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
 
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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.com<mailto: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.edu<mailto: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.com<mailto: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?
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Message: 2
Date: Tue, 12 Jun 2018 21:08:20 +0000
From: "Alexopoulos, Dimitrios" <dimitriosalexopoulos@wustl.edu>
Subject: [Freesurfer] tractstats2table - all tracts for multiple
        subjects
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CY1PR0201MB1914D2CDCDE64F2A2093AC89D67F0@CY1PR0201MB1914.namprd02.prod.outlook.com>
       
Content-Type: text/plain; charset="us-ascii"

        External Email - Use Caution       

Hi,


For a group analysis, it possible to use 'tractstats2table' to generate a single table that contains all the tracts for multiple subjects?



It's not intuitively obvious looking at the options with the 'tractstats2table' utility.



Jim


"The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email."


________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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Message: 3
Date: Tue, 12 Jun 2018 21:30:05 +0000
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] tractstats2table - all tracts for multiple
        subjects
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BLUPR0401MB1713489D7CE131B99D103EED8A7F0@BLUPR0401MB1713.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="windows-1252"

Hi Jim - You can use the --load-pathstats-from-file option, as in the tutorial, to pass a text file that contains the paths to all the stats files that you want to include in the table. These can be from multiple subjects and/or tracts.


http://freesurfer.net/fswiki/FsTutorial/TraculaStatistics


Best,

a.y

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alexopoulos, Dimitrios <dimitriosalexopoulos@wustl.edu>
Sent: Tuesday, June 12, 2018 5:08:20 PM
To: Freesurfer support list
Subject: [Freesurfer] tractstats2table - all tracts for multiple subjects


        External Email - Use Caution

Hi,



For a group analysis, it possible to use ?tractstats2table? to generate a single table that contains all the tracts for multiple subjects?



It?s not intuitively obvious looking at the options with the ?tractstats2table? utility.



Jim





?The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.?





________________________________

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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Message: 4
Date: Tue, 12 Jun 2018 21:33:17 +0000
From: "Daumail, Loic Jean" <LDAUMAIL@mgh.harvard.edu>
Subject: [Freesurfer] dwi.ecclog file
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <F1DCEE78C79E7046AC0B5BA33993892801009BEA@PHSX10MB2.partners.org>
Content-Type: text/plain; charset="iso-8859-1"

Hello,

I have several questions regarding the dwi.ecclog file data from Tracula, using the FreeSurfer version V6.0.0.

1) Does Tracula still use eddy_correct from FSL, or was it updated with the new eddy function from FSL?

2) Are the values for each slice of dwi.ecclog relative to the first slice or to the previous slice, or to another template? is it the same for both rotation and translation values?

3) What is the coordinate system for the rotation values? Is there a way to determine the total rotation from these 9 values?

Thanks,

Sincerely,

Loic Daumail
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Message: 5
Date: Tue, 12 Jun 2018 21:40:17 +0000
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] dwi.ecclog file
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BLUPR0401MB1713FB9BD0AD965D70F7272B8A7F0@BLUPR0401MB1713.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="us-ascii"

Hi Loic - The command that computes the motion measures is dmri_motion, and it can take either the eddy_correct or eddy format as input. The former format contains affine registration matrices with respect to the reference frame (which usually is the first b=0). The latter format contains the shift/rotation/etc. parameters of the registration rather than the matrix itself. You can run dmri_motion without arguments to see details.


Best,

a.y

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Daumail, Loic Jean <LDAUMAIL@mgh.harvard.edu>
Sent: Tuesday, June 12, 2018 5:33:17 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] dwi.ecclog file

Hello,

I have several questions regarding the dwi.ecclog file data from Tracula, using the FreeSurfer version V6.0.0.

1) Does Tracula still use eddy_correct from FSL, or was it updated with the new eddy function from FSL?

2) Are the values for each slice of dwi.ecclog relative to the first slice or to the previous slice, or to another template? is it the same for both rotation and translation values?

3) What is the coordinate system for the rotation values? Is there a way to determine the total rotation from these 9 values?

Thanks,

Sincerely,

Loic Daumail
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Message: 6
Date: Tue, 12 Jun 2018 21:50:59 +0000
From: "Alexopoulos, Dimitrios" <dimitriosalexopoulos@wustl.edu>
Subject: Re: [Freesurfer] tractstats2table - all tracts for multiple
        subjects
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CY1PR0201MB191466973DA1B7223811FAA0D67F0@CY1PR0201MB1914.namprd02.prod.outlook.com>
       
Content-Type: text/plain; charset="us-ascii"

        External Email - Use Caution       

Thx Anastasia.

