Hi,
I have a large dataset for which I run freesurfer and confirmed that the apar+aseg.mgz file is satisfactory. Can someone please recommend the best way to aggregate all of the volumes/other values generated by freesurfer into a single table for this dataset? (e.g. subjects as Rows and values by columns).
Best wishes,
Sla
use asegstats2table and aparcstats2table. This will give you 3 tables which you could then merge into 1. doug
On 8/4/13 12:22 PM, Salil Soman wrote:
Hi,
I have a large dataset for which I run freesurfer and confirmed that the apar+aseg.mgz file is satisfactory. Can someone please recommend the best way to aggregate all of the volumes/other values generated by freesurfer into a single table for this dataset? (e.g. subjects as Rows and values by columns).
Best wishes,
Sla
Thank you Doug!
-S
On Sun, Aug 4, 2013 at 10:09 AM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
use asegstats2table and aparcstats2table. This will give you 3 tables which you could then merge into 1. doug
On 8/4/13 12:22 PM, Salil Soman wrote:
Hi,
I have a large dataset for which I run freesurfer and confirmed that the apar+aseg.mgz file is satisfactory. Can someone please recommend the best way to aggregate all of the volumes/other values generated by freesurfer into a single table for this dataset? (e.g. subjects as Rows and values by columns).
Best wishes,
Sla
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/**compliancelinehttp://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.
try asegstats2table
cheers Bruce On Sun, 4 Aug 2013, Salil Soman wrote:
Hi, I have a large dataset for which I run freesurfer and confirmed that the apar+aseg.mgz file is satisfactory. Can someone please recommend the best way to aggregate all of the volumes/other values generated by freesurfer into a single table for this dataset? (e.g. subjects as Rows and values by columns).
Best wishes,
Sla
Dear Doug and Bruce,
Thank you for your emails. I have also run the -hippo-subfields option on my freesurfer processing. How do I extract those values as tables as well?
Best wishes,
Sal
On Sun, Aug 4, 2013 at 11:10 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
try asegstats2table
cheers Bruce
On Sun, 4 Aug 2013, Salil Soman wrote:
Hi,
I have a large dataset for which I run freesurfer and confirmed that the apar+aseg.mgz file is satisfactory. Can someone please recommend the best way to aggregate all of the volumes/other values generated by freesurfer into a single table for this dataset? (e.g. subjects as Rows and values by columns).
Best wishes,
Sla
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/**compliancelinehttp://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.
Good question:). It does not look like we are currently creating a stats file for the subfields, which means you will have to do it yourself. You can do it with something like
cd $SUBJECTS_DIR/subject mri_segstats --seg mri/hippsubfieldseg.mgz --sum stats/hipposub.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject --surf-wm-vol --etiv --ctab $FREESURFERHOME/FreeSurferColorLUT.txt
You can then run asegstats2table specifying hipposub.stats as the stats file
doug
On 8/5/13 3:39 PM, Salil Soman wrote:
Dear Doug and Bruce,
Thank you for your emails. I have also run the -hippo-subfields option on my freesurfer processing. How do I extract those values as tables as well?
Best wishes,
Sal
On Sun, Aug 4, 2013 at 11:10 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
try asegstats2table cheers Bruce On Sun, 4 Aug 2013, Salil Soman wrote: Hi, I have a large dataset for which I run freesurfer and confirmed that the apar+aseg.mgz file is satisfactory. Can someone please recommend the best way to aggregate all of the volumes/other values generated by freesurfer into a single table for this dataset? (e.g. subjects as Rows and values by columns). Best wishes, Sla 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.-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
Thank you!
-Sal
On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
Good question:). It does not look like we are currently creating a stats file for the subfields, which means you will have to do it yourself. You can do it with something like
cd $SUBJECTS_DIR/subject mri_segstats --seg mri/hippsubfieldseg.mgz --sum stats/hipposub.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject --surf-wm-vol --etiv --ctab $FREESURFERHOME/FreeSurferColorLUT.txt
You can then run asegstats2table specifying hipposub.stats as the stats file
doug
On 8/5/13 3:39 PM, Salil Soman wrote:
Dear Doug and Bruce,
Thank you for your emails. I have also run the -hippo-subfields option on my freesurfer processing. How do I extract those values as tables as well?
