 10/14/16 6:36 AM, Damien MARIE wrote:
Hi,
Just adding a word about the e-mail of ma colleague Josue. What he meant is that he extracted volumes for exactly the same ROI (a merging of destrieux labels of Hechl’s gyrus, Heschl's sulcus and planum temporale) using 1- a .curv file of this ROI, mri_binarize and mri_segstats or 2- a .label file of this ROI and mris_anatomical_stats.
We get a different volume output (ratio of difference between the 2 methods = approx. 2.5, similar to mean thickness I would say…), so we would like to understand what is happening exactly.
Using the method 1, it’s actually a surface measurement we get no?
Would that be possible to convert a .cuvr file to a .label file ?
Thank you and best, Damien
Josue Luiz Dalboni Da Rocha Wed, 12 Oct 2016 07:26:32 -0700 Dear Doug,
Thank you very much for your advice! We get to extract results for the volumes from a ".curv file encoded ROI" using your recommended command lines (mri_binarize and mri_segstats ), but unfortunately the results are much smaller (around 3 times) than when we extract total gray matter volumes from a respective ".label file encoded ROI" using mris_anatomical_stats . Example: Volumes from a ".curv file encoded ROI" using your recommended command lines (mri_binarize and mri_segstats): Subject1 = 1090 Subject2 = 1181 Subject3 = 713 Subject4 = 1230 Volumes from a respective ".label file encoded ROI" (mris_anatomical_stats): Subject1 = 3497 Subject2 = 3786 Subject3 = 2268 Subject4 = 3491
Are the volumes extracted from a ".curv file encoded ROI" (using mri_binarize and mri_segstats) an estimation of the total gray matter volumes? Why these values are differing that much?
Thank you very much, Josue Dalboni ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu> Sent: Wednesday, October 5, 2016 5:19 PM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes
I would binarize the curv file with
mri_binarize --i lh.yourcurvfile --abs --min .0000001 --o lh.yourcurvfilebin.mgh
Then compute the volume with
mri_segstats --seg lh.yourcurvfilebin.mgh --id 1 --i lh.volume --accumulate --sum lh.vol.yourcurv.sum
On 10/05/2016 09:09 AM, Josue Luiz Dalboni Da Rocha wrote:
Dear Douglas,
I have a ".curv" file that contains the curvature information
inside an
automatically delineated ROI and 0 everywhere else. I would like to calculate the volume of this ROI,
Can I extract statistics directly from the ".curv" file?
Best regards, Josue ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu
http://nmr.mgh.harvard.edu> on behalf of Douglas N Greve
<gr...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu> Sent: Tuesday, October 4, 2016 9:41 PM To: freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Quantifying volumes
What is the nature of the segmentation? Is it just a binary (1=in, 0=out) segmentation? And what file format? In general we don't use .w anymore, but it can be converted into something else.
doug
On 10/03/2016 12:35 PM, Josue Luiz Dalboni Da Rocha wrote:
Dear Douglas,
I have a segmented gyrus curvature file (.curv or .w) and I would like to calculate the volume (and other statistics) of this gyrus.
I currently only know mris_anatomical_stats to perform that, but requiring a '.label' file.
Can I extract statistics directly from the ".curv" file?
Or can I convert directly from .curv to .label in order to extract these statistics?
As another option, is it feasible to convert the '.curv' file to nifti volume (mri_surf2vol), binarize it (mri_binarize), and then convert to label (mri_cor2label)?
What does the output nifti file from 'mri_surf2vol' contain? Does it contain the complete volume behind the surface? Or does it only contain the surface over the 3D space?
Thank you very much in advance for your help!
Best regards,
Josue
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://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 mailto: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 mailto: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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug,
Thank you for your reply!
This label on this specific case is basically the sum of the labels from Heschl's Gyrus, Heschl's Sulcus and Planum temporale.
The labels from Heschl's Gyrus, Heschl's Sulcus and Planum temporale are firstly produced inside 'Recon-all'.
The aggregation of these 3 labels is produced by the following command line:
mri_mergelabels -i $SUBJECTS_DIR/$subj/label/labelsAtlas2009/lh.G_temp_sup-G_T_transv.label -i $SUBJECTS_DIR/$subj/label/labelsAtlas2009/lh.G_temp_sup-Plan_tempo.label -i $SUBJECTS_DIR/$subj/label/labelsAtlas2009/lh.S_temporal_transverse.label -o $SUBJECTS_DIR/$subj/label/labelsAtlas2009/lh_masked_all.label
The volume calculated by 'mris_anatomical_stats' of the aggregated label is equal to the sum of the volumes from these 3 labels produced during "Recon-all'.
But the issue is these values differ from the one obtained using "mri_binarize" and "mri_segstats" based on the '.curv' file of the portion of surface (Heschl's Gyrus + Heschl's Sulcus + Planum temporale).