This the command I used and the error:

[hellerml@login01 processed_data]$ tractstats2table --load-pathstats-from-file /scratch/jimalex/freesurfer6_0_chd_auck_6yr/processed_data/test.list --overall --tablefile test.table
Parsing the .stats files
Building the table..
ERROR: all stats files need to have the same pathwayname. try verbose option
These are the pathwaynames found: ['fmajor', 'fminor', 'lh.atr', 'lh.cab', 'lh.ccg', 'lh.cst', 'lh.ilf', 'lh.slfp', 'lh.slft', 'lh.unc', 'rh.atr', 'rh.cab', 'rh.ccg', 'rh.cst', 'rh.ilf', 'rh.slfp', 'rh.slft', 'rh.unc']

For example, the test .list input file I used for a single subject is below:
--------------------------------
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/fminor_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.atr_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.cab_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.ccg_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.slft_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.atr_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.cab_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.ccg_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.cst_AS_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.slft_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt



"The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email."

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, June 12, 2018 4:30 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] tractstats2table - all tracts for multiple subjects


Hi Jim - You can use the --load-pathstats-from-file option, as in the tutorial, to pass a text file that contains the paths to all the stats files that you want to include in the table. These can be from multiple subjects and/or tracts.



http://freesurfer.net/fswiki/FsTutorial/TraculaStatistics



Best,

a.y

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Alexopoulos, Dimitrios <dimitriosalexopoulos@wustl.edu<mailto:dimitriosalexopoulos@wustl.edu>>
Sent: Tuesday, June 12, 2018 5:08:20 PM
To: Freesurfer support list
Subject: [Freesurfer] tractstats2table - all tracts for multiple subjects


        External Email - Use Caution

Hi,



For a group analysis, it possible to use 'tractstats2table' to generate a single table that contains all the tracts for multiple subjects?



It's not intuitively obvious looking at the options with the 'tractstats2table' utility.



Jim





"The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email."





________________________________

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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Message: 7
Date: Tue, 12 Jun 2018 18:07:17 -0700
From: Matthew Peverill <mrpeverill@gmail.com>
Subject: Re: [Freesurfer] Missing Control Points and QATools
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CABnnpkMeW5ZrtszCDSz99=JbS1+JVqWyLiPqGB8h+5nt0KaWpA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hi all,
Sorry for the bump but I wanted to take one more shot at this. We're making
it back but we've lost many, many hours of editing work. Has anyone else
had experiences with QAtools, or other FreeSurfer utilities, removing
control point data, or discovered any way to recover control.dat from other
files? Thank you,
   -Matt

On Mon, May 21, 2018 at 11:35 AM Matthew Peverill <mrpeverill@gmail.com>
wrote:

> Hello,
> We are finishing up manual inspection and editing of our dataset. As part
> of this process, we used QATools to generate QA reports. While we were
> running our reports the tmp/control.dat file was deleted from many of our
> subject directories (the brains had already been recon'd, so the corrected
> surfaces were not affected). The timing certainly suggests these were
> related, but we have no way of knowing if something else unrelated to
> QAtools happened that caused these files to be deleted. So two questions:
>
> 1) Has anyone else had an experience with QAtools where the control.dat
> file was deleted, or have any insight about why this could have happened?
> 2) Is the data in control.dat stored anywhere else? For example, can it be
> recovered from mri/ctrl_pts.mgz? We are mostly fine, but a few brains will
> need to have control points re-applied.
>
> Something of a shot in the dark, but we would love any suggestions. Thanks,
>    -Matt
>
> Version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> uname -a: Linux vmpfc 3.16.0-4-amd64 #1 SMP Debian 3.16.39-1+deb8u2
> (2017-03-07) x86_64 GNU/Linux
>
>
> --
> Matthew Peverill
> mrpeverill@gmail.com (preferred)
>


--
Matthew Peverill
857-277-9083
mrpeverill@gmail.com (preferred)
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Message: 8
Date: Tue, 12 Jun 2018 21:17:42 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Missing Control Points and QATools
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <alpine.LRH.2.20.1806122114340.32555@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Matt

I'm sorry to hear it. I've never heard of anything of ours deleting the
control.dat unless you run recon-all with the appropriate -clean switch.

I don't know an easy way to recover them. Do you need them back? You could
do something like copy the subject, run the intensity normalization on the
copy, then look for points that are exactly 110 in the old
(control-point-normalized) brain.mgz and the new one without control
points, that are also wm in the aseg.mgz. This won't be exactly the control
points, but would let you rerun without losing too much if that is what you
are worried about

cheers
Bruce



On Tue, 12 Jun 2018, Matthew Peverill wrote:

