Re: [Freesurfer] The results of your email commands

[Dave Yas]

Hello,

The files didnt work!

Here is the error after trying 2 participants, one with each mri_segstats you 
attached.
same error for both.


Could you please let me know what to do next?


n#-
#@# Curvature Stats rh Tue May 24 08:13:18 JST 2016
/Users/dave/Documents/tot/Studies/ASD_Struct/Kj/Surf_test/PSY1012fs/surf
\n mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats 
-F smoothwm PSY1012fs rh curv sulc \n
 Toggling save flag on curvature files   [ ok ]
 Outputting results using filestem   [ ../stats/rh.curv.stats ]
 Toggling save flag on curvature files   [ ok ]
   Setting surface[ PSY1012fs/rh.smoothwm ]
Reading surface...   [ ok ]
   Setting texture [ curv ]
Reading texture...   [ ok ]
   Setting texture [ sulc ]
Reading texture...Gb_filter = 0
   [ ok ]
  Calculating Discrete Principal Curvatures...
   Determining geometric order for vertex faces... [] [ ok ]
  Determining KH curvatures... [] [ ok ]
Determining k1k2 curvatures... [] [ ok ]
   deltaViolations  [ 260 ]
Gb_filter = 0

WARN:S lookup   min:  -0.175830
WARN:S explicit min:  0.00vertex = 422
#
#@# ASeg Stats Tue May 24 08:13:23 JST 2016
\nINFO: mri_segstats will not calculate Supratentorial
  due to missing ribbon.mgz file
/Users/dave/Documents/tot/Studies/ASD_Struct/kj/Surf_test/PSY1012fs
\n mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz 
--empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 
--excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm 
--in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler 
--ctab /Applications/freesurfer/ASegStatsLUT.txt --subject PSY1012fs \n

$Id: mri_segstats.c,v 1.110.2.3 2015/07/02 20:12:19 zkaufman Exp $
cwd 
cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg 
--excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz 
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol 
--surf-ctx-vol --totalgray --euler --ctab 
/Applications/freesurfer/ASegStatsLUT.txt --subject PSY1012fs 
sysname  Darwin
hostname daves-Mac-Pro.local
machine  x86_64
user dave
UseRobust  0
atlas_icv (eTIV) = 1512862 mm^3(det: 1.287696 )
Computing euler number
orig.nofix lheno = -122, rheno = -128
orig.nofix lhholes =   62, rhholes = 65
Loading mri/aseg.mgz
Warning: cannot find 
/Users/dave/Documents/tot/Studies/ASD_Struct/kj/Surf_test/PSY1012fs/mri/ribbon.mgz,
 not computing whole brain stats
Loading mri/norm.mgz
Loading mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found  50 segmentations
Computing statistics for each segmentation

Reporting on  45 segmentations
Using PrintSegStat
mri_segstats done

#--

Started at Mon May 23 11:43:42 JST 2016 
Ended   at Tue May 24 08:16:38 JST 2016
#@#%# recon-all-run-time-hours 20.549
recon-all -s PSY1012fs finished without error at Tue May 24 08:16:38 JST 2016
done
[daves-Mac-Pro:ASD_Struct/kj/Surf_test] dave% 

From: davema...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Fri, 20 May 2016 01:07:28 +
Subject: Re: [Freesurfer] The results of your email commands





Thanks a lot. 
Does the snowleaopard version work on El Capitan? 
So by replacing the version already found in bin/mrisegstats, with the leopard 
one after Chomd +x, it should work?
I thought i would get a link for something like mri_segstats.ElCapitan?

Yas
  

> To: freesurfer@nmr.mgh.harvard.edu
> From: gr...@nmr.mgh.harvard.edu
> Date: Thu, 19 May 2016 11:07:40 -0400
> Subject: Re: [Freesurfer] The results of your email commands
> 
> I've refreshed those links
> 
> On 05/18/2016 10:44 PM, Dave Yas wrote:
> > Dear Doug,
> >
> > I'm getting mri_segstats error [mghread(...ribbon.mgz) at the end of 
> > -autorecon2.
> > I saw your answer for others about this Q before and i know how to 
> > solve this *IF* i was able to access to the links you posted.
> >
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.centos6
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.snowleopard
> >
> > I thought that these should give me some kind of a pop up to prompt me 
> > to enter as a guest and get the file to put it in 

Re: [Freesurfer] ERROR: cannot unpack mosiacs without ASCII header

[Douglas N Greve]

Have the dicom files changed in any way? In the failure, the problem 
maybe that it thinks that the series is truncated (the header thing is 
not a problem). Do you still have perms to all the files in that folder? 
I noticed in the analysis that succeeded had a bunch of these statements 
(never seen it before):

Agreeing to the Xcode/iOS license requires admin privileges, please 
re-run as root via sudo.

