Dear Freesurfer developers,
I would like to run Local Gyrification Index analysis for a group of healthy controls and a single patient. After running recon-all -s <subj> -localGI command, we get lh.pial_lgi and rh.pial_lgi surf files. In the last stage of this analysis, local gyrification index values are calculated at each pial vertices.
In the wiki, it is said that the next process should be done in qdec, but since I have only one patient, GLM analysis would not be suitable. Thus, I would like to get the LGI values of each subject as e.g. text files (like stats files for curvature, thickness, gm volume), and use them for my own analysis (not in qdec). I know that we can get parcel-wise anaysis values using this command: mri_segstats --annot CASE lh aparc \
--i $SUBJECTS_DIR/CASE/surf/lh.pial_lgi \
--sum lh.aparc.pial_lgi.stats
But I would like to use vertex-wise analysis values for my won analysis. Is it possible? Can I learn the command I need to use to get these values for each subject?
Thank you, Buse
Dear Freesurfers,
I have two questions:
1) In the last stage of the recon-all -s <subj> -localGI analysis, local gyrification index values are calculated at each pial vertices. Is there any way (command?) to extract *vertex-wise local gyrification index values* (of individual subjects) *before running GLM analysis in Qdec*? GLM analysis is not suitable for my study (single-case), so I need to extract values for each subject and use them for my own statistical analysis.
2) As far as I know we can extract *parcel-wise lGI* values using the following command:
mri_segstats --annot *subjID* lh aparc \
--i $SUBJECTS_DIR/*subjID*/surf/lh.pial_lgi \
--sum lh.aparc.pial_lgi.stats
Running this command provides "Intensity Mean, Intensity STD, Intensity Max, Intensity Min, Intensity Range" values for each parcellated area. Can you explain these values and what they mean?
Thanks,
-Buse
On 5 November 2017 at 19:54, Buse Merve Ürgen buseurgen@gmail.com wrote:
Dear Freesurfer developers,
I would like to run Local Gyrification Index analysis for a group of healthy controls and a single patient. After running recon-all -s <subj> -localGI command, we get lh.pial_lgi and rh.pial_lgi surf files. In the last stage of this analysis, local gyrification index values are calculated at each pial vertices.
In the wiki, it is said that the next process should be done in qdec, but since I have only one patient, GLM analysis would not be suitable. Thus, I would like to get the LGI values of each subject as e.g. text files (like stats files for curvature, thickness, gm volume), and use them for my own analysis (not in qdec). I know that we can get parcel-wise anaysis values using this command: mri_segstats --annot CASE lh aparc \
--i $SUBJECTS_DIR/CASE/surf/lh.pial_lgi \
--sum lh.aparc.pial_lgi.stats
But I would like to use vertex-wise analysis values for my won analysis. Is it possible? Can I learn the command I need to use to get these values for each subject?
Thank you, Buse
--
Buse Urgen
Intensity Mean will be the mean value of the input (lGI) averaged over the ROI.
STD, Max, Min, and Range are the intensity stddev maximimum mininum andrange=max-min over the ROI
On 11/07/2017 12:57 PM, Buse Merve Ürgen wrote:
Dear Freesurfers,
I have two questions:
- In the last stage of the recon-all -s <subj> -localGI analysis,
local gyrification index values are calculated at each pial vertices. Is there any way (command?) to extract /vertex-wise local gyrification index values/ (of individual subjects) /before running GLM analysis in Qdec/? GLM analysis is not suitable for my study (single-case), so I need to extract values for each subject and use them for my own statistical analysis.
- As far as I know we can extract /parcel-wise lGI/ values using the
following command:
mri_segstats --annot /subjID/ lh aparc \
--i $SUBJECTS_DIR//subjID//surf/lh.pial_lgi \
--sum lh.aparc.pial_lgi.stats
Running this command provides "Intensity Mean, Intensity STD, Intensity Max, Intensity Min, Intensity Range" values for each parcellated area. Can you explain these values and what they mean?
Thanks,
-Buse
On 5 November 2017 at 19:54, Buse Merve Ürgen <buseurgen@gmail.com mailto:buseurgen@gmail.com> wrote:
Dear Freesurfer developers, I would like to run Local Gyrification Index analysis for a group of healthy controls and a single patient. After running recon-all -s <subj> -localGI command, we get lh.pial_lgi and rh.pial_lgi surf files. In the last stage of this analysis, local gyrification index values are calculated at each pial vertices. In the wiki, it is said that the next process should be done in qdec, but since I have only one patient, GLM analysis would not be suitable. Thus, I would like to get the LGI values of each subject as e.g. text files (like stats files for curvature, thickness, gm volume), and use them for my own analysis (not in qdec). I know that we can get parcel-wise anaysis values using this command: mri_segstats --annot CASE lh aparc \ --i $SUBJECTS_DIR/CASE/surf/lh.pial_lgi \ --sum lh.aparc.pial_lgi.stats But I would like to use vertex-wise analysis values for my won analysis. Is it possible? Can I learn the command I need to use to get these values for each subject? Thank you, Buse -- Buse Urgen--
Buse M. Ürgen
Ph.D. Candidate Neuroscience Graduate Program National Magnetic Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research Center Bilkent University Ankara, 06800 Turkey
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you so much! Can I also learn whether running vertex-wise analysis without GLM analysis in Qdec is possible or not? As I said, I will compare a single patient with a group of healthy controls, so GLM would not work. What would you suggest for this? Is it possible to extract lGI values from surface data?
Thank you for your help, Buse
—
Douglas N Greve greve@nmr.mgh.harvard.edu şunları yazdı (7 Kas 2017 21:12):
Intensity Mean will be the mean value of the input (lGI) averaged over the ROI.