>
> ????????External Email - Use Caution????????
>
> Hi all,Sorry for the bump but I wanted to take one more shot at this. We're making it back but we've
> lost many, many hours of editing work. Has anyone else had experiences with QAtools, or other
> FreeSurfer utilities, removing control point data, or discovered any way to recover control.dat from
> other files? Thank you,
> ? ?-Matt
>
> On Mon, May 21, 2018 at 11:35 AM Matthew Peverill <mrpeverill@gmail.com> wrote:
>       Hello,
>       We are finishing up manual inspection and editing of our dataset. As part of this
>       process, we used QATools to generate QA reports. While we were running our reports the
>       tmp/control.dat file was deleted from many of our subject directories (the brains had
>       already been recon'd, so the corrected surfaces were not affected). The timing certainly
>       suggests these were related, but we have no way of knowing if something else unrelated
>       to QAtools happened that caused these files to be deleted. So two questions:
>
> 1) Has anyone else had an experience with QAtools where the control.dat file was deleted, or
> have any insight about why this could have happened?
> 2) Is the data in control.dat stored anywhere else? For example, can it be recovered
> from?mri/ctrl_pts.mgz? We are mostly fine, but a few brains will need to have control points
> re-applied.
>
> Something of a shot in the dark, but we would love any suggestions. Thanks,
> ? ?-Matt
>
> Version:?freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> uname -a:?Linux vmpfc 3.16.0-4-amd64 #1 SMP Debian 3.16.39-1+deb8u2 (2017-03-07) x86_64
> GNU/Linux
>
>
> --
> Matthew Peverill
> mrpeverill@gmail.com (preferred)
>
>
>
> --
> Matthew Peverill
> 857-277-9083
> mrpeverill@gmail.com (preferred)
>
>

------------------------------

Message: 9
Date: Wed, 13 Jun 2018 11:19:38 +0000
From: "Erik O'Hanlon" <erikohanlon@rcsi.ie>
Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <AM0PR07MB4209CF0074F152A501ECF7C8A37E0@AM0PR07MB4209.eurprd07.prod.outlook.com>
       
Content-Type: text/plain; charset="us-ascii"

        External Email - Use Caution       

Sorry Bruce,


Yep Thanks. I didn't spot that label just the 216. Worked perfectly.


Thanks again


Erik

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Sent: 12 June 2018 19:04:32
To: Freesurfer support list
Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask

I think you can use 1006 (left) and 2006 (right)

cheers
Bruce
On Tue, 12 Jun 2018, Erik
O'Hanlon wrote:

>        External Email - Use Caution
>
> Hi Bruce,
>
>
> Thanks. So if I use the following command
>
> mri_extract_Label aparc+aseg.mgz 216 EC.mgz
>
> would that give me both L and right EC extracted? is there any way to get the left and right separately?
>
>
> Thanks so much for the help
>
>
> cheers
>
>
> Erik
>

Erik O'Hanlon
Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont D9 Ireland
T: 8093740
E: erikohanlon@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/>


Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018>


RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]


> ________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> Sent: 12 June 2018 14:56:41
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask
>
> Hi Erik
>
> yes, you can apply mri_extract_label to the aparc+aseg.mgz to extract EC
> as a volume mask
>
> cheers
> Bruce
> On Tue, 12 Jun 2018, Erik O'Hanlon wrote:
>
>>        External Email - Use Caution
>>
>> Hi FS experts ,
>>
>>
>> I'd like to make masks for the entorhinal cortex to use for tractography. Can you advise what FS tool should be used? I've used the mri_extract_label for my hippocampal masks but not sure what files to use to extract EC ? I'm sure it's straightforward
>>
>>
>> Thanks for any advice
>>
>>
>> Best regards
>>
>>
>> Erik
>>
>> Erik O'Hanlon
>> Postdoctoral researcher
>>
>> [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]
>>
>> RCSI Psychiatry
>> Royal College of Surgeons in Ireland
>> Beaumont Road, Beaumont D9 Ireland
>> T: 8093740
>> E: erikohanlon@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/>
>>
>>
>> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018>
>>
>>
>> RCSI LEADING THE WORLD TO BETTER HEALTH
>>
>> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]
>>
>>
> _______________________________________________
> 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.
>
>
> Erik O'Hanlon
> Postdoctoral researcher
>
> [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]
>
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont D9 Ireland
> T: 8093740
> E: erikohanlon@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/>
>
>
> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018>
>
>
> RCSI LEADING THE WORLD TO BETTER HEALTH
>
> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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------------------------------

Message: 10
Date: Wed, 13 Jun 2018 12:57:38 +0100
From: Walter Hugo Lopez Pinaya <walhugolp@gmail.com>
Subject: [Freesurfer] PREDOCTORAL POSITION at King's College London
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAN7TPXWEP4ywrZBPa3VVwkwH07YrGGC+d=FHQD=tJD-4pGG1yw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Dear colleagues,


We are looking for a predoctoral research assistant with knowledge of
neuroimaging to work on a research project involving the application of
machine learning techniques to neuroanatomical data.

The project will lead to the development of a practical and flexible
web-based tool for measuring neuroanatomical alterations in any brain-based
disorders.

The successful applicant will have previous experience in the handling of
multiple structural neuroimaging datasets within the same project. Previous
experience of using machine learning would be considered a strength but is
not a requisite. The post holder will join a multi-disciplinary team
including neuroscientists, psychologists and computer scientists.