Best wishes,
Sal
On Sun, Aug 4, 2013 at 11:10 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
try asegstats2table
cheers Bruce
On Sun, 4 Aug 2013, Salil Soman wrote:
Hi,
I have a large dataset for which I run freesurfer and confirmed that the apar+aseg.mgz file is satisfactory. Can someone please recommend the best way to aggregate all of the volumes/other values generated by freesurfer into a single table for this dataset? (e.g. subjects as Rows and values by columns).
Best wishes,
Sla
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.
-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
mri/hippsubfieldseg.mgz
Thank you Doug. Just to clarify the code you suggested earlier, should "mri/hippsubfieldseg.mgz" be replaced with each of the specific hipposubfields:
posterior_Left-Cerebral-Cortex.mgz posterior_Left-Cerebral-White-Matter.mgz posterior_Left-Hippocampus.mgz posterior_Right-Cerebral-Cortex.mgz posterior_Right-Cerebral-White-Matter.mgz posterior_Right-Hippocampus.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_CA4_DG.mgz posterior_left_fimbria.mgz posterior_left_hippocampal_fissure.mgz posterior_left_presubiculum.mgz posterior_left_subiculum.mgz posterior_right_CA1.mgz posterior_right_CA2_3.mgz posterior_right_CA4_DG.mgz posterior_right_fimbria.mgz posterior_right_hippocampal_fissure.mgz posterior_right_presubiculum.mgz posterior_right_subiculum.mgz
If not, I do not see a file called mri/hippsubfieldseg.mgz for my output, and any advice on where I could find it would be great.
Best wishes,
Sal
oh, sorry, you are right. I had thought that they generated a single file with the segmentations. In this case, you will need to threshold at some value of the posterior probability. Alternatively, you could generate a segmentation file by selecting the seg at a voxel that has the highest post prob using mri_concat with the --max-index-prune option. You'd then create your own LUT and run mri_segstats using the seg volume and the LUT doug
On 08/06/2013 03:09 PM, Salil Soman wrote:
On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
mri/hippsubfieldseg.mgzThank you Doug. Just to clarify the code you suggested earlier, should "mri/hippsubfieldseg.mgz" be replaced with each of the specific hipposubfields:
posterior_Left-Cerebral-Cortex.mgz posterior_Left-Cerebral-White-Matter.mgz posterior_Left-Hippocampus.mgz posterior_Right-Cerebral-Cortex.mgz posterior_Right-Cerebral-White-Matter.mgz posterior_Right-Hippocampus.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_CA4_DG.mgz posterior_left_fimbria.mgz posterior_left_hippocampal_fissure.mgz posterior_left_presubiculum.mgz posterior_left_subiculum.mgz posterior_right_CA1.mgz posterior_right_CA2_3.mgz posterior_right_CA4_DG.mgz posterior_right_fimbria.mgz posterior_right_hippocampal_fissure.mgz posterior_right_presubiculum.mgz posterior_right_subiculum.mgz
If not, I do not see a file called mri/hippsubfieldseg.mgz for my output, and any advice on where I could find it would be great.
Best wishes,
Sal
-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
Hi Doug,
I realize now that I was unclear of the function of kvlQuantifyHippocampalSubfieldSegmentations.sh
It creates a summary file of volumes for the left and right subfields as volumeStats_X.txt (where x is left or right). It writes the files into the mri subdirectory. Is there a scripted way to combine these stat files into a table format for a group?
Thank you for all your help.