Feel free to tar up the dicom folder and send it to me at our file drop.


On 05/23/2016 06:35 PM, Aloi, Joseph wrote:
> Hi Doug,
>
> I've attached the recon-all log for an analysis on a research subject 
> that I successfully ran a few weeks ago and then the recon-all log 
> when I try to run the exact same analysis on the exact same subject 
> now.  Thanks so much for taking a look at these.
>
> The log files you can just attach to the email to the list (or to me
> directly if there is something in there that you don't want to post)
> On 05/20/2016 04:02 PM, Aloi, Joseph wrote:
> > Excellent, thank you!  To do that, do I send an e-mail to the listserv
> > with the log files attached or do I use the filedrop?
> >
> > yea, can you post the log file of both the successful and failing runs?
> >
> > On 05/19/2016 11:28 AM, Aloi, Joseph wrote:
> > >
> > > Hi Doug,
> > >
> > > No that’s not how I usually store my files- I have a folder for the
> > > particular study that I am working on then the dicoms for each subject
> > > in that study are stored in individual subject folders within the
> > > study folder.
> > >
> > > I got a chance to look around the recon-all logs this morning for a
> > > subject that I had successfully processed in the past (but that I get
> > > the error when I try to process this same dataset now).  From
> > > comparing the recon-all log from when recon-all ran successfully
> > > versus now, things are running fine up until it gets to MRI_convert.
> > > However, it looks like things are actually starting to go haywire
> > > during MRI_convert even before I get the warning about the ASCII
> > > header and recon-all exits.  It appears that MRI_convert is having
> > > some trouble with extracting some of the information it needs from the
> > > dicom file, resulting in the error that I posted.  I know you guys are
> > > busy, but would you be able to take a look at the log files?  I’ve
> > > only been using freesurfer a few weeks, so I would definitely
> > > appreciate any insights you might have from looking at the log files.
> > >
> > > Thank you!
> > >
> > > I don't have any idea what is going wrong. I noticed that the file
> > > that it is having problems with is here
> > > /Users/alojos/Applications/freesurfer/subjects/sub_.dcm
> > > Do you really keep all your dicom files in that location?
> > >
> > >
> > >
> > > On 05/17/2016 11:47 PM, Aloi, Joseph wrote:
> > > > Hi Doug,
> > > > Sorry- I've added entire correspondence onto the end of this
> > > e-mail.  I don't think the disk filled up as I am on a 3 TB hard drive
> > > and I still have ~2 TB of free space on my disk.  Anything else you
> > > think it could be?
> > > > Thanks!
> > > > Joseph Aloi
> > > > Please remember to include previous correspondence otherwise we can't
> > > > keep track of the problem!
> > > > Eg, I don't have the previous email to see what the error was. Is it
> > > > possible that the disk filled up?
> > > > On 05/17/2016 09:49 AM, Aloi, Joseph wrote:
> > > > > Hi Doug,
> > > > >
> > > > > Yes, you are correct- data I have previously processed without any
> > > > > problems is no longer being processed.
> > > > >
> > > > > My version of freesurfer is 5.3.0; I only downloaded it a few weeks
> > > > > ago so I have not changed my freesurfer version recently.
> > > > >
> > > > > Thanks!
> > > > >
> > > > > Joseph Aloi
> > > > > Graduate Student, MD/PhD Scholars Program
> > > > > Department of Pharmacology and Experimental Neuroscience
> > > > > University of Nebraska Medical Center
> > > > >
> > > > > Neurobehavioral Research Assistant, Center For Neurobehavioral
> > > Research
> > > > > Boys Town National Research Hospital
> > > > So the exact same data set is now generating an error whereas it ran
> > > > smoothly before? What version of FS are you using? Did you change
> > > versions?
> > > > doug
> > > > On 05/16/2016 09:49 AM, Aloi, Joseph wrote:
> > > > >
> > > > > Hi freesurfer experts,
> > > > >
> > > > > I have recently begun to use freesurfer to do structural MRI
> > > > > analyses.  I have been able to successfully process about 40
> > > > > structural scans with recon-all thus far, but starting a few days ago,
> > > > > I started getting this error whenever I run recon-all:
> > > > >
> > > > > WARNING: file
> > > > > /Users/alojos/Applications/freesurfer/subjects/sub_.dcm does not
> > > > > contain a Siemens ASCII header
> > > > >
> > > > > has this file been anonymized?
> > > > >
> > > > > ERROR: cannot unpack mosiacs without ASCII header
> > > > >
> > > > > Darwin nerc130622.local 14.5.0 