This project is a collaboration between King?s College London, UK (Dr.
Andrea Mechelli), the University of New Mexico, USA (Prof. Vince Calhoun)
and the Universidade Federal do ABC, Brazil (Prof Jo?o Sato) and is funded
by an Innovator Award from the Wellcome Trust. The post holder will be
based at the Institute of Psychiatry, Psychology & Neuroscience (King?s
College London).


For more information, please see
https://www.hirewire.co.uk/HE/1061247/MS_JobDetails.aspx?JobID=79233

Best wishes,

Walter Hugo Diaz Sanz
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------------------------------

Message: 11
Date: Wed, 13 Jun 2018 09:45:50 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <alpine.LRH.2.20.1806130945470.12577@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed

glad to hear it
Bruce
On Wed, 13 Jun 2018, Erik O'Hanlon wrote:

>        External Email - Use Caution
>
> Sorry Bruce,
>
>
> Yep Thanks. I didn't spot that label just the 216. Worked perfectly.
>
>
> Thanks again
>
>
> Erik
>
> ________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> Sent: 12 June 2018 19:04:32
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask
>
> I think you can use 1006 (left) and 2006 (right)
>
> cheers
> Bruce
> On Tue, 12 Jun 2018, Erik
> O'Hanlon wrote:
>
>>        External Email - Use Caution
>>
>> Hi Bruce,
>>
>>
>> Thanks. So if I use the following command
>>
>> mri_extract_Label aparc+aseg.mgz 216 EC.mgz
>>
>> would that give me both L and right EC extracted? is there any way to get the left and right separately?
>>
>>
>> Thanks so much for the help
>>
>>
>> cheers
>>
>>
>> Erik
>>
>
> Erik O'Hanlon
> Postdoctoral researcher
>
> [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]
>
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont D9 Ireland
> T: 8093740
> E: erikohanlon@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/>
>
>
> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018>
>
>
> RCSI LEADING THE WORLD TO BETTER HEALTH
>
> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]
>
>
>> ________________________________
>> From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu>
>> Sent: 12 June 2018 14:56:41
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask
>>
>> Hi Erik
>>
>> yes, you can apply mri_extract_label to the aparc+aseg.mgz to extract EC
>> as a volume mask
>>
>> cheers
>> Bruce
>> On Tue, 12 Jun 2018, Erik O'Hanlon wrote:
>>
>>>        External Email - Use Caution
>>>
>>> Hi FS experts ,
>>>
>>>
>>> I'd like to make masks for the entorhinal cortex to use for tractography. Can you advise what FS tool should be used? I've used the mri_extract_label for my hippocampal masks but not sure what files to use to extract EC ? I'm sure it's straightforward
>>>
>>>
>>> Thanks for any advice
>>>
>>>
>>> Best regards
>>>
>>>
>>> Erik
>>>
>>> Erik O'Hanlon
>>> Postdoctoral researcher
>>>
>>> [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]
>>>
>>> RCSI Psychiatry
>>> Royal College of Surgeons in Ireland
>>> Beaumont Road, Beaumont D9 Ireland
>>> T: 8093740
>>> E: erikohanlon@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/>
>>>
>>>
>>> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018>
>>>
>>>
>>> RCSI LEADING THE WORLD TO BETTER HEALTH
>>>
>>> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]
>>>
>>>
>> _______________________________________________
>> 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.
>>
>>
>> Erik O'Hanlon
>> Postdoctoral researcher
>>
>> [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]
>>
>> RCSI Psychiatry
>> Royal College of Surgeons in Ireland
>> Beaumont Road, Beaumont D9 Ireland
>> T: 8093740
>> E: erikohanlon@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/>
>>
>>
>> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018>
>>
>>
>> RCSI LEADING THE WORLD TO BETTER HEALTH
>>
>> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]
>>
>>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>


------------------------------

Message: 12
Date: Wed, 13 Jun 2018 16:34:58 +0200
From: Tudor Popescu <tudor3@gmail.com>
Subject: Re: [Freesurfer] "WARNING: Image geometries differ across
        time" upon running base step of longitudinal pipeline
To: free surfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAGBir40vNFk6zTXB7ByHx5qf_WumrHJA4qKVZDWeBF8okL0bpg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hi Bruce,

I am guessing that Martin might be unavailable for now, judging by the date
of his last input to the list.

However, my intuition is that there is something really trivial that's
causing this chain of (circular!) errors...

For any more ideas of what I could try, I'd remain really indebted!

