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Today's Topics:

   1. Longitudinal stream with v6 but cross with v5.3
      (Matthieu Vanhoutte)
   2. Re: Hippocampal Subfields Segmentation Error
      (Iglesias Gonzalez, Eugenio)
   3. Re: longitudinal tracula error (Yendiki, Anastasia)
   4. Re: freesurfer 6.0 with some of the analyses (Rizvi, Batool)
   5. Re: Command for Reverse Normalizing with mri_vol2vol Using
      CVS m3z Morphs (Lilla Zollei)
   6. Re: freesurfer 6.0 with some of the analyses (Adam Martersteck)
   7. Re: freesurfer 6.0 with some of the analyses
      (Iglesias Gonzalez, Eugenio)


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

Message: 1
Date: Thu, 26 Jan 2017 09:58:30 +0100
From: Matthieu Vanhoutte <matthieuvanhoutte@gmail.com>
Subject: [Freesurfer] Longitudinal stream with v6 but cross with v5.3
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAF6uKJSd96orkeH+WWX5T6jz3xeYtTNiJ80i96C_5do1L8CWqA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear FS's experts,

I have run all my cross with v5.3 and hesitate to run all longitudinal
process with v6. Does that make sense and will improve the process or would
it be risky to do this ?

Many thanks for your lights !

Best regards,
Matthieu
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Message: 2
Date: Thu, 26 Jan 2017 12:15:44 +0000
From: "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.uk>
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <4751AE9C-2F68-4149-A252-717D257B071C@ucl.ac.uk>
Content-Type: text/plain; charset="windows-1252"

I have never tried this. Does the rest of recon-all -all run without errors?
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/



On 25 Jan 2017, at 11:45, Michel Hu <aoul@live.nl<mailto:aoul@live.nl>> wrote:

Dear  Juan,

I actually followed the guide on the following website in order to make it work on windows 10.
It seems to be a linux BASH shell with ubuntu 14.05.
http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/

Installing and running FreeSurfer on Windows 10 - Imaging ...<http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/>

nuclear-imaging.info<http://nuclear-imaging.info/>
Before I get into how to install FreeSurfer, I must thank the author at K-Lab for the post on ?How to run FSL on Windows 10?. That post describes how to install ...

Sincerely,
Michel hu



________________________________
Van: 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>> namens Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk<mailto:e.iglesias@ucl.ac.uk>>
Verzonden: woensdag 25 januari 2017 12:30
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Hippocampal Subfields Segmentation Error

Dear Michel,
What exact platform are you using? Ubuntu 14.04 installed on a virtual machine running on Windows 10?
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


On 24 Jan 2017, at 12:47, Michel Hu <aoul@live.nl<mailto:aoul@live.nl>> wrote:

Dear Freesurfer Developers,

For my research I'm trying to run the hippocampal subfield segmentation analysis however, I keep running into the following error. I tried to solve it by myself however I had no luck ( I tried by removing the exec flag from the files ).

I'm using the following sofftware
Freesurfer : freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
Ubuntu: 14.04.5 LTS
WIndows 10

michel@-:~$ recon-all -s bob -hippocampal-subfields-T1
Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-rw-r-- 1 michel 1590 1249629 Jan 24 13:40 /usr/local/freesurfer/subjects/bob/scripts/recon-all.log
Linux - 3.4.0+ #1 PREEMPT Thu Aug 1 17:06:05 CST 2013 x86_64 x86_64 x86_64 GNU/Linux
'/usr/local/freesurfer/bin/recon-all' -> '/usr/local/freesurfer/subjects/bob/scripts/recon-all.local-copy'
#--------------------------------------------
#@# Hippocampal Subfields processing (T1 only) left Tue Jan 24 13:43:46 STD 2017

 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 /usr/local/freesurfer bob /usr/local/freesurfer/subjects left

See log file: /usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML: error while loading shared libraries: libut.so: cannot enable executable stack as shared object requires: Invalid argument
#--------------------------------------------
#@# Hippocampal Subfields processing (T1 only) right Tue Jan 24 13:43:46 STD 2017

 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 /usr/local/freesurfer bob /usr/local/freesurfer/subjects right

See log file: /usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML: error while loading shared libraries: libut.so: cannot enable executable stack as shared object requires: Invalid argument

Started at Tue Jan 24 13:43:45 STD 2017
Ended   at Tue Jan 24 13:43:47 STD 2017
#@#%# recon-all-run-time-hours 0.001
recon-all -s bob finished without error at Tue Jan 24 13:43:47 STD 2017
done

Sincerely,
Michel


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The information in this e-mail is intended only for the person to whom it is
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Message: 3
Date: Thu, 26 Jan 2017 13:51:59 +0000
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] longitudinal tracula error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <AF49D39E2A7A3142903EC64E43DC0FAB749220D2@PHSX10MB10.partners.org>
Content-Type: text/plain; charset="windows-1252"

Glad to hear it, thanks for checking! If the final 6.0 works, there's no need to dig up the beta.