Sal
On Tue, Aug 6, 2013 at 12:17 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
oh, sorry, you are right. I had thought that they generated a single file with the segmentations. In this case, you will need to threshold at some value of the posterior probability. Alternatively, you could generate a segmentation file by selecting the seg at a voxel that has the highest post prob using mri_concat with the --max-index-prune option. You'd then create your own LUT and run mri_segstats using the seg volume and the LUT doug
On 08/06/2013 03:09 PM, Salil Soman wrote:
On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve <greve@nmr.mgh.harvard.edu<mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote:
mri/hippsubfieldseg.mgzThank you Doug. Just to clarify the code you suggested earlier, should "mri/hippsubfieldseg.mgz" be replaced with each of the specific hipposubfields:
posterior_Left-Cerebral-**Cortex.mgz posterior_Left-Cerebral-White-**Matter.mgz posterior_Left-Hippocampus.mgz posterior_Right-Cerebral-**Cortex.mgz posterior_Right-Cerebral-**White-Matter.mgz posterior_Right-Hippocampus.**mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_CA4_DG.mgz posterior_left_fimbria.mgz posterior_left_hippocampal_**fissure.mgz posterior_left_presubiculum.**mgz posterior_left_subiculum.mgz posterior_right_CA1.mgz posterior_right_CA2_3.mgz posterior_right_CA4_DG.mgz posterior_right_fimbria.mgz posterior_right_hippocampal_**fissure.mgz posterior_right_presubiculum.**mgz posterior_right_subiculum.mgz
If not, I do not see a file called mri/hippsubfieldseg.mgz for my output, and any advice on where I could find it would be great.
Best wishes,
Sal
-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://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/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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/**compliancelinehttp://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.
I can add that after running "kvlQuantifyHippocampalSubfield Segmentations.sh" I cannot find the nonPartialVolumeStatsLeft.txt and nonPartialVolumeStatsRigt.txt files mentioned on the tutorial page:
http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation
I only have the volumeStats_left.txt and volumeStats_right.txt files in the mri subdirectory.
Again, any pointers on how to generate group stats into a table would be a great help.
Best wishes,
Sal
On Tue, Aug 6, 2013 at 12:33 PM, Salil Soman salsoman@stanford.edu wrote:
Hi Doug,
I realize now that I was unclear of the function of kvlQuantifyHippocampalSubfieldSegmentations.sh
It creates a summary file of volumes for the left and right subfields as volumeStats_X.txt (where x is left or right). It writes the files into the mri subdirectory. Is there a scripted way to combine these stat files into a table format for a group?
Thank you for all your help.
Sal
On Tue, Aug 6, 2013 at 12:17 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
oh, sorry, you are right. I had thought that they generated a single file with the segmentations. In this case, you will need to threshold at some value of the posterior probability. Alternatively, you could generate a segmentation file by selecting the seg at a voxel that has the highest post prob using mri_concat with the --max-index-prune option. You'd then create your own LUT and run mri_segstats using the seg volume and the LUT doug
On 08/06/2013 03:09 PM, Salil Soman wrote:
On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve <greve@nmr.mgh.harvard.edu<mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote:
mri/hippsubfieldseg.mgzThank you Doug. Just to clarify the code you suggested earlier, should "mri/hippsubfieldseg.mgz" be replaced with each of the specific hipposubfields:
posterior_Left-Cerebral-**Cortex.mgz posterior_Left-Cerebral-White-**Matter.mgz posterior_Left-Hippocampus.mgz posterior_Right-Cerebral-**Cortex.mgz posterior_Right-Cerebral-**White-Matter.mgz posterior_Right-Hippocampus.**mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_CA4_DG.mgz posterior_left_fimbria.mgz posterior_left_hippocampal_**fissure.mgz posterior_left_presubiculum.**mgz posterior_left_subiculum.mgz posterior_right_CA1.mgz posterior_right_CA2_3.mgz posterior_right_CA4_DG.mgz posterior_right_fimbria.mgz posterior_right_hippocampal_**fissure.mgz posterior_right_presubiculum.**mgz posterior_right_subiculum.mgz
If not, I do not see a file called mri/hippsubfieldseg.mgz for my output, and any advice on where I could find it would be great.