Cheers,
Tudor

On Mon, 11 Jun 2018 at 16:03, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:

> Hi Tudor
>
> I think Martin is probably better able to sort this out than I am.
>
> Bruce
>
>
> On Mon, 11 Jun 2018, Tudor Popescu wrote:
>
> >
> >         External Email - Use Caution
> >
> > Hi Bruce,
> > I assumed a subject-specific target for the mri_convert, so I used this
> command to realign
> > subject1's post to his pre:
> >       mri_convert -rl 01_1.nii.gz 01_2.nii.gz 01_2resampled.nii.gz
> >
> > (and renamed the resampled file to 01_2). However, then the base step
> >       recon-all -base 01 -tp 01_1 -tp 01_2 -all
> >
> > still gives the same warning about geometries differing across time; and
> also in addition, this
> > error message (which might have been there earlier too but had gone
> unnoticed):
> >       mghRead(/media/FS/01_1/mri/norm.mgz, -1): could not open file
> > MultiRegistration::loadMovables: could not open input volume
> /media/FS/01_1/mri/norm.mgz.
> >
> > Inside /media/FS/01_1/mri/ (where /media/FS is my $SUBJECTS_DIR), there
> is indeed no norm.mgz, which
> > suggests something in my previous commands:
> >       recon-all -i 01_1.nii.gz -subjid 01_1
> > recon-all -i 01_2.nii.gz -subjid 01_2
> > recon-all -subjid 01_1 -all
> > recon-all -subjid 01_2 -all
> >
> > ..has gone wrong despite these having produced no errors. Although I
> thought the base step already
> > does autorecon1 as part of the longitudinal pipeline, I tried doing it
> manually:
> >       recon-all -autorecon1 -subjid 01
> >
> > however this returns:
> >       ERROR: It appears that this subject ID is an existing
> base/template from longitudinal
> >       processing (-base). Please make sure you pass all necessary flags.
> For example, if you
> >       are trying to re-run a -base: \' -base <templateid> -tp <tpNid>
> ... \'
> >
> > ..and running autorecon1 and 2 for the first timepoint instead,
> >       recon-all -autorecon1  -autorecon2 -subjid 01_1
> >
> > returns
> >       mri_em_register: could not open input volume nu.mgz
> >
> >
> > Not sure what to do at this stage!.. Thanks again for any pointers!
> >
> > Cheers,
> > Tudor
> >
> > On Thu, 7 Jun 2018 at 18:16, Tudor Popescu <tudor3@gmail.com> wrote:
> >       Hi Bruce,
> > Thanks for your answer! Before seeing this warning (rather: error, as no
> output is produced),
> > I'd not have thought the pre-post images have different geometries, as
> I'm pretty sure their
> > acquisition parameters were the same. The pre and post of any one
> subject, as well as the
> > different subjects' images, all seem to have identical voxel size
> (1x1x1) and image size
> > (176x224x160). Furthemore, the (0,0,0) point seems to always overlap
> well-enough on the
> > anterior commissure...
> >
> > This all suggests to me the geometry differences are trivial, so the
> resampling is worth a
> > try. However, I'm unsure whether, in the call to mri_convert -rl, the
> target would have to
> > be subject-specific (e.g. resample each 'post' to the 'pre' baseline),
> or if I should use a
> > single target for all the pre&post images in the study, a bit like the
> study-specific template
> > used by VBM?
> >
> > Cheers,
> > Tudor
> >
> >
> >
> > On 6 June 2018 at 16:37, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> wrote:
> >       Hi Tudor
> >
> >       if you are sure that the differences are trivial you can resample
> the images to
> >       all have exactly the same geometries and rerun (I think
> mri_convert -rl <target
> >       vol> <source vol> <source vol resampled>
> >
> >       should do it (-rl is "reslice like"). If they are not trivial
> though you may find
> >       effects that only reflect the acquisition differences.
> >
> >       cheers
> >       Bruce
> >
> >       On Wed, 6 Jun 2018, Tudor Popescu wrote:
> >
> >
> >                     External Email - Use Caution
> >
> >             Hello,
> >             If any more information is needed to address my question,
> please do
> >             let me know. I hope to hear back and once again
> >             thanks a lot for any assistance with this.
> >
> >             Best wishes,
> >             Tudor
> >
> >             On 1 June 2018 at 16:07, Tudor Popescu <tudor3@gmail.com>
> wrote:
> >                   Dear all,
> >             I have pre and post-intervention data for a single group of
> subjects,
> >             and I'd like to extract the cortical
> >             thickness pre and post, for all standard regions in the
> atlas, and use
> >             those in subsequent analyses.
> >
> >             Following the standard approach for longitudinal studies, I
> used the
> >             following types of commands:
> >              1. recon-all -i 01_1.nii.gz -subjid 01_1
> >                 recon-all -i 01_2.nii.gz -subjid 01_2
> >                 recon-all -i 02_1.nii.gz -subjid 02_1
> >                 ..
> >                 where e.g. 01 is the subj code, and _1 and _2 represent
> pre and
> >             post scans
> >              2. recon-all -subjid 01_1 -all
> >                 recon-all -subjid 01_2 -all
> >                 ..
> >              3. recon-all -base 01 -tp 01_1 -tp 01_2 -all
> >                 ..
> >              4. recon-all -long 01_1 01 -all
> >                 recon-all -long 01_2 01 -all
> >                 ..
> >             However, the base step has led to warnings of the type:
> "WARNING:
> >             Image geometries differ across time, maybe
> >             due to aquisition changes?  This can potentially bias a
> longitudinal
> >             study! ", and consequently to an empty
> >             /stats folder -- even though my pre and post images are
> aligned and
> >             have similar acquisition parameters.
> >
> >             Have I done something wrong, and how can I fix this
> warning/error?
> >             Many thanks in advance for any help.
> >
> >             Best wishes,
> >             Tudor
> >
> >
> >
> >
> >       _______________________________________________
> >       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
>
>
> 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.
>
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------------------------------