STD, Max, Min, and Range are the intensity stddev maximimum mininum andrange=max-min over the ROI
On 11/07/2017 12:57 PM, Buse Merve Ürgen wrote: Dear Freesurfers,
I have two questions:
- In the last stage of the recon-all -s <subj> -localGI analysis,
local gyrification index values are calculated at each pial vertices. Is there any way (command?) to extract /vertex-wise local gyrification index values/ (of individual subjects) /before running GLM analysis in Qdec/? GLM analysis is not suitable for my study (single-case), so I need to extract values for each subject and use them for my own statistical analysis.
- As far as I know we can extract /parcel-wise lGI/ values using the
following command:
mri_segstats --annot /subjID/ lh aparc \
--i $SUBJECTS_DIR//subjID//surf/lh.pial_lgi \
--sum lh.aparc.pial_lgi.stats
Running this command provides "Intensity Mean, Intensity STD, Intensity Max, Intensity Min, Intensity Range" values for each parcellated area. Can you explain these values and what they mean?
Thanks,
-Buse
On 5 November 2017 at 19:54, Buse Merve Ürgen <buseurgen@gmail.com mailto:buseurgen@gmail.com> wrote:
Dear Freesurfer developers,
I would like to run Local Gyrification Index analysis for a group of healthy controls and a single patient. After running recon-all -s <subj> -localGI command, we get lh.pial_lgi and rh.pial_lgi surf files. In the last stage of this analysis, local gyrification index values are calculated at each pial vertices.
In the wiki, it is said that the next process should be done in qdec, but since I have only one patient, GLM analysis would not be suitable. Thus, I would like to get the LGI values of each subject as e.g. text files (like stats files for curvature, thickness, gm volume), and use them for my own analysis (not in qdec). I know that we can get parcel-wise anaysis values using this command: mri_segstats --annot CASE lh aparc \
--i $SUBJECTS_DIR/CASE/surf/lh.pial_lgi \ --sum lh.aparc.pial_lgi.statsBut I would like to use vertex-wise analysis values for my won analysis. Is it possible? Can I learn the command I need to use to get these values for each subject?
Thank you, Buse
--
Buse
Urgen
--
Buse M. Ürgen
Ph.D. Candidate Neuroscience Graduate Program National Magnetic Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research Center Bilkent University Ankara, 06800 Turkey
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 greve@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.
Don't know what you mean by "extract lGI values from surface data" if not using mri_segstats as we've discussed. I think you can do the comparison you want in the GLM using a "two group" analysis where one group only has one subject.
On 11/09/2017 01:46 AM, Buse Merve Ürgen wrote:
Thank you so much! Can I also learn whether running vertex-wise analysis without GLM analysis in Qdec is possible or not? As I said, I will compare a single patient with a group of healthy controls, so GLM would not work. What would you suggest for this? Is it possible to extract lGI values from surface data?
Thank you for your help, Buse
—
Douglas N Greve greve@nmr.mgh.harvard.edu şunları yazdı (7 Kas 2017 21:12):
Intensity Mean will be the mean value of the input (lGI) averaged over the ROI.
STD, Max, Min, and Range are the intensity stddev maximimum mininum andrange=max-min over the ROI
On 11/07/2017 12:57 PM, Buse Merve Ürgen wrote: Dear Freesurfers,
I have two questions:
- In the last stage of the recon-all -s <subj> -localGI analysis,
local gyrification index values are calculated at each pial vertices. Is there any way (command?) to extract /vertex-wise local gyrification index values/ (of individual subjects) /before running GLM analysis in Qdec/? GLM analysis is not suitable for my study (single-case), so I need to extract values for each subject and use them for my own statistical analysis.
- As far as I know we can extract /parcel-wise lGI/ values using the
following command:
mri_segstats --annot /subjID/ lh aparc \
--i $SUBJECTS_DIR//subjID//surf/lh.pial_lgi \
--sum lh.aparc.pial_lgi.stats
Running this command provides "Intensity Mean, Intensity STD, Intensity Max, Intensity Min, Intensity Range" values for each parcellated area. Can you explain these values and what they mean?
Thanks,
-Buse
On 5 November 2017 at 19:54, Buse Merve Ürgen <buseurgen@gmail.com mailto:buseurgen@gmail.com> wrote:
Dear Freesurfer developers, I would like to run Local Gyrification Index analysis for a group of healthy controls and a single patient. After running recon-all -s <subj> -localGI command, we get lh.pial_lgi and rh.pial_lgi surf files. In the last stage of this analysis, local gyrification index values are calculated at each pial vertices. In the wiki, it is said that the next process should be done in qdec, but since I have only one patient, GLM analysis would not be suitable. Thus, I would like to get the LGI values of each subject as e.g. text files (like stats files for curvature, thickness, gm volume), and use them for my own analysis (not in qdec). I know that we can get parcel-wise anaysis values using this command: mri_segstats --annot CASE lh aparc \ --i $SUBJECTS_DIR/CASE/surf/lh.pial_lgi \ --sum lh.aparc.pial_lgi.stats But I would like to use vertex-wise analysis values for my won analysis. Is it possible? Can I learn the command I need to use to get these values for each subject? Thank you, Buse -- Buse Urgen--
Buse M. Ürgen
Ph.D. Candidate Neuroscience Graduate Program National Magnetic Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research Center Bilkent University Ankara, 06800 Turkey
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 greve@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
freesurfer@nmr.mgh.harvard.edu
-
Buse Merve Ürgen -
Douglas N Greve