Dear FreeSurfer experts,
We have a longitudinal study design with up to 5 time points. However, we both want to do a baseline cross-sectional analysis and later a longitudinal analysis. All subjects have been run through the longitudinal pipeline (only the base was edited). We want to start analysing baseline cross-sectionally using QDEC. I have read through the wiki guides but would like to make sure that we are doing it correctly. We have done/plan to do the following:
1. The [CROSS], edited [BASE] and [LONG] is processed.
2. We will create a qdec table called qdec.table.dat. However, because we want to use the improved longitudinal runs [LONG] (i.e., because the [BASE] has been edited] the first column in the QDEC table (i.e., fsid) has been changed to include the longitudinal names (please see below). In addition, we have included the line *SUBJECTS_DIR /my/path/to/subject/data* to let FreeSurfer know that it is the longitudinal directories that should be used (is this the correct why to let FreeSurfer know that it is the "longitudinal runs" which should be used?).
SUBJECTS_DIR /my/path/to/subject/data fsid Gender Group Age d115a.long.d115_base 1 1 19 d120a.long.d120_base 0 1 22 ...
2. We transfer the default fsaverage to the subject directory. 3. To presmooth the data onto the target we run the following command: *recon-all -long <tpid> <baseid> -qcache*
When the above steps are done we plan to load it into QDEC.
Is the above steps correct for doing a cross-sectional group analysis in QDEC?
Best regards, Kasper Jessen MD, PhD student
Hi Kasper,
short answer: yes.
long answer 1. yes 2. yes (you need to create a table in cross sectional format (no fsid-base column) and the fsid needs to be the tp.long.base names for baseline visit. the path should point to where these *.long.* directories are located). 2. yes (fsaverage should be linked there anyway, right?) 3. yes
;-) Martin
On 03/09/2016 03:42 PM, Kasper Jessen wrote:
Dear FreeSurfer experts,
We have a longitudinal study design with up to 5 time points. However, we both want to do a baseline cross-sectional analysis and later a longitudinal analysis. All subjects have been run through the longitudinal pipeline (only the base was edited). We want to start analysing baseline cross-sectionally using QDEC. I have read through the wiki guides but would like to make sure that we are doing it correctly. We have done/plan to do the following:
The [CROSS], edited [BASE] and [LONG] is processed.
We will create a qdec table called qdec.table.dat. However, because
we want to use the improved longitudinal runs [LONG] (i.e., because the [BASE] has been edited] the first column in the QDEC table (i.e., fsid) has been changed to include the longitudinal names (please see below). In addition, we have included the line /SUBJECTS_DIR /my/path/to/subject/data/ to let FreeSurfer know that it is the longitudinal directories that should be used (is this the correct why to let FreeSurfer know that it is the "longitudinal runs" which should be used?).
SUBJECTS_DIR /my/path/to/subject/data fsid Gender Group Age d115a.long.d115_base 1 1 19 d120a.long.d120_base 0 1 22 ...
- We transfer the default fsaverage to the subject directory.
- To presmooth the data onto the target we run the following command:
*recon-all -long <tpid> <baseid> -qcache*
When the above steps are done we plan to load it into QDEC.
Is the above steps correct for doing a cross-sectional group analysis in QDEC?
Best regards, Kasper Jessen MD, PhD student
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Martin,
Thanks for the answer :-)
To presmooth the data onto target, with the following command:
recon-all -long <tpid> <baseid> -qcache
The <tpdi>, does that have to be the longitudinal name (d115a.long.d115_base) or the cross-sectional name (d115a)?
Best wishes Kasper
2016-03-09 22:38 GMT+01:00 Martin Reuter mreuter@nmr.mgh.harvard.edu:
Hi Kasper,
short answer: yes.
long answer
- yes
- yes (you need to create a table in cross sectional format (no fsid-base
column) and the fsid needs to be the tp.long.base names for baseline visit. the path should point to where these *.long.* directories are located). 2. yes (fsaverage should be linked there anyway, right?) 3. yes
;-) Martin
On 03/09/2016 03:42 PM, Kasper Jessen wrote:
Dear FreeSurfer experts,
We have a longitudinal study design with up to 5 time points. However, we both want to do a baseline cross-sectional analysis and later a longitudinal analysis. All subjects have been run through the longitudinal pipeline (only the base was edited). We want to start analysing baseline cross-sectionally using QDEC. I have read through the wiki guides but would like to make sure that we are doing it correctly. We have done/plan to do the following:
The [CROSS], edited [BASE] and [LONG] is processed.
We will create a qdec table called qdec.table.dat. However, because we
want to use the improved longitudinal runs [LONG] (i.e., because the [BASE] has been edited] the first column in the QDEC table (i.e., fsid) has been changed to include the longitudinal names (please see below). In addition, we have included the line *SUBJECTS_DIR /my/path/to/subject/data* to let FreeSurfer know that it is the longitudinal directories that should be used (is this the correct why to let FreeSurfer know that it is the "longitudinal runs" which should be used?).