Re: [Freesurfer] Brainmask edit error

[Sabrina Yu]

Thank you for your explanation. Would it be possible to find a workaround? I 
want to generate stats on intensity over an ROI for these stroke subjects. For 
the brain matter not included in the surface, can I create a volume label file 
in freeview instead of trying to edit the surfaces?

Thank you,
Sabrina

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Monday, May 23, 2016 12:30:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Brainmask edit error

because it violates too many of our assumptions about the topology and
geometry of the brain.

cheers
Bruce
On Mon, 23 May 2016, Sabrina Yu
wrote:

>
> Hi Bruce,
>
> Thank you for your reply. I've uploaded the .mgz and surfaces using FTP to 
> FreeSurfer. Why is it that it may not be possible to get good surfaces with 
> extensive strokes?
>
> Thank you,
> Sabrina
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bruce Fischl 
> 
> Sent: Thursday, May 19, 2016 11:24:51 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Brainmask edit error
>
> Hi Sabrina
>
> it's tough to tell from just the 2 slices. If you upload the subject one
> of us will take a look, but it may not be possible to get good surfaces
> with that extensive a stroke
>
> cheers
> Bruce
> On Wed, 18 May 2016, Sabrina Yu wrote:
>
>>
>> Hello,
>>
>>
>> I'm having problems with regenerating the surfaces for stroke cases after
>> editing the brainmask.mgz file. In the aseg.mgz file, the brain matter
>> around lesion area is correctly classified as brain matter. In the pial
>> surface, this brain matter is not included.
>>
>>
>> I've tried to edit the brainmask.mgz file to include this region, but when I
>> run: recon-all -subjid  -autorecon2-pial, the surfaces generated
>> are not changed at all.
>>
>>
>> I have attached some images to this email. I'm new to Freesurfer, so any
>> help would be greatly appreciated.
>>
>>
>> Thank you.
>>
>>
>>
>>
>>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

[Douglas N Greve]

If you seek help with this problem, make sure to send:
   1. Your command line:
 mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C 
**G2V2.mtx --surf fsaverage lh --cortex --glmdir lh.**G2V2.dods_sm15.glmdir
   2. The FSGD file (if using one)
   3. And the design matrix above

On 05/21/2016 04:57 PM, Hanbyul Cho wrote:
> Dear FreeSurfer Team,
>
> I processed the Group analysis by FreeSurfer 5.3.0
>
> Our data has two groups (Patient, Control) and two covariate values 
> (age, extra value)
> mtx, contrast is 1 -1 0 0 0 0
> The mris_preproc, and mri_surf2surf command were completed without error.
>
> mris_preproc --fsgd **G2V2.fsgd --target fsaverage --hemi lh --meas 
> thickness --out lh.**G2V2.dods.mgh
> mri_surf2surf --hemi lh --s fsaverage --sval lh.**G2V2.dods.mgh --fwhm 
> 15 --cortex --tval lh.**G2V2.dods_sm15.mgh
> mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C 
> **G2V2.mtx --surf fsaverage lh --cortex --glmdir 
> lh.**G2V2.dods_sm15.glmdir
>
> After mri_glmfit command, I saw the error message.
>
> =
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
> 
> 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 lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C 
> **G2V2.mtx --surf fsaverage lh --cortex --glmdir 
> lh.**G2V2.dods_sm15.glmdir
>   2. The FSGD file (if using one)
>   3. And the design matrix above
> =
>
> I think our fsgd and mtx compositions are equal to the g2v2.fsgd which 
> FreeSurfer wiki example.
> (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V)
>
> In this situation, how can I correct my fsgd or mtx files? Is there 
> any other command option?
>
> Best Regards,
>
> Han
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] freeview, tkmedit won't start

[Julian Jäckle]

Dear all

I installed freesurfer as supposed for linux (ubuntu). When I tried to run
freeview an error for tcsh occured. Apparenty I fixed that one but still
freeview doesn't start.
Typing the command: "freeview" nothing happens (I did export and source
freesurfer correctly).
Further trying to run tkmedit it says command not found. How can I get
freeview and tkmedit to run?