Message: 13
Date: Wed, 13 Jun 2018 15:09:11 +0000
From: "Daumail, Loic Jean" <LDAUMAIL@mgh.harvard.edu>
Subject: Re: [Freesurfer] dwi.ecclog file
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <F1DCEE78C79E7046AC0B5BA33993892801009C34@PHSX10MB2.partners.org>
Content-Type: text/plain; charset="iso-8859-1"

Dear Mrs Yendiki,

thank you for your response.
However, for my configuration file, containing :
"
setenv SUBJECTS_DIR /autofs/space/avadhuti_001/users/gdesbord/CALM_data/CALM_001

set subjlist = ( 02_recon )

set dcmlist = ( /autofs/space/avadhuti_001/users/gdesbord/CALM_data/Qball_data/raw_DICOMs/CALM_001/02/892000-000015-000001.dcm)

set doeddy = 1

set dorotbvecs = 1

"

Did "doeddy = 1" use eddy_correct or eddy format?
Also, I am not sure about the units, is it in mm and degrees for the values in dwi.ecclog file?

Thank you,

Sincerely,

Loic


________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu]
Sent: Tuesday, June 12, 2018 5:40 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dwi.ecclog file


Hi Loic - The command that computes the motion measures is dmri_motion, and it can take either the eddy_correct or eddy format as input. The former format contains affine registration matrices with respect to the reference frame (which usually is the first b=0). The latter format contains the shift/rotation/etc. parameters of the registration rather than the matrix itself. You can run dmri_motion without arguments to see details.


Best,

a.y

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Daumail, Loic Jean <LDAUMAIL@mgh.harvard.edu>
Sent: Tuesday, June 12, 2018 5:33:17 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] dwi.ecclog file

Hello,

I have several questions regarding the dwi.ecclog file data from Tracula, using the FreeSurfer version V6.0.0.

1) Does Tracula still use eddy_correct from FSL, or was it updated with the new eddy function from FSL?

2) Are the values for each slice of dwi.ecclog relative to the first slice or to the previous slice, or to another template? is it the same for both rotation and translation values?

3) What is the coordinate system for the rotation values? Is there a way to determine the total rotation from these 9 values?

Thanks,

Sincerely,

Loic Daumail
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Message: 14
Date: Wed, 13 Jun 2018 11:20:16 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Running qcache on old FS data
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <6877f84e-1e94-65f2-3de6-e66c96774474@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"; format=flowed

I have no idea how to make it work with data that old. You can "fool" it
by copying or soft linking lh.curv to lh.white.K. You can probably get
it to at least finish.


On 06/06/2018 03:41 PM, Jamie Hanson wrote:
>
> ????????External Email - Use Caution
>
>
> Hello all,
>
> I was trying to run?qcache?on some previously processed Freesurfer
> data from a colleague, but ran into some issues with missing files and
> wondered how best to proceed.
>
> Details:
> -The data was processed with (Freesurfer) v4.5.0 and I would ideally
> like to not reprocess it with a newer version (to keep in concordance
> with past published work, and also it's a large number of subjects,
> n=800+).
> -The qcache flag was not used with the data previously (to my
> knowledge), so I was attempting to run this command: recon-all -s
> $subj -qcache
> -When I try that command, I get an error regarding a
> missing?lh.white.K file.
>
> I've uploaded the log file here:
> https://www.dropbox.com/s/94mnsy7wrps5ce2/recon-all.log?dl=0
>
> I wondered if it was possible to complete qcache with the data as is?
> I searched on the list previously and saw one or two other folks had
> run into this issues; I, however, didn't see a final solution to
> things. Any thoughts or suggestions are greatly appreciated! Thanks much!
>
> Best,
> Jamie.
>
> --
> Jamie Hanson
> Assistant Professor, Psychology
> Research Scientist, Learning Research and Development Center
> University of Pittsburgh
> Personal website: jamiehanson.org <http://jamiehanson.org>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



------------------------------

Message: 15
Date: Wed, 13 Jun 2018 11:52:52 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Group Analysis Covariates
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <fe0de347-e3a3-2c18-af56-47dc48e9e37a@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"; format=flowed