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of B?rbara Avelar Pereira [barbara.avelar.pereira@ki.se]
Sent: Thursday, January 26, 2017 3:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your help! Sorry for the delay in replying -- just wanted to make sure the was problem was indeed solved. Since I'm using a server for which I have no administrative rights, I had to wait before the update was installed. It seems to run perfectly now.
I can't find the beta version I was using at the time (just deleted it once I realised I was having the same problem), but if I manage to trace it back, I'll let you know.

Once again, thanks, I'm super grateful!

________________________________
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 Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu<mailto:AYENDIKI@mgh.harvard.edu>]
Sent: Sunday, January 22, 2017 7:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Barbara - If you're using the 5.3 version, then you'll have to download the update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was having the same problem, please let me know (by sending the trac-all copy of that version) so I can fix that asap.

Thanks!

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 B?rbara Avelar Pereira [barbara.avelar.pereira@ki.se<mailto:barbara.avelar.pereira@ki.se>]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine whether the error was possibly version-related, but that doesn?t seem to be the case? I'm actually working with version 5.3 so I'll send attach the trac-all.local-copy for that if that?s OK. Once again, thank you!

On 20 Jan 2017, at 23:52, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu<mailto:AYENDIKI@mgh.harvard.edu>> wrote:

Hi Barbara - If you take out the "set baselist" part, you'll run the cross-sectional TRACULA stream, i.e., analyze each time point independently. So you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may not be used, but the files under the base template's directory are used. Longitudinal TRACULA maps between the base space to the space of each DWI time point, as described in the paper.

Can you please attach the file scripts/trac-all.local-copy? Since there's no official 6.0 version yet but multiple beta versions of it, it's hard to know which one you used.

Thanks,
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 B?rbara Avelar Pereira [barbara.avelar.pereira@ki.se<mailto:barbara.avelar.pereira@ki.se>]
Sent: Friday, January 20, 2017 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal tracula error

Dear FreeSurfer experts,

I?m running tracula on longitudinal data but I?ve encountered the following error at the ?trac-all -prep? stage:  ERROR: flag ; unrecognized (see below)

trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log /Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd /Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log /Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd /Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c /Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log /Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd /Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ;
ERROR: flag ; unrecognized

As an example, I defined the parameters in my dmrirc file as:
set subjlist = ( S0001.01_T1 \
       S0001.01_T2 \
       S0004.00_T1 \
       S0004.00_T2 )

set baselist = ( S0001.01 \
        S0001.01 \
        S0004.00 \
        S0004.00 )

set dcmlist =  ( S0001.01_T1/DTI.nii \
        S0001.01_T2/DTI.nii \
        S0004.00_T1/DTI.nii \
        S0004.00_T2/DTI.nii )

>From the mailing list, it seems a similar issue has been fixed in previous updates but I have tried both version 5.3 and 6.0 and still get this error...

My tracula directory contains 3 directories per participant: 2 with the *.long.* output for timepoint 1 and 2, and a directory with the base. Including the base gives the error above, but if I take it out, it asks for it: ERROR: cannot find /Documents/TRACULA/TEST/S0001.01

>From what I understand, the base is not necessary to run any analysis, but it has to be there anyhow (?): https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45332.html Maybe I am understanding this incorrectly?

Since the base is used to create the longitudinal output (*long*), including the aparc+aseg.mgz file, and those are then used in tracula, I thought I could run things without it. I decided to take out the ?set baselist? part from the configuration file ? this way it seems to run fine (so far). But I assume it?s there for a reason so I?m not sure this is a solution at all...

Any help would be much appreciated!

Details:
1) freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) platform: CentOS release 6.8 (Final)
3) Operating system details (kernel name, release, version, etc.): Linux 2.6.32-642.11.1.el6.x86_64 #1 SMP Fri Nov 18 19:25:05 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
_______________________________________________
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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
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Message: 4
Date: Thu, 26 Jan 2017 14:36:03 +0000
From: "Rizvi, Batool" <br2499@cumc.columbia.edu>
Subject: Re: [Freesurfer] freesurfer 6.0 with some of the analyses
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <04BA39A2E56E2B45A28A08CD188272F534882A55@SGVWAEXM101.mc.cumc.columbia.edu>
       
Content-Type: text/plain; charset="iso-8859-1"

Hi,
Can anyone comment on my question below?
I think the FAQ page mentions that the same version should be used to process all cases within a dataset, but my question is whether I can have the same dataset used for two different versions for separate analyses? This is considering that I've already processed all my data with 5.3, but am interested in getting hippocampal subfields through 6.0.


Thanks so much!
Batool
________________________________
From: Rizvi, Batool
Sent: Wednesday, January 25, 2017 12:54 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: freesurfer 6.0 with some of the analyses

Hi,
I'm wondering if it's okay to run some of the analyses within one study on v.5.3 and the other hippocampal analyses on 6.0? Or do you recommend us starting over for the analyses we've already done in 5.3 for that study?

Thank you!
Batool
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Message: 5
Date: Thu, 26 Jan 2017 09:42:06 -0500 (EST)
From: Lilla Zollei <lzollei@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Command for Reverse Normalizing with
        mri_vol2vol Using CVS m3z Morphs
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <alpine.LRH.2.20.1701260938470.25404@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-15"


Hi Doug,

In order to compute and apply the inverse of an m3z transform you would
need to use the --inv-morph flag instead of the --m3z and reverse your
targ and mov inputs. With the current implementation of mri_vol2vol though
I do not think that you can specify the order of the transforms (which is
important here), so you would need to apply the inverse non-linear
trasform first and then the inverse rigid.