Best regards,
Josue
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu Sent: Friday, October 14, 2016 7:01 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes
How did you create the label ?
On 10/14/16 12:43 PM, Josue Luiz Dalboni Da Rocha wrote:
Dear Doug,
From the curvature file of the ROI (selected portion of surface), we extract the volume using this 2 command lines:
mri_binarize --i $D_load/lh_masked_all.curv --max -.0000001 --o $D_load/lh_masked_all_bin.mgh mri_segstats --seg $D_load/lh_masked_all_bin.mgh --id 1 --i $SUBJECTS_DIR/$subj/surf/lh.volume --accumulate --sum $D_load/lh_masked_all_bin.txt
From the label file of the same ROI, we extract the volume using the following command line: mris_anatomical_stats -l $SUBJECTS_DIR/$subj/label/labelsAtlas2009/lh_masked_all.label -f $outD/lh_masked_all_Volume $subj lh
As the '.curv' file and the '.label' file represent the same ROI, we were expecting to get the same volume (total gray matter volume of the selected portion of surface). But the results using the first method are always about 3 time higher than using the second method.
We would like to understand what is going on, because for some selected portions of ROI we just have the '.curv' file to extract the volume from.
Thank you very much for your help!
Best regards, Josue
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Sent: Friday, October 14, 2016 5:54 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes
please send command lines
On 10/14/16 6:36 AM, Damien MARIE wrote: Hi,
Just adding a word about the e-mail of ma colleague Josue. What he meant is that he extracted volumes for exactly the same ROI (a merging of destrieux labels of Hechl’s gyrus, Heschl's sulcus and planum temporale) using 1- a .curv file of this ROI, mri_binarize and mri_segstats or 2- a .label file of this ROI and mris_anatomical_stats.
We get a different volume output (ratio of difference between the 2 methods = approx. 2.5, similar to mean thickness I would say…), so we would like to understand what is happening exactly.
Using the method 1, it’s actually a surface measurement we get no?
Would that be possible to convert a .cuvr file to a .label file ?
Thank you and best, Damien
Josue Luiz Dalboni Da Rocha Wed, 12 Oct 2016 07:26:32 -0700 Dear Doug,
Thank you very much for your advice! We get to extract results for the volumes from a ".curv file encoded ROI" using your recommended command lines (mri_binarize and mri_segstats ), but unfortunately the results are much smaller (around 3 times) than when we extract total gray matter volumes from a respective ".label file encoded ROI" using mris_anatomical_stats . Example: Volumes from a ".curv file encoded ROI" using your recommended command lines (mri_binarize and mri_segstats): Subject1 = 1090 Subject2 = 1181 Subject3 = 713 Subject4 = 1230 Volumes from a respective ".label file encoded ROI" (mris_anatomical_stats): Subject1 = 3497 Subject2 = 3786 Subject3 = 2268 Subject4 = 3491
Are the volumes extracted from a ".curv file encoded ROI" (using mri_binarize and mri_segstats) an estimation of the total gray matter volumes? Why these values are differing that much?
Thank you very much, Josue Dalboni ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu> Sent: Wednesday, October 5, 2016 5:19 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes
I would binarize the curv file with
mri_binarize --i lh.yourcurvfile --abs --min .0000001 --o lh.yourcurvfilebin.mgh
Then compute the volume with
mri_segstats --seg lh.yourcurvfilebin.mgh --id 1 --i lh.volume --accumulate --sum lh.vol.yourcurv.sum
On 10/05/2016 09:09 AM, Josue Luiz Dalboni Da Rocha wrote:
Dear Douglas,
I have a ".curv" file that contains the curvature information inside an automatically delineated ROI and 0 everywhere else. I would like to calculate the volume of this ROI,
Can I extract statistics directly from the ".curv" file?
Best regards, Josue ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu> Sent: Tuesday, October 4, 2016 9:41 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes
What is the nature of the segmentation? Is it just a binary (1=in, 0=out) segmentation? And what file format? In general we don't use .w anymore, but it can be converted into something else.
doug
On 10/03/2016 12:35 PM, Josue Luiz Dalboni Da Rocha wrote:
Dear Douglas,
I have a segmented gyrus curvature file (.curv or .w) and I would like to calculate the volume (and other statistics) of this gyrus.
I currently only know mris_anatomical_stats to perform that, but requiring a '.label' file.
Can I extract statistics directly from the ".curv" file?
Or can I convert directly from .curv to .label in order to extract these statistics?
As another option, is it feasible to convert the '.curv' file to nifti volume (mri_surf2vol), binarize it (mri_binarize), and then convert to label (mri_cor2label)?
What does the output nifti file from 'mri_surf2vol' contain? Does it contain the complete volume behind the surface? Or does it only contain the surface over the 3D space?
Thank you very much in advance for your help!
Best regards,
Josue
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