Re: [Freesurfer] external WM and GM masks as input to recon-all?

[Diamond, Bram Ryder]

Hi Shadia,


How did you make the externally-derived ribbons?  Can you please send us your 
recon-all.log and your subject directory so we can take a look? 
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange


Thanks,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of MIKHAEL Shadia 

Sent: Sunday, January 21, 2018 1:58:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] external WM and GM masks as input to recon-all?

Dear Bruce,

Thank you for your reply at 
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2018-January/055512.html 
regarding the use of grey and white matter masks.

Since you were suggesting that this may be difficult, I have instead tried to 
introduce external masks at a later stage (ribbons) in the process as follows:
running recon-all once (run1), all the way through, then replacing 
?h.ribbon.nii and ?h.ribbon.mgz with externally-derived ribbons, before calling 
recon-all a second time (run2) in FreeSurfer 6.0 as follows:

recon-all -autorecon-pial -parcstats -cortparc2 -parcstats2 -cortparc3 
-parcstats3 -subjid s1-freesurfer60-run2-external_ribbon

I have experimented with the following 2 setups for this 2nd run of recon-all:
1. run2-setup1: keeping all the files in the 'mri' directory generated by run 
1, except for ?h.ribbon.nii and ?h.ribbon.mgz which I'm replacing by the 
externally-derived ones
2. run2-setup2: keeping only the files in the 'mri' directory generated by run 
1  before ?h.ribbon.nii and ?h.ribbon.mgz. Files generated after those 2 were 
deleted, and the ribbons were replaced by the externally-derived ones

I have found that in both cases, the ?h.ribbon.mgz are getting modified by the 
recon-all process, and the stats file is identical to that of run 1, which is 
not what I was hoping for. Altering the ribbons did not alter the parcellation 
& corresponding stats.

Could you please advise on the steps that I've missed/done wrongly in order for 
the ribbon changes to get incorporated? Should I be clearing the 'stats' 
directory? And is the 2nd run of recon-all correct? Any tips would be greatly 
appreciated.

Thank you in advance.

Shadia



--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


-Original Message-
From: MIKHAEL Shadia
Sent: 12 January 2018 18:43
To: freesurfer@nmr.mgh.harvard.edu
Subject: external WM and GM masks as input to recon-all?

Dear FreeSurfer experts,

Could you please advise on whether it would be possible to run recon-all in 
FreeSurfer 6.0 using externally-derived probabilistic white matter and grey 
matter masks, both of which include the cerebellum but not the ventricles, and 
if so, how? Would the flag -autorecon2-pial suffice?

Thank you in advance.

Shadia


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Re: [Freesurfer] recon-all exited with error

[Trisanna Sprung-Much]

Hi there

I uploaded these last week to the file drop and used Bruce's email as it
said it requires a  ".nmr.mgh.harvard.edu" email type.

Please let me know if you received icbm-202 and icbm-205 as tar.gz files.
As I mentioned, I was able to get surfaces for both of these but they
seemed to end at the labeling step.



best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Jan 19, 2018 at 10:42 AM, Hoopes, Andrew 
wrote:

> You can send it to either my email (ahoo...@mgh.harvard.edu) or Bruce’s
>
> best,
> Andrew
>
> On Jan 19, 2018, at 10:12 AM, Trisanna Sprung-Much <
> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
>
>
> thanks Andrew. I had seen that and will give it a go - just wanted to make
> sure that my recipient email would be the FreeSurfer support list.
>
> Trisanna
>
> On Fri, Jan 19, 2018 at 9:59 AM, Hoopes, Andrew 
> wrote:
>
>> Hi Trisanna,
>>
>> Okay - if your file is less than 2GiB, I suggest sending your data via
>> the Martinos file drop (directions at the bottom of this page:
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange).
>>
>> best
>> Andrew
>>
>> On Jan 18, 2018, at 11:53 AM, Trisanna Sprung-Much <
>> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>>
>>
>> Hi Andrew
>>
>> Thank you for your response. I gave it a go and still no luck, unless I
>> am missing something completely obvious here
>>
>> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
>> surfer.nmr.mgh.harvard.edu
>> Connected to surfer.nmr.mgh.harvard.edu.
>> 220-This is the Martinos Center Anonymous FTP service. Use of this
>> site
>> 220-shows implicit consent to our Acceptable Use Policy outlined
>> at
>> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
>>
>> 220-
>> 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
>> 220-
>> 220-229 Entering Extended Passive Mode
>> 220-
>> 220-   and nothing happens OR
>> 220-
>> 220-229 Entering Extended Passive Mode
>> 220-500 Bad EPRT protocol.
>> 220-
>> 220-  try issuing the EPSV command prior to GET or PUT.
>> 220-
>> 220
>> Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
>> 331 Please specify the password.
>> Password:
>> 230 Login successful.
>> Remote system type is UNIX.
>> Using binary mode to transfer files.
>> ftp> cd transfer/incoming
>> 250 Directory successfully changed.
>> ftp> quote PASV
>> 227 Entering Passive Mode (132,183,202,158,147,251).
>> ftp> put icbm-205.tar.gz
>> local: icbm-205.tar.gz remote: icbm-205.tar.gz
>> 200 PORT command successful. Consider using PASV.
>> 425 Failed to establish connection.
>>
>>
>>
>>
>>
>> On Wed, Jan 17, 2018 at 5:59 PM, Hoopes, Andrew 
>> wrote:
>>
>>> Hi Trisanna,
>>>
>>> Try running 'quote PASV' in ftp before running 'put' - that should
>>> hopefully clear up this issue.
>>>
>>> best,
>>> Andrew
>>>
>>>
>>> On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much <
>>> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>>>
>>> Sorry, Bruce. ignore my last email. Not sure what happened there.
>>>
>>> I now am trying to upload icbm-205.tar.gz (the subject that failed) but
>>> I get the following and it happens over and over. Any idea what the problem
>>> could be?
>>>
>>> trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/
>>> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls
>>> fsaverage  icbm-109  icbm-118  icbm-127  icbm-142  icbm-202
>>> icbm-102   icbm-110  icbm-119  icbm-131  icbm-143  icbm-202.tar.gz
>>> icbm-103   icbm-111  icbm-120  icbm-133  icbm-144  icbm-203
>>> icbm-104   icbm-112  icbm-121  icbm-135  icbm-146  icbm-204
>>> icbm-105   icbm-113  icbm-122  icbm-137  icbm-150  icbm-205
>>> icbm-106   icbm-114  icbm-123  icbm-139  icbm-158  icbm-205.tar.gz
>>> icbm-107   icbm-115  icbm-125  icbm-140  icbm-200  icbm-206
>>> icbm-108   icbm-117  icbm-126  icbm-141  icbm-201
>>> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
>>> surfer.nmr.mgh.harvard.edu
>>> Connected to surfer.nmr.mgh.harvard.edu.
>>> 220-This is the Martinos Center Anonymous FTP service. Use of this
>>> site
>>> 220-shows implicit consent to our Acceptable Use Policy outlined
>>> at
>>> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/compute
>>> r/nmr-aup.php
>>> 220-
>>> 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
>>> 220-
>>> 220-229 Entering Extended Passive Mode
>>> 220-
>>> 220-   and nothing happens OR
>>> 220-
>>> 220-229 Entering Extended Passive Mode
>>> 220-500 Bad EPRT protocol.
>>> 220-
>>> 220-  try issuing the EPSV command prior to GET or PUT.
>>> 220-
>>> 220
>>> Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
>>> 331 Please specify the password.
>>> Password:
>>> 230 Login successful.
>>> Remote system type is UNIX.
>>> Using binary mode to transfer files.
>>> ftp> cd transfer/incoming
>>> 

Re: [Freesurfer] [CVS_register] Warp field reading through Matlab

[Bruce Fischl]

Hi Stefano

Lilla is going to be out of touch for a while I expect. Have you 
downloaded the FreeSurfer source code? That might be a good place to 
start. I think you can also load a .m3z warp into freeview and it will 
display it as a 3-frame volume.