Help would be appreciated

Julian
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] ERROR: dimension mismatch between input volume and seg

[Douglas N Greve]

Try it without the --reshape option in mri_surf2surf

On 05/20/2016 05:51 PM, Kari Parsons wrote:
> Hi,
>
>   I'm trying to get some cortical thickness volumes for an ROI that I 
> have (I'm pretty much following the instructions at 
> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness 
> verbatim), but for some of my subjects I'm getting errors that look like this 
> when I run mdi_segstats:
>
> ERROR: dimension mismatch between input volume and seg
>input 1 1 145283
>seg   145283 1 1
>
>   Does anyone have any thoughts on how to trouble-shoot this one?
>
> Thanks!
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] ERROR: cannot unpack mosiacs without ASCII header

[Douglas N Greve]

The log files you can just attach to the email to the list (or to me 
directly if there is something in there that you don't want to post)


On 05/20/2016 04:02 PM, Aloi, Joseph wrote:
> Excellent, thank you!  To do that, do I send an e-mail to the listserv 
> with the log files attached or do I use the filedrop?
>
> yea, can you post the log file of both the successful and failing runs?
>
> On 05/19/2016 11:28 AM, Aloi, Joseph wrote:
> >
> > Hi Doug,
> >
> > No that’s not how I usually store my files- I have a folder for the
> > particular study that I am working on then the dicoms for each subject
> > in that study are stored in individual subject folders within the
> > study folder.
> >
> > I got a chance to look around the recon-all logs this morning for a
> > subject that I had successfully processed in the past (but that I get
> > the error when I try to process this same dataset now).  From
> > comparing the recon-all log from when recon-all ran successfully
> > versus now, things are running fine up until it gets to MRI_convert.
> > However, it looks like things are actually starting to go haywire
> > during MRI_convert even before I get the warning about the ASCII
> > header and recon-all exits.  It appears that MRI_convert is having
> > some trouble with extracting some of the information it needs from the
> > dicom file, resulting in the error that I posted.  I know you guys are
> > busy, but would you be able to take a look at the log files?  I’ve
> > only been using freesurfer a few weeks, so I would definitely
> > appreciate any insights you might have from looking at the log files.
> >
> > Thank you!
> >
> > I don't have any idea what is going wrong. I noticed that the file
> > that it is having problems with is here
> > /Users/alojos/Applications/freesurfer/subjects/sub_.dcm
> > Do you really keep all your dicom files in that location?
> >
> >
> >
> > On 05/17/2016 11:47 PM, Aloi, Joseph wrote:
> > > Hi Doug,
> > > Sorry- I've added entire correspondence onto the end of this
> > e-mail.  I don't think the disk filled up as I am on a 3 TB hard drive
> > and I still have ~2 TB of free space on my disk.  Anything else you
> > think it could be?
> > > Thanks!
> > > Joseph Aloi
> > > Please remember to include previous correspondence otherwise we can't
> > > keep track of the problem!
> > > Eg, I don't have the previous email to see what the error was. Is it
> > > possible that the disk filled up?
> > > On 05/17/2016 09:49 AM, Aloi, Joseph wrote:
> > > > Hi Doug,
> > > >
> > > > Yes, you are correct- data I have previously processed without any
> > > > problems is no longer being processed.
> > > >
> > > > My version of freesurfer is 5.3.0; I only downloaded it a few weeks
> > > > ago so I have not changed my freesurfer version recently.
> > > >
> > > > Thanks!
> > > >
> > > > Joseph Aloi
> > > > Graduate Student, MD/PhD Scholars Program
> > > > Department of Pharmacology and Experimental Neuroscience
> > > > University of Nebraska Medical Center
> > > >
> > > > Neurobehavioral Research Assistant, Center For Neurobehavioral
> > Research
> > > > Boys Town National Research Hospital
> > > So the exact same data set is now generating an error whereas it ran
> > > smoothly before? What version of FS are you using? Did you change
> > versions?
> > > doug
> > > On 05/16/2016 09:49 AM, Aloi, Joseph wrote:
> > > >
> > > > Hi freesurfer experts,
> > > >
> > > > I have recently begun to use freesurfer to do structural MRI
> > > > analyses.  I have been able to successfully process about 40
> > > > structural scans with recon-all thus far, but starting a few days ago,
> > > > I started getting this error whenever I run recon-all:
> > > >
> > > > WARNING: file
> > > > /Users/alojos/Applications/freesurfer/subjects/sub_.dcm does not
> > > > contain a Siemens ASCII header
> > > >
> > > > has this file been anonymized?
> > > >
> > > > ERROR: cannot unpack mosiacs without ASCII header
> > > >
> > > > Darwin nerc130622.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan
> > > > 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64
> > > >
> > > > recon-all -s sub_ exited with ERRORS at Mon May 16 08:43:24
> > CDT 2016
> > > >
> > > > Here are a few of the troubleshooting steps I’ve tried to track down
> > > > the cause of the error:
> > > >
> > > > -- Re-run recon-all with a couple of scans from my dataset that I have
> > > > already successfully processed
> > > >
> > > > - - Re-run recon-all the same datasets but on a different computer
> > > >
> > > > - - Re-convert the scans from .ima files to dicoms in osirix, then
> > > > run recon-all
> > > >
> > > >
> > > > For all of these steps, I have gotten the exact same error message.
> > > > The files should be anonymized, since I used osirix’s “anonymize and
> > > > convert” function to generate the dicom files (the scans were given to
> > > > me as .ima files).
> > > >
> > > > Any suggestions on what to try next?
> > > >
> > > > 