SUBJECTS_DIR /my/path/to/subject/data fsid Gender Group Age d115a.long.d115_base 1 1 19 d120a.long.d120_base 0 1 22 ...
- We transfer the default fsaverage to the subject directory.
- To presmooth the data onto the target we run the following command: *recon-all
-long <tpid> <baseid> -qcache*
When the above steps are done we plan to load it into QDEC.
Is the above steps correct for doing a cross-sectional group analysis in QDEC?
Best regards, Kasper Jessen MD, PhD student
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
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 Kasper,
That needs to be the cross-sectinal name (whenever you also pass a base, it will automatically create the ..long.. names internally).
cheers, Martin
On 03/11/2016 08:51 AM, Kasper Jessen wrote:
Hi Martin,
Thanks for the answer :-)
To presmooth the data onto target, with the following command:
recon-all -long <tpid> <baseid> -qcache
The <tpdi>, does that have to be the longitudinal name (d115a.long.d115_base) or the cross-sectional name (d115a)?
Best wishes Kasper
2016-03-09 22:38 GMT+01:00 Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu>:
Hi Kasper, short answer: yes. long answer 1. yes 2. yes (you need to create a table in cross sectional format (no fsid-base column) and the fsid needs to be the tp.long.base names for baseline visit. the path should point to where these *.long.* directories are located). 2. yes (fsaverage should be linked there anyway, right?) 3. yes ;-) Martin On 03/09/2016 03:42 PM, Kasper Jessen wrote:Dear FreeSurfer experts, We have a longitudinal study design with up to 5 time points. However, we both want to do a baseline cross-sectional analysis and later a longitudinal analysis. All subjects have been run through the longitudinal pipeline (only the base was edited). We want to start analysing baseline cross-sectionally using QDEC. I have read through the wiki guides but would like to make sure that we are doing it correctly. We have done/plan to do the following: 1. The [CROSS], edited [BASE] and [LONG] is processed. 2. We will create a qdec table called qdec.table.dat. However, because we want to use the improved longitudinal runs [LONG] (i.e., because the [BASE] has been edited] the first column in the QDEC table (i.e., fsid) has been changed to include the longitudinal names (please see below). In addition, we have included the line /SUBJECTS_DIR /my/path/to/subject/data/ to let FreeSurfer know that it is the longitudinal directories that should be used (is this the correct why to let FreeSurfer know that it is the "longitudinal runs" which should be used?). SUBJECTS_DIR /my/path/to/subject/data fsid Gender Group Age d115a.long.d115_base 1 1 19 d120a.long.d120_base 0 1 22 ... 2. We transfer the default fsaverage to the subject directory. 3. To presmooth the data onto the target we run the following command: *recon-all -long <tpid> <baseid> -qcache* * * When the above steps are done we plan to load it into QDEC. * * Is the above steps correct for doing a cross-sectional group analysis in QDEC? Best regards, Kasper Jessen MD, PhD student * * * * * * * * _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> Web :http://reuter.mit.edu _______________________________________________ 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.-- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j@cnsr.dk mailto:kasper_j@cnsr.dk eller kasper.jessen@regionh.dk mailto:kasper.jessen@regionh.dk
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Martin, When doing cross-sectional analysis on a longitudinal data set and the qdec table is ordered as followed:
fsid Gender Group Age d115a.long.d115_base 1 1 19 d120a.long.d120_base 0 1 22
Why does the presmoothing not have to be: recon-all -s d115a.long.d115_base -qcache recon-all -s d120a.long.d120_base -qcache
instead of
recon-all -long d115a d115_base -qcache recon-all -long d120a d120_base -qcache
Cheers, Kasper
2016-03-11 17:52 GMT+01:00 Martin Reuter mreuter@nmr.mgh.harvard.edu:
Hi Kasper,
That needs to be the cross-sectinal name (whenever you also pass a base, it will automatically create the ..long.. names internally).
cheers, Martin
On 03/11/2016 08:51 AM, Kasper Jessen wrote:
Hi Martin,
Thanks for the answer :-)
To presmooth the data onto target, with the following command:
recon-all -long <tpid> <baseid> -qcache
The <tpdi>, does that have to be the longitudinal name ( d115a.long.d115_base) or the cross-sectional name (d115a)?
Best wishes Kasper
2016-03-09 22:38 GMT+01:00 Martin Reuter mreuter@nmr.mgh.harvard.edu:
Hi Kasper,
short answer: yes.
long answer
- yes
- yes (you need to create a table in cross sectional format (no
fsid-base column) and the fsid needs to be the tp.long.base names for baseline visit. the path should point to where these *.long.* directories are located). 2. yes (fsaverage should be linked there anyway, right?) 3. yes
;-) Martin
On 03/09/2016 03:42 PM, Kasper Jessen wrote:
Dear FreeSurfer experts,
We have a longitudinal study design with up to 5 time points. However, we both want to do a baseline cross-sectional analysis and later a longitudinal analysis. All subjects have been run through the longitudinal pipeline (only the base was edited). We want to start analysing baseline cross-sectionally using QDEC. I have read through the wiki guides but would like to make sure that we are doing it correctly. We have done/plan to do the following:
The [CROSS], edited [BASE] and [LONG] is processed.