On 06/11/2018 11:07 PM, Hua, Jessica wrote:
>
>
> Dear Freesurfer Experts:
>
>
> I analyzed my data following the guidelines on the FSL Tutorial/Group
> Analysis page . I am trying to plot the adjusted values (covariates:
> age, sex, and ICV)?for the significant clusters for each of my
> participants.
>
I assume you mean FreeSurfer, not FSL?
>
>
> I set up the contrast to test group differences. So testing whether
> there is a difference between groups regressing out the effects of
> sex, age, and ICV. Contrasts?created were? [1 -1 0 0 0 0 0 0] and [-1
> 1 0 0 0 0 0 0].
>
>
> I?then extracted values from this file
> (cache.th20.abs.sig.y.ocn.dat;?i.e., the average value of each subject
> in each cluster) into my dataset. I believe these are the unadjusted
> values, correct?
>
These are the average thickness data (assuming you are using thickness
as input --y)
>
> I calculated total volume and total surface area by multiplying these
> values by the total number of vertices in each cluster.
>
Not sure what you mean here or how it works.
>
> To adjust for covariates, I ran a regression with the
> ExtractedClusterValues as the DV and?Group, Sex, Age, and ICV as
> predictors. Looking at the output, there was no significant effect of
> group (p = .769; whereas in FreeSurfer the cluster-wise p < .001).
>
What were you using to do this test? You really need to have exactly the
same design matrix and contrast matrix.
>
> Also when I plotted the predicted values adjusting for covariates, the
> means between the groups were very similar.
>
>
> Why am I getting a p = .769 when I adjust for covariates, but
> FreeSurfer has a cluster-wise p < .001? Or is there a way to calculate
> adjusted values in FreeSurfer?
>
>
> Best,
>
>
> Jessica
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



------------------------------

Message: 16
Date: Wed, 13 Jun 2018 11:54:08 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Error during QDEC
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <c755a260-8d08-eb9c-91a2-b17f6df17f25@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"; format=flowed

can you send the fsgd file?