Best wishes,
Sal
-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://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/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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/**compliancelinehttp://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.
-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
Hi Doug,
Turns out the kvlQuantifyHippocampalSubfieldSegmentations.sh was crashing before it got a chance to write the summary files. It crashed after trying to go into fsaverage/mri. I edited the file to specifically only go into my current study folders (they all have a common prefix), and then the script worked and generated the 2 summary files.
Best wishes,
Sal
On Tue, Aug 6, 2013 at 12:40 PM, Salil Soman salsoman@stanford.edu wrote:
I can add that after running "kvlQuantifyHippocampalSubfield Segmentations.sh" I cannot find the nonPartialVolumeStatsLeft.txt and nonPartialVolumeStatsRigt.txt files mentioned on the tutorial page:
http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation
I only have the volumeStats_left.txt and volumeStats_right.txt files in the mri subdirectory.
Again, any pointers on how to generate group stats into a table would be a great help.
Best wishes,
Sal
On Tue, Aug 6, 2013 at 12:33 PM, Salil Soman salsoman@stanford.eduwrote:
Hi Doug,
I realize now that I was unclear of the function of kvlQuantifyHippocampalSubfieldSegmentations.sh
It creates a summary file of volumes for the left and right subfields as volumeStats_X.txt (where x is left or right). It writes the files into the mri subdirectory. Is there a scripted way to combine these stat files into a table format for a group?
Thank you for all your help.
Sal
On Tue, Aug 6, 2013 at 12:17 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
oh, sorry, you are right. I had thought that they generated a single file with the segmentations. In this case, you will need to threshold at some value of the posterior probability. Alternatively, you could generate a segmentation file by selecting the seg at a voxel that has the highest post prob using mri_concat with the --max-index-prune option. You'd then create your own LUT and run mri_segstats using the seg volume and the LUT doug
On 08/06/2013 03:09 PM, Salil Soman wrote:
On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
mri/hippsubfieldseg.mgzThank you Doug. Just to clarify the code you suggested earlier, should "mri/hippsubfieldseg.mgz" be replaced with each of the specific hipposubfields:
posterior_Left-Cerebral-**Cortex.mgz posterior_Left-Cerebral-White-**Matter.mgz posterior_Left-Hippocampus.mgz posterior_Right-Cerebral-**Cortex.mgz posterior_Right-Cerebral-**White-Matter.mgz posterior_Right-Hippocampus.**mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_CA4_DG.mgz posterior_left_fimbria.mgz posterior_left_hippocampal_**fissure.mgz posterior_left_presubiculum.**mgz posterior_left_subiculum.mgz posterior_right_CA1.mgz posterior_right_CA2_3.mgz posterior_right_CA4_DG.mgz posterior_right_fimbria.mgz posterior_right_hippocampal_**fissure.mgz posterior_right_presubiculum.**mgz posterior_right_subiculum.mgz
If not, I do not see a file called mri/hippsubfieldseg.mgz for my output, and any advice on where I could find it would be great.
Best wishes,
Sal
-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://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/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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/**compliancelinehttp://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.
-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
I actually have not used the hipposubfields yet, so I'm not familiar with the output. If it is the same format as the aseg.stats file, then you can use asegstats2table. Maybe Eugenio knows. doug
On 08/06/2013 03:33 PM, Salil Soman wrote:
Hi Doug,
I realize now that I was unclear of the function of kvlQuantifyHippocampalSubfieldSegmentations.sh
It creates a summary file of volumes for the left and right subfields as volumeStats_X.txt (where x is left or right). It writes the files into the mri subdirectory. Is there a scripted way to combine these stat files into a table format for a group?
Thank you for all your help.