Re: [Freesurfer] Brainmask edit error

[Sabrina Yu]

Hi Bruce,

Thank you for your reply. I've uploaded the .mgz and surfaces using FTP to 
FreeSurfer. Why is it that it may not be possible to get good surfaces with 
extensive strokes?

Thank you,
Sabrina

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Thursday, May 19, 2016 11:24:51 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Brainmask edit error

Hi Sabrina

it's tough to tell from just the 2 slices. If you upload the subject one
of us will take a look, but it may not be possible to get good surfaces
with that extensive a stroke

cheers
Bruce
On Wed, 18 May 2016, Sabrina Yu wrote:

>
> Hello,
>
>
> I'm having problems with regenerating the surfaces for stroke cases after
> editing the brainmask.mgz file. In the aseg.mgz file, the brain matter
> around lesion area is correctly classified as brain matter. In the pial
> surface, this brain matter is not included.
>
>
> I've tried to edit the brainmask.mgz file to include this region, but when I
> run: recon-all -subjid  -autorecon2-pial, the surfaces generated
> are not changed at all.
>
>
> I have attached some images to this email. I'm new to Freesurfer, so any
> help would be greatly appreciated.
>
>
> Thank you.
>
>
>
>
>

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[Freesurfer] Deadline to sign up for Copenhagen Course is near!

[Allison Stevens]

Hi everyone,
There is just a week and a half left before the deadline to sign up for 
the FreeSurfer course being held in Copenhagen, Denmark on August 10th 
through the 12th. The deadline is June 1st.

We still have a few places left! You can sign up for one here:
   https://fscph.nru.dk/registration.html


This will be a 3 day course, very similar to the course we hold in Boston 
twice a year. The course will be taught by Lilla Zollei, Martin Reuter, 
Emily Lindemer, and myself.

If you've had any trouble registering or have any questions, feel free to 
contact me or Melanie (fs-cph AT nru.dk)

Allison
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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] hippocampal subfields analysis took 10 min

[Eugenio Iglesias]

Hi Jiook, 
That is a bit weird. What was the error that you got on the left hemisphere? 
In any case, 10 mins sounds about right. Does the output segmentation look ok? 
Cheers, 
Eugenio 

Juan Eugenio Iglesias 

Honorary Senior Research Associate 
Translational Imaging Group 
University College London 
and 
Postdoctoral researcher BCBL 

http://www.jeiglesias.com 
http://cmictig.cs.ucl.ac.uk/ 

www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Jiook Cha"  
To: "Eugenio Iglesias" , "Freesurfer support list" 
 
Sent: Saturday, May 21, 2016 1:33:59 PM 
Subject: hippocampal subfields analysis took 10 min 

Dear Eugenio, 

I had to run the hippocampal subfield segmentation analysis in Freesurfer v6 
manually by running segmentSF_T1.sh program. When I call it through recon-all, 
it only processed the left hemisphere but not the right. The issue is that 
running segmentSF only took 10 min per hemisphere. I didn't use multicores. 
Although the analysis resulted in all the files correctly, I am just concerned 
if running this manually completed the analysis prematurely. 


Sincerely, 
Jiook 
ᐧ 

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