On 06/12/2018 02:32 AM, Seung-Gul Kang (???) wrote:
> Dear Freesurfer experts,
>
> I see the error message when I perform QDEC.
> The error message is as below.
>
> Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
>
> cwd /home/sgk
>
> cmdline mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh
> --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods
> --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh
> --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat
> --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat
> --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat
> --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat
> --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat
> --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat
> --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat
>
>
> sysnameLinux
>
> hostname localhost.localdomain
>
> machinex86_64
>
> usersgk
>
> FixVertexAreaFlag = 1
>
> UseMaskWithSmoothing1
>
> OneSampleGroupMean 0
>
> y/mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh
>
> logyflag 0
>
> usedti0
>
> FSGD /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd
>
> labelmask/mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label
>
> maskinv 0
>
> glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI
>
> IllCondOK 0
>
> ReScaleX 1
>
> DoFFx 0
>
> Creating output directory /mnt/hgfs/share/suicide/qdec/LH_area_SSI
>
> Loading y from /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh
>
> INFO: gd2mtx_method is dods
>
> Saving design matrix to /mnt/hgfs/share/suicide/qdec/LH_area_SSI/Xg.dat
>
> Normalized matrix condition is 24522.5
>
> Design matrix ------------------
>
> 1.0000.0000.0000.00015.0000.0000.0000.00024.0000.0000.0000.00021.0000.0000.0000.000149457.5940.0000.0000.000;
>
> 1.0000.0000.0000.00019.0000.0000.0000.00050.0000.0000.0000.00020.0000.0000.0000.000161540.2030.0000.0000.000;
>
> 1.0000.0000.0000.0007.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000167295.9060.0000.0000.000;
>
> 0.0000.0001.0000.0000.0000.00010.0000.0000.0000.00031.0000.0000.0000.00027.0000.0000.0000.000175241.7030.000;
>
> 0.0000.0001.0000.0000.0000.00015.0000.0000.0000.00059.0000.0000.0000.00023.0000.0000.0000.000165616.7970.000;
>
> 0.0000.0001.0000.0000.0000.00011.0000.0000.0000.00057.0000.0000.0000.00022.0000.0000.0000.000183255.5940.000;
>
> 1.0000.0000.0000.00026.0000.0000.0000.00037.0000.0000.0000.00023.0000.0000.0000.000159212.2030.0000.0000.000;
>
> 0.0000.0001.0000.0000.0000.00014.0000.0000.0000.00050.0000.0000.0000.00022.0000.0000.0000.000170017.0940.000;
>
> 0.0000.0001.0000.0000.0000.00016.0000.0000.0000.00026.0000.0000.0000.00019.0000.0000.0000.000190217.9060.000;
>
> 0.0000.0001.0000.0000.0000.0001.0000.0000.0000.00039.0000.0000.0000.00019.0000.0000.0000.000156341.0000.000;
>
> 1.0000.0000.0000.00018.0000.0000.0000.00049.0000.0000.0000.00032.0000.0000.0000.000168844.2970.0000.0000.000;
>
> 1.0000.0000.0000.00021.0000.0000.0000.00039.0000.0000.0000.00026.0000.0000.0000.000149945.4060.0000.0000.000;
>
> 1.0000.0000.0000.00011.0000.0000.0000.00039.0000.0000.0000.00022.0000.0000.0000.000166132.9060.0000.0000.000;
>
> 1.0000.0000.0000.00017.0000.0000.0000.00041.0000.0000.0000.00025.0000.0000.0000.000139924.4060.0000.0000.000;
>
> 1.0000.0000.0000.00027.0000.0000.0000.00045.0000.0000.0000.00034.0000.0000.0000.000133331.7970.0000.0000.000;
>
> 1.0000.0000.0000.00011.0000.0000.0000.00047.0000.0000.0000.00024.0000.0000.0000.000164844.7030.0000.0000.000;
>
> 1.0000.0000.0000.00023.0000.0000.0000.00046.0000.0000.0000.00026.0000.0000.0000.000163024.2030.0000.0000.000;
>
> 0.0000.0001.0000.0000.0000.00031.0000.0000.0000.00042.0000.0000.0000.00033.0000.0000.0000.000140203.7970.000;
>
> 0.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00029.0000.0000.0000.000186282.2970.000;
>
> 0.0000.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00017.0000.0000.0000.000171746.094;
>
> 0.0001.0000.0000.0000.00017.0000.0000.0000.00034.0000.0000.0000.00015.0000.0000.0000.000145005.2030.0000.000;
>
> 0.0000.0000.0001.0000.0000.0000.00015.0000.0000.0000.00054.0000.0000.0000.00027.0000.0000.0000.000168633.203;
>
> 0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00027.0000.0000.0000.00020.0000.0000.0000.000186731.297;
>
> 0.0001.0000.0000.0000.0001.0000.0000.0000.00061.0000.0000.0000.00028.0000.0000.0000.000154627.5000.0000.000;
>
> 0.0001.0000.0000.0000.00010.0000.0000.0000.00044.0000.0000.0000.00022.0000.0000.0000.000154626.2970.0000.000;
>
> 0.0000.0000.0001.0000.0000.0000.0004.0000.0000.0000.00059.0000.0000.0000.00020.0000.0000.0000.000177918.500;
>
> 0.0001.0000.0000.0000.0004.0000.0000.0000.00056.0000.0000.0000.00027.0000.0000.0000.000157687.7970.0000.000;
>
> 0.0000.0000.0001.0000.0000.0000.0008.0000.0000.0000.00058.0000.0000.0000.00032.0000.0000.0000.000173899.094;
>
> 0.0000.0000.0001.0000.0000.0000.00021.0000.0000.0000.00020.0000.0000.0000.00018.0000.0000.0000.000175980.500;
>
> 0.0001.0000.0000.0000.0000.0000.0000.0000.00059.0000.0000.0000.00028.0000.0000.0000.000162526.7030.0000.000;
>
> 0.0000.0000.0001.0000.0000.0000.0002.0000.0000.0000.00037.0000.0000.0000.00020.0000.0000.0000.000198622.797;
>
> 0.0001.0000.0000.0000.0003.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000157633.9060.0000.000;
>
> 0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00021.0000.0000.0000.00021.0000.0000.0000.000164236.297;
>
> 0.0001.0000.0000.0000.00022.0000.0000.0000.00046.0000.0000.0000.00023.0000.0000.0000.000144559.7030.0000.000;
>
> 0.0001.0000.0000.0000.0007.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000156151.5000.0000.000;
>
> 0.0000.0000.0001.0000.0000.0000.00016.0000.0000.0000.00046.0000.0000.0000.00027.0000.0000.0000.000154306.406;
>
> 0.0000.0000.0001.0000.0000.0000.0000.0000.0000.0000.00019.0000.0000.0000.00020.0000.0000.0000.000188334.203;
>
> 0.0001.0000.0000.0000.00020.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000134977.4060.0000.000;
>
> --------------------------------
>
> ERROR: matrix is ill-conditioned or badly scaled, condno = 24522.5
>
> --------------------------------
>
> Possible problem with experimental design:
>
> Check for duplicate entries and/or lack of range of
>
> continuous variables within a class.
>
> If you seek help with this problem, make sure to send:
>
> 1. Your command line:
>
> mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label
> /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat
> --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat
> --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat
> --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat
> --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat--C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat
> --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat
>
>
> 2. The FSGD file (if using one)
>
> 3. And the design matrix above
>
> Error in Analyze: command failed: mri_glmfit --y
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label
> /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat
> --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat
> --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat
> --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat
> --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat
> --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat
> --C
> /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat
>
> I also attach the error message.
>
> Could you tell me how I can fix this problem?
>
> I am looking forward to receiving your reply.
>
> Best regards,
> Seung-Gul
>
> *S**eung-Gul Kang, M.D., Ph.D. *
> Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center
> ?????. Dean, Department of Research Affairs; Gachon University
> College of Medicine
> ????????????.?Director, Incheon Suicide Prevention Center
> 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea
>
> ?
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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End of Freesurfer Digest, Vol 172, Issue 21
*******************************************