Sal
On Tue, Aug 6, 2013 at 12:17 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
oh, sorry, you are right. I had thought that they generated a single file with the segmentations. In this case, you will need to threshold at some value of the posterior probability. Alternatively, you could generate a segmentation file by selecting the seg at a voxel that has the highest post prob using mri_concat with the --max-index-prune option. You'd then create your own LUT and run mri_segstats using the seg volume and the LUT doug On 08/06/2013 03:09 PM, Salil Soman wrote: On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: mri/hippsubfieldseg.mgz Thank you Doug. Just to clarify the code you suggested earlier, should "mri/hippsubfieldseg.mgz" be replaced with each of the specific hipposubfields: posterior_Left-Cerebral-Cortex.mgz posterior_Left-Cerebral-White-Matter.mgz posterior_Left-Hippocampus.mgz posterior_Right-Cerebral-Cortex.mgz posterior_Right-Cerebral-White-Matter.mgz posterior_Right-Hippocampus.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_CA4_DG.mgz posterior_left_fimbria.mgz posterior_left_hippocampal_fissure.mgz posterior_left_presubiculum.mgz posterior_left_subiculum.mgz posterior_right_CA1.mgz posterior_right_CA2_3.mgz posterior_right_CA4_DG.mgz posterior_right_fimbria.mgz posterior_right_hippocampal_fissure.mgz posterior_right_presubiculum.mgz posterior_right_subiculum.mgz If not, I do not see a file called mri/hippsubfieldseg.mgz for my output, and any advice on where I could find it would be great. Best wishes, Sal -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel: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/ 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.-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
Hi Sal, when you run kvlQuantifyHippocampalSubfieldSegmentations.sh, two things happen: 1. First, the script goes subject by subject and creates the files you mentioned (volumeStats_X.txt). 2. Goes along those files and combines the outputs into a single table which you can find in two files: "nonPartialVolumeStatsLeft.txt" and "nonPartialVolumeStatsRight.txt" If you're sure that those files haven't been written, please send me the output from kvlQuantifyHippocampalSubfieldSegmentations.sh and I'll take a look Cheers, /Eugenio
On 08/06/2013 04:12 PM, Douglas N Greve wrote:
I actually have not used the hipposubfields yet, so I'm not familiar with the output. If it is the same format as the aseg.stats file, then you can use asegstats2table. Maybe Eugenio knows. doug
On 08/06/2013 03:33 PM, Salil Soman wrote:
Hi Doug,
I realize now that I was unclear of the function of kvlQuantifyHippocampalSubfieldSegmentations.sh
It creates a summary file of volumes for the left and right subfields as volumeStats_X.txt (where x is left or right). It writes the files into the mri subdirectory. Is there a scripted way to combine these stat files into a table format for a group?
Thank you for all your help.
Sal
On Tue, Aug 6, 2013 at 12:17 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
oh, sorry, you are right. I had thought that they generated a single file with the segmentations. In this case, you will need to threshold at some value of the posterior probability. Alternatively, you could generate a segmentation file by selecting the seg at a voxel that has the highest post prob using mri_concat with the --max-index-prune option. You'd then create your own LUT and run mri_segstats using the seg volume and the LUT doug On 08/06/2013 03:09 PM, Salil Soman wrote: On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: mri/hippsubfieldseg.mgz Thank you Doug. Just to clarify the code you suggested earlier, should "mri/hippsubfieldseg.mgz" be replaced with each of the specific hipposubfields: posterior_Left-Cerebral-Cortex.mgz posterior_Left-Cerebral-White-Matter.mgz posterior_Left-Hippocampus.mgz posterior_Right-Cerebral-Cortex.mgz posterior_Right-Cerebral-White-Matter.mgz posterior_Right-Hippocampus.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_CA4_DG.mgz posterior_left_fimbria.mgz posterior_left_hippocampal_fissure.mgz posterior_left_presubiculum.mgz posterior_left_subiculum.mgz posterior_right_CA1.mgz posterior_right_CA2_3.mgz posterior_right_CA4_DG.mgz posterior_right_fimbria.mgz posterior_right_hippocampal_fissure.mgz posterior_right_presubiculum.mgz posterior_right_subiculum.mgz If not, I do not see a file called mri/hippsubfieldseg.mgz for my output, and any advice on where I could find it would be great. Best wishes, Sal -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel: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/ 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.-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
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