Lilla

On Wed, 25 Jan 2017, Douglas Merkitch wrote:

> Hello Freesurfer experts,
> From your wiki page, I understand how to normalize volumes in subject diffusion space to the CVS template:
>
> mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \
>             --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \
>             --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \
>             --mov fa-masked.mgz \
>             --o fa-masked.ANAT+CVS-to-avg35.mgz \
>             --interp trilin --no-save-reg
>
> However, how would one take take a volume in CVS?template?space and reverse normalize it back to subject diffusion space? Is this possible? If so, what would that command look like and what other st
> eps would be necessary to get the required inputs?
>
> Thanks,
>
> Doug
>
> Douglas Merkitch
> Neurological Sciences
> Rush University Medical Center
> Email:?Douglas_Merkitch@rush.edu
>
>
>
>
>
>
>

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

Message: 6
Date: Thu, 26 Jan 2017 15:55:18 +0000
From: Adam Martersteck <acmarter@gmail.com>
Subject: Re: [Freesurfer] freesurfer 6.0 with some of the analyses
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CANxh5+xV19h5cCYN0mkQAG171=PDN5TVaGsr2i1ehr2W7zXtLA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

I believe Dr. Iglesias previous responses on this exact question have been,
"yes it's possible, but your results may be harder to reproduce"
e.g. If someone wanted to replicate your study they may have a harder time
having to download 2 different versions of freesurfer to achieve comparable
results with your study.

I think the general consensus is "how many subjects do you have?" -- if
it's less than 50, you may want to just rerun v6 on your subjects as it
should preserve the edits -- but it's recommended you still open them up
and double check.

-Adam

On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool <br2499@cumc.columbia.edu>
wrote:

>
>
>
>
>
>
>
>
>
>
>
>
> Hi,
>
> Can anyone comment on my question below?
>
>
> I think the FAQ page mentions that the same version should be used to
> process all cases within a dataset, but my question is whether I can have
> the same dataset used for two different versions for separate analyses?
> This is considering that I've already
>
> processed all my data with 5.3, but am interested in getting hippocampal
> subfields through 6.0.
>
>
>
>
>
>
>
>
>
>
>
>
> Thanks so much!
>
>
> Batool
>
>
>
>
> ------------------------------
>
>
> *From:* Rizvi, Batool
>
>
> *Sent:* Wednesday, January 25, 2017 12:54 PM
>
>
> *To:* freesurfer@nmr.mgh.harvard.edu
>
>
> *Subject:* freesurfer 6.0 with some of the analyses
>
>
>
>
>
>
>
>
>
>
>
>
>
> Hi,
>
>
> I'm wondering if it's okay to run some of the analyses within one study
> on v.5.3 and the other hippocampal analyses on 6.0?
>
> Or do you recommend us starting over for the analyses we've already done
> in 5.3 for that study?
>
>
>
>
>
>
> Thank you!
>
>
> Batool
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
> 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: 7
Date: Thu, 26 Jan 2017 16:01:54 +0000
From: "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.uk>
Subject: Re: [Freesurfer] freesurfer 6.0 with some of the analyses
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <91B2E7DE-58C7-48C4-889F-F8402F98ABC6@ucl.ac.uk>
Content-Type: text/plain; charset="utf-8"

Dear Batool,
Sorry for missing your message.
And dear Adam:
Thanks for covering me! That?s exactly my standard answer to that question ;-)

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 26 Jan 2017, at 15:55, Adam Martersteck <acmarter@gmail.com<mailto:acmarter@gmail.com>> wrote:

I believe Dr. Iglesias previous responses on this exact question have been, "yes it's possible, but your results may be harder to reproduce"
e.g. If someone wanted to replicate your study they may have a harder time having to download 2 different versions of freesurfer to achieve comparable results with your study.

I think the general consensus is "how many subjects do you have?" -- if it's less than 50, you may want to just rerun v6 on your subjects as it should preserve the edits -- but it's recommended you still open them up and double check.

-Adam

On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool <br2499@cumc.columbia.edu<mailto:br2499@cumc.columbia.edu>> wrote:












Hi,

Can anyone comment on my question below?


I think the FAQ page mentions that the same version should be used to process all cases within a dataset, but my question is whether I can have the same dataset used for two different versions for separate analyses? This is considering that I've already

processed all my data with 5.3, but am interested in getting hippocampal subfields through 6.0.












Thanks so much!


Batool




________________________________


From: Rizvi, Batool


Sent: Wednesday, January 25, 2017 12:54 PM


To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>


Subject: freesurfer 6.0 with some of the analyses













Hi,


I'm wondering if it's okay to run some of the analyses within one study on v.5.3 and the other hippocampal analyses on 6.0?

Or do you recommend us starting over for the analyses we've already done in 5.3 for that study?






Thank you!


Batool










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