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Thank you for your response!
Just to clarify: if my input is volume, does the cache.th20.abs.sig.y.ocn.dat contain the average unadjusted volume values for each participant in each significant cluster?
Since the file I just mentioned contains the average values, I used mri_segstats to calculate total volume for the cluster.
mri_segstats --i <pathway to rh.volume.Study.10.mgh> --seg cache.th20.abs.sig.ocn.mgh --excludeid 0 --sumwf ClusterVolumeValues.dat
However, this just calculates the sum of the unadjusted values in the cluster. I guess my main question is, is there a way to extract or calculate the adjusted values for each participant in each cluster after accounting for covariates (age, sex, and ICV)?
---
Jessica
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu freesurfer-request@nmr.mgh.harvard.edu Sent: Wednesday, June 13, 2018 11:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 172, Issue 21
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You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
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Today's Topics:
1. Re: crypt_gkey = (null) (Dicamillo, Robert) 2. tractstats2table - all tracts for multiple subjects (Alexopoulos, Dimitrios) 3. Re: tractstats2table - all tracts for multiple subjects (Yendiki, Anastasia) 4. dwi.ecclog file (Daumail, Loic Jean) 5. Re: dwi.ecclog file (Yendiki, Anastasia) 6. Re: tractstats2table - all tracts for multiple subjects (Alexopoulos, Dimitrios) 7. Re: Missing Control Points and QATools (Matthew Peverill) 8. Re: Missing Control Points and QATools (Bruce Fischl) 9. Re: Extract the entorhinal cortex as a mask (Erik O'Hanlon) 10. PREDOCTORAL POSITION at King's College London (Walter Hugo Lopez Pinaya) 11. Re: Extract the entorhinal cortex as a mask (Bruce Fischl) 12. Re: "WARNING: Image geometries differ across time" upon running base step of longitudinal pipeline (Tudor Popescu) 13. Re: dwi.ecclog file (Daumail, Loic Jean) 14. Re: Running qcache on old FS data (Douglas N. Greve) 15. Re: Group Analysis Covariates (Douglas N. Greve) 16. Re: Error during QDEC (Douglas N. Greve)
----------------------------------------------------------------------
Message: 1 Date: Tue, 12 Jun 2018 19:52:52 +0000 From: "Dicamillo, Robert" RDICAMILLO@mgh.harvard.edu Subject: Re: [Freesurfer] crypt_gkey = (null) To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 5024346D-6C53-4E0F-8189-FAAE089D2108@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Hello Aaron,
The build timestamp from the output below shows mri_convert is from 8/2014. When I look at the build timestamp on our stable 5.3 version of mri_convert I see it is from 5/2013. So the version that you listed is about 1 year newer than the 5.3 release I can see. It is possible that someone downloaded a daily/dev build of freesurfer at that time.
You might want to consider running the latest 6.0 release of Freesurfer (released in January 2017), which should be fine on CentOS 7. It can be downloaded from, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
I also suggest that you start out in a default/clean shell, set FREESURFER_HOME, and then source the setup script for linux, You can see the instructions on that same web page under ?Setup and Configuration?. The setup steps should work for version 5 or 6.
- rob
On Jun 12, 2018, at 2:43 PM, Aaron Tanenbaum <aaron.b.tanenbaum@gmail.commailto:aaron.b.tanenbaum@gmail.com> wrote:
External Email - Use Caution
I checked my system is not encrypted. I had someone else run the command on the same machine. It worked for them. So I changed my BASH environment to a default environment. I still get the same error.
I tried this again but with a different FreeSurfer 5.3. turns out the one I was using has been altered version of FreeSurfer. I do not know how it was altered. It worked. so it has to do with the altered FreeSurfer. I ran the command mri_convert -version on both FreeSurfer.
for the unaltered i get the out put mri_convert -version stable5 altered version i get mri_convert -version dev build (use --all-info flag for full version info)
with this output i type in mri_convert --all-info mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/06/12-18:32:17-GMT BuildTimeStamp: Aug 22 2014 21:04:47 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: tanenbauma Machine: rocky Platform: Linux PlatformVersion: 3.10.0-862.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Wondering is this version of mri_convert a developmental version? Also both version are the CentOS 6 build.
On Tue, Jun 12, 2018 at 1:01 PM Dicamillo, Robert <RDICAMILLO@mgh.harvard.edumailto:RDICAMILLO@mgh.harvard.edu> wrote: Hello Aaron,
You could check to see if the CentOS 7 system is using disk encryption, e.g., if the following command return 1, then it would mean encryption is in use (which can be an issue with FreeSurfer).
$ cat /proc/sys/crypto/fips_enabled
If it returns zero, it could be an issue with a system library like glibc on CentOS 7.5 (that does not happen on older versions of CentOS).
Either way, this is not your doing ;-)
On Jun 12, 2018, at 11:51 AM, Aaron Tanenbaum <aaron.b.tanenbaum@gmail.commailto:aaron.b.tanenbaum@gmail.com> wrote:
External Email - Use Caution
I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3. When i get to the part where MRI_convert is creating the the orig001.mgz its gives me a segmentation fault. if i run this on a centos 6 system it works fine. below is the output of the program.
/data/gizmo/data1/freesurfer5.3/bin/mri_convert /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm /data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm... crypt_gkey = (null) Segmentation fault (core dumped)
Did I do anything wrong? _______________________________________________ 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
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
The value in the ocn.dat file totally depends on what you used as input (--y) to mri_glmfit. If you used thickness, then it is thickness. That mri_segstats command is almost correct. You will need to add --accumulate so that it gives you the total volume rather than the average
On 06/13/2018 12:47 PM, Hua, Jessica wrote:
External Email - Use Caution
Thank you for your response!