We will create a qdec table called qdec.table.dat. However, because we
want to use the improved longitudinal runs [LONG] (i.e., because the [BASE] has been edited] the first column in the QDEC table (i.e., fsid) has been changed to include the longitudinal names (please see below). In addition, we have included the line *SUBJECTS_DIR /my/path/to/subject/data* to let FreeSurfer know that it is the longitudinal directories that should be used (is this the correct why to let FreeSurfer know that it is the "longitudinal runs" which should be used?).
SUBJECTS_DIR /my/path/to/subject/data fsid Gender Group Age d115a.long.d115_base 1 1 19 d120a.long.d120_base 0 1 22 ...
- We transfer the default fsaverage to the subject directory.
- To presmooth the data onto the target we run the following command: *recon-all
-long <tpid> <baseid> -qcache*
When the above steps are done we plan to load it into QDEC.
Is the above steps correct for doing a cross-sectional group analysis in QDEC?
Best regards, Kasper Jessen MD, PhD student
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
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.
-- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j@cnsr.dk eller kasper.jessen@regionh.dk kasper.jessen@regionh.dk
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
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 Kasper,
because that is the way it is designed. Whenever recon-all runs on longitudinal data, it needs to know where the cross and base are (just in case that this info is needed somewhere). So the correct call is the one with the -long telling it that this is a longituidnal run (and not just a cross sectional run that happens to have "long" in the name).
Best, Martin
On 03/29/2016 05:58 AM, Kasper Jessen wrote:
Hi Martin, When doing cross-sectional analysis on a longitudinal data set and the qdec table is ordered as followed:
fsid Gender Group Age d115a.long.d115_base 1 1 19 d120a.long.d120_base 0 1 22
Why does the presmoothing not have to be: recon-all -s d115a.long.d115_base -qcache recon-all -s d120a.long.d120_base -qcache
instead of
recon-all -long d115a d115_base -qcache recon-all -long d120a d120_base -qcache
Cheers, Kasper
2016-03-11 17:52 GMT+01:00 Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu>:
Hi Kasper, That needs to be the cross-sectinal name (whenever you also pass a base, it will automatically create the ..long.. names internally). cheers, Martin On 03/11/2016 08:51 AM, Kasper Jessen wrote:Hi Martin, Thanks for the answer :-) To presmooth the data onto target, with the following command: recon-all -long <tpid> <baseid> -qcache * * The <tpdi>, does that have to be the longitudinal name (d115a.long.d115_base) or the cross-sectional name (d115a)? Best wishes Kasper 2016-03-09 22:38 GMT+01:00 Martin Reuter <mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>: Hi Kasper, short answer: yes. long answer 1. yes 2. yes (you need to create a table in cross sectional format (no fsid-base column) and the fsid needs to be the tp.long.base names for baseline visit. the path should point to where these *.long.* directories are located). 2. yes (fsaverage should be linked there anyway, right?) 3. yes ;-) Martin On 03/09/2016 03:42 PM, Kasper Jessen wrote:Dear FreeSurfer experts, We have a longitudinal study design with up to 5 time points. However, we both want to do a baseline cross-sectional analysis and later a longitudinal analysis. All subjects have been run through the longitudinal pipeline (only the base was edited). We want to start analysing baseline cross-sectionally using QDEC. I have read through the wiki guides but would like to make sure that we are doing it correctly. We have done/plan to do the following: 1. The [CROSS], edited [BASE] and [LONG] is processed. 2. We will create a qdec table called qdec.table.dat. However, because we want to use the improved longitudinal runs [LONG] (i.e., because the [BASE] has been edited] the first column in the QDEC table (i.e., fsid) has been changed to include the longitudinal names (please see below). In addition, we have included the line /SUBJECTS_DIR /my/path/to/subject/data/ to let FreeSurfer know that it is the longitudinal directories that should be used (is this the correct why to let FreeSurfer know that it is the "longitudinal runs" which should be used?). SUBJECTS_DIR /my/path/to/subject/data fsid Gender Group Age d115a.long.d115_base 1 1 19 d120a.long.d120_base 0 1 22 ... 2. We transfer the default fsaverage to the subject directory. 3. To presmooth the data onto the target we run the following command: *recon-all -long <tpid> <baseid> -qcache* * * When the above steps are done we plan to load it into QDEC. * * Is the above steps correct for doing a cross-sectional group analysis in QDEC? Best regards, Kasper Jessen MD, PhD student * * * * * * * * _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> Web :http://reuter.mit.edu _______________________________________________ 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. -- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j@cnsr.dk <mailto:kasper_j@cnsr.dk> eller kasper.jessen@regionh.dk <mailto:kasper.jessen@regionh.dk> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 <tel:%2B1-617-724-5652> Web : http://reuter.mit.edu _______________________________________________ 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.-- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j@cnsr.dk mailto:kasper_j@cnsr.dk eller kasper.jessen@regionh.dk mailto:kasper.jessen@regionh.dk
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Kasper Jessen -
Martin Reuter