I think the representation is that we keep a target volume coordinate for 
every atlas node


cheers
Bruce


On Tue, 23 Jan 2018, Stefano Zappalà wrote:



To whom it may concern,

I am Stefano Zappalà, a second year PhD student at Cardiff University. I would 
like to use the CVS
registration tool of the FreeSurfer software for elastic registration. I was 
very impressed by its
accuracy even in aligning fiber tracts.

My project is based on reading the warp field files as output of elastic 
registration for estimating
displacement fields. I wrote to Lilla Zollei few months ago who kindly shared 
with me a Matlab
script for reading .m3z files, output of cvs_register. I played with it for 
several months, without
being able to properly read the deformation field. What I obtain does not 
represent the real warp
(that i can extract and compare with, using another software). By checking the 
output image, I can
tell that the registration was successful, so I am expecting the warp field to 
be consistent with
the real one.

When I use the Matlab function given me by Ms Zollei, I notice a gradient in 
each of the component
(x,y,z) of the vector field, that varies according to the coordinate of each 
voxel (as you can see
in Figure1 attached). I therefore subtracted, for each voxel, its coordinate to 
the corresponding
component of the vector, using the cycle:
 
T=zeros(256,256,256,3);
for k=1:256
    for j=1:256
        for i=1:256
            T(i,j,k,:)=squeeze(vol_orig(i,j,k,:))-[i;j;k];
        end
    end
end
where vol_orig is the output of the function you gave me [vol_orig, vol_dest, 
vol_ind0, spacing,
exp_k] = mris_read_m3z('FILELOC'). The result is compared to vol_orig in 
Figure1.  

By doing so I obtained something acceptable but still distant from the truth 
(which comparison is
reported in Figure2, where the truth is the right vector field). 
In the attachment you can find the function, as well as Figure1 representing a 
slice of vol_orig on
the left and the modified version where the coordinates are subtracted to each 
component of the
vectors. Finally, in Figure2 you can find the warp field estimated with 
cvs_register and the
corresponding truth. The two warp fields seem different, unfortunately.

I was wondering if you have any suggestion on how to properly read it, or if 
you could confirm that
what I have done is correct. 

Thank you for your consideration.

Best regards,
Stefano.



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Re: [Freesurfer] Loading talairach-space images into FSL

[Douglas N Greve]

I've never used FSLeyes so I can't say


On 01/23/2018 01:05 PM, Helen Beaumont wrote:
> Hi
>
> I have a series of T1 images that I have transformed in Freesurfer to
> .nii.gz images in talairach space with mri_convert -at
> transforms/talairach.xfm. I am using the skull-stripped image brain.mgz
> produced by recon-all.
>
> When I view them in freeview they look well-registered, and similarly
> when I view them in MRIcron. However, if I use FSLeyes they seem to have
> a different origin for each subject, and fslmerge complains that they
> have Inconsistent orientations.
>
> Is there any inconsistency that you know of between freeview and FSLeyes?
>
> Helen Beaumont PhD
>
> ___
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>
>

-- 
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] Value of ROIs different between FreeSurfer versions?

[Bruce Fischl]

Hi Kaley

no, it is inevitable that there will be differences as we are always 
trying to improve the algorithms.


cheers
Bruce
On Tue, 23 Jan 2018, KALEY E ELLIS wrote:



Hello FreeSurfer Developers,


I am extracting ROIs of cross-sectional data using FreeSurfer v6.0.  We looked 
at this data
preliminarily about 2 years ago using FreeSurfer v5.3. It looks like there are 
slight differences in
the values of the same subject (see below). Do you know the reason for this 
difference and whether
there is something I should do differently?


Subject 2000_1, lh_G_and_S_frontomargin_thickness:

v5.3 = 2.416

v6.0 = 2.482


command used: 

aparcstats2table --hemi lh --subjects $subjectlist --skip --delimiter comma 
--meas thickness --parc
aparc.a2009s --tablefile /PATH/lh_aparc-destrieux-thickness-table.csv


Thank you for your time!

Kaley Ellis


Associate Research Specialist
Center for Healthy Minds
Waisman Center for Brain Imaging and Behavior
University of Wisconsin-Madison

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[Freesurfer] [error] no installation candidates for curl

[Darko Komnenić]

Dear FreeSurfer experts,
I am trying to perform hippocampal subfield segmentation with
FreeSurfer 6. I followed the instructions found on this page:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields which
said that I first need to download Matlab Runtime. Which brought me to
this page: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime

I reach the stage where I type in
curl 
"https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile=get=runtime2012bLinux.tar.gz;
-o "runtime.tar.gz"
after which I receive the following:
Die Anwendung »curl« ist momentan nicht installiert.  Sie können sie
durch folgende Eingabe installieren:
sudo apt-get install curl

(my computer is in German, it basically says that curl is not
installed and that I can install it via apt-get command).
When I then type in that command and give my password, I receive:

Paketlisten werden gelesen... Fertig
Abhängigkeitsbaum wird aufgebaut
Status-Informationen einlesen... Fertig
Paket curl ist nicht verfügbar, wird aber von einem anderen Paket
referenziert. Das kann heißen, dass das Paket fehlt, dass es veraltet
ist oder nur aus einer anderen Quelle verfügbar ist.
E: Paket curl hat keinen Installationskandidaten

Which roughly translates to: reading package lists... done
building a dependency tree
reading status information... done
Package curl is not available, but is referred to by another package.
This could mean that the package is missing, outdated or available
only from a different source.
E: Package curl has no installation candidates.

I would be grateful for any solution suggestions!
Best,
Darko

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[Freesurfer] Loading talairach-space images into FSL

[Helen Beaumont]

Hi

I have a series of T1 images that I have transformed in Freesurfer to 
.nii.gz images in talairach space with mri_convert -at 
transforms/talairach.xfm. I am using the skull-stripped image brain.mgz 
produced by recon-all.

When I view them in freeview they look well-registered, and similarly 
when I view them in MRIcron. However, if I use FSLeyes they seem to have 
a different origin for each subject, and fslmerge complains that they 
have Inconsistent orientations.

Is there any inconsistency that you know of between freeview and FSLeyes?

Helen Beaumont PhD

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Re: [Freesurfer] recon-all error

[Douglas N Greve]

Try setting the FS_LOAD_DWI env var to 0, eg,

setenv FS_LOAD_DWI 0

or

export FS_LOAD_DWI=0


On 01/23/2018 10:43 AM, Bruce Fischl wrote:
>
>
>
> we don't have much experience with it. Can you cc the FS list so that 
> others can answer? I'll do so on this email. Maybe try some other tool 
> for conversion? If recon-all fails it is not surprising that 
> mri_convert also fails since they use the same DICOM code
>
> cheers
> Bruce
>
> On Tue, 23 Jan 2018, Julia Ströhlein wrote:
>
>>
>>  Hi Bruce,
>>
>>  thank you very much for your reply.
>>
>>
>>
>>  I’m sure that I use the right series.  I tried to convert my DICOM 
>> files to
>>  nifti, but this produces
>>  the same error and the command also doesn`t create the NIFTI file.
>>
>>
>>
>>  Julias-MacBook-Air:~ Jule$ cd
>>  /Applications/freesurfer/subjects/MRtest2/001/001/9
>>
>>  Julias-MacBook-Air:9 Jule$ mri_convert 00010001 00010001.nii
>>
>>  mri_convert.bin 00010001 00010001.nii
>>
>>  $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
>>
>>  reading from 00010001...
>>
>>  Starting DICOMRead2()
>>
>>  dcmfile = /Applications/freesurfer/subjects/MRtest2/001/001/9/00010001
>>
>>  dcmdir = /Applications/freesurfer/subjects/MRtest2/001/001/9
>>
>>  ERROR: don't know how to get DWI parameters from --Hitachi Medical
>>  Corporation --
>>
>>  ERROR: GetDICOMInfo(): dcmGetDWIParams() 1
>>
>>  DICOM File: 
>> /Applications/freesurfer/subjects/MRtest2/001/001/9/00010001
>>
>>  break DICOMRead.c:5228
>>
>>  Ref Series No = 9
>>
>>  Found 302 files, checking for dicoms
>>
>>  ERROR: don't know how to get DWI parameters from --Hitachi Medical
>>  Corporation –
>>
>>
>>
>>  Do you know problems like this with this type of MR scanner?
>>
>>
>>
>>  Kind regards,
>>
>>  Julia
>>
>>
>>
>>  Unbenannt
>>
>>
>>
>>
>>
>
>
> ___
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-- 
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] [Re] medial wall label in Freesurfer 6

[M del Mar Velasco]

Yes, it solves medial_wall label problem but not mri_aparc2aseg error.log. I 
attached you in a previous message: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg56610.html


Many thanks,


M del Mar

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[Freesurfer] Value of ROIs different between FreeSurfer versions?

[KALEY E ELLIS]

Hello FreeSurfer Developers,


I am extracting ROIs of cross-sectional data using FreeSurfer v6.0.  We looked 
at this data preliminarily about 2 years ago using FreeSurfer v5.3. It looks 
like there are slight differences in the values of the same subject (see 
below). Do you know the reason for this difference and whether there is 
something I should do differently?


Subject 2000_1, lh_G_and_S_frontomargin_thickness:

v5.3 = 2.416

v6.0 = 2.482


command used:

aparcstats2table --hemi lh --subjects $subjectlist --skip --delimiter comma 
--meas thickness --parc aparc.a2009s --tablefile 
/PATH/lh_aparc-destrieux-thickness-table.csv


Thank you for your time!

Kaley Ellis


Associate Research Specialist
Center for Healthy Minds
Waisman Center for Brain Imaging and Behavior
University of Wisconsin-Madison
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Re: [Freesurfer] recon-all error

[Bruce Fischl]

we don't have much experience with it. Can you cc the FS list so that others 
can answer? I'll do so on this email. Maybe try some other tool for conversion? 
If recon-all fails it is not surprising that mri_convert also fails since they 
use the same DICOM code


cheers
Bruce

On Tue, 23 Jan 2018, Julia Ströhlein wrote:



 Hi Bruce,

 thank you very much for your reply.

  

 I’m sure that I use the right series.  I tried to convert my DICOM files to
 nifti, but this produces
 the same error and the command also doesn`t create the NIFTI file.

  

 Julias-MacBook-Air:~ Jule$ cd
 /Applications/freesurfer/subjects/MRtest2/001/001/9

 Julias-MacBook-Air:9 Jule$ mri_convert 00010001 00010001.nii

 mri_convert.bin 00010001 00010001.nii 

 $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

 reading from 00010001...

 Starting DICOMRead2()

 dcmfile = /Applications/freesurfer/subjects/MRtest2/001/001/9/00010001

 dcmdir = /Applications/freesurfer/subjects/MRtest2/001/001/9

 ERROR: don't know how to get DWI parameters from --Hitachi Medical
 Corporation --

 ERROR: GetDICOMInfo(): dcmGetDWIParams() 1

 DICOM File: /Applications/freesurfer/subjects/MRtest2/001/001/9/00010001

 break DICOMRead.c:5228

 Ref Series No = 9

 Found 302 files, checking for dicoms

 ERROR: don't know how to get DWI parameters from --Hitachi Medical
 Corporation –

  

 Do you know problems like this with this type of MR scanner?

  

 Kind regards,

 Julia

  

 Unbenannt

  


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Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

[m . bahri]

Dear Bruce,

Thank you very much for your kind help!

Best regards

- Mail original -
De: "Bruce Fischl" 
À: "Freesurfer support list" 
Envoyé: Lundi 22 Janvier 2018 16:12:10
Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

oh, then I think you are just showing the surface-based label, which will 
only fill voxels that intersect with the white surface I believe. To 
sample it into the volume try mri_label2vol with the --fill-ribbon flag 
(the help is pretty extensive).

cheers
Bruce
On Mon, 22 Jan 2018, m.ba...@uliege.be 
wrote:

> Dear Bruce,
>
> Thank you for your answer!
>
> I just display the "T1.mgz" image (mri folder) using Freeview and then loaded 
> the "lh/rh.perirhinal_exvivo.label" rois (label folder).