Just to clarify: if my input is volume, does the cache.th20.abs.sig.y.ocn.dat contain the average unadjusted volume values for each participant in each significant cluster?
Since the file I just mentioned contains the average values, I used mri_segstats to calculate total volume for the cluster.
mri_segstats --i <pathway to rh.volume.Study.10.mgh> --seg cache.th20.abs.sig.ocn.mgh --excludeid 0 --sumwf ClusterVolumeValues.dat
However, this just calculates the sum of the unadjusted values in the cluster. I guess my main question is, is there a way to extract or calculate the adjusted values for each participant in each cluster after accounting for covariates (age, sex, and ICV)?
Jessica
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu freesurfer-request@nmr.mgh.harvard.edu *Sent:* Wednesday, June 13, 2018 11:00 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Freesurfer Digest, Vol 172, Issue 21 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Re: crypt_gkey = (null) (Dicamillo, Robert) 2. tractstats2table - all tracts for multiple subjects (Alexopoulos, Dimitrios) 3. Re: tractstats2table - all tracts for multiple subjects (Yendiki, Anastasia) 4. dwi.ecclog file (Daumail, Loic Jean) 5. Re: dwi.ecclog file (Yendiki, Anastasia) 6. Re: tractstats2table - all tracts for multiple subjects (Alexopoulos, Dimitrios) 7. Re: Missing Control Points and QATools (Matthew Peverill) 8. Re: Missing Control Points and QATools (Bruce Fischl) 9. Re: Extract the entorhinal cortex as a mask (Erik O'Hanlon) 10. PREDOCTORAL POSITION at King's College London (Walter Hugo Lopez Pinaya) 11. Re: Extract the entorhinal cortex as a mask (Bruce Fischl) 12. Re: "WARNING: Image geometries differ across time" upon running base step of longitudinal pipeline (Tudor Popescu) 13. Re: dwi.ecclog file (Daumail, Loic Jean) 14. Re: Running qcache on old FS data (Douglas N. Greve) 15. Re: Group Analysis Covariates (Douglas N. Greve) 16. Re: Error during QDEC (Douglas N. Greve)
Message: 1 Date: Tue, 12 Jun 2018 19:52:52 +0000 From: "Dicamillo, Robert" RDICAMILLO@mgh.harvard.edu Subject: Re: [Freesurfer] crypt_gkey = (null) To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 5024346D-6C53-4E0F-8189-FAAE089D2108@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Hello Aaron,
The build timestamp from the output below shows mri_convert is from 8/2014. When I look at the build timestamp on our stable 5.3 version of mri_convert I see it is from 5/2013. So the version that you listed is about 1 year newer than the 5.3 release I can see. It is possible that someone downloaded a daily/dev build of freesurfer at that time.
You might want to consider running the latest 6.0 release of Freesurfer (released in January 2017), which should be fine on CentOS 7. It can be downloaded from, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
I also suggest that you start out in a default/clean shell, set FREESURFER_HOME, and then source the setup script for linux, You can see the instructions on that same web page under ?Setup and Configuration?. The setup steps should work for version 5 or 6.
- rob
On Jun 12, 2018, at 2:43 PM, Aaron Tanenbaum <aaron.b.tanenbaum@gmail.commailto:aaron.b.tanenbaum@gmail.com> wrote:
External Email - Use Caution
I checked my system is not encrypted. I had someone else run the command on the same machine. It worked for them. So I changed my BASH environment to a default environment. I still get the same error.
I tried this again but with a different FreeSurfer 5.3. turns out the one I was using has been altered version of FreeSurfer. I do not know how it was altered. It worked. so it has to do with the altered FreeSurfer. I ran the command mri_convert -version on both FreeSurfer.
for the unaltered i get the out put mri_convert -version stable5 altered version i get mri_convert -version dev build (use --all-info flag for full version info)
with this output i type in mri_convert --all-info mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/06/12-18:32:17-GMT BuildTimeStamp: Aug 22 2014 21:04:47 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: tanenbauma Machine: rocky Platform: Linux PlatformVersion: 3.10.0-862.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Wondering is this version of mri_convert a developmental version? Also both version are the CentOS 6 build.
On Tue, Jun 12, 2018 at 1:01 PM Dicamillo, Robert <RDICAMILLO@mgh.harvard.edumailto:RDICAMILLO@mgh.harvard.edu> wrote: Hello Aaron,
You could check to see if the CentOS 7 system is using disk encryption, e.g., if the following command return 1, then it would mean encryption is in use (which can be an issue with FreeSurfer).
$ cat /proc/sys/crypto/fips_enabled
If it returns zero, it could be an issue with a system library like glibc on CentOS 7.5 (that does not happen on older versions of CentOS).
Either way, this is not your doing ;-)
On Jun 12, 2018, at 11:51 AM, Aaron Tanenbaum <aaron.b.tanenbaum@gmail.commailto:aaron.b.tanenbaum@gmail.com> wrote:
External Email - Use Caution
I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3. When i get to the part where MRI_convert is creating the the orig001.mgz its gives me a segmentation fault. if i run this on a centos 6 system it works fine. below is the output of the program.
/data/gizmo/data1/freesurfer5.3/bin/mri_convert /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm /data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm... crypt_gkey = (null) Segmentation fault (core dumped)
Did I do anything wrong? _______________________________________________ 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
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@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Hua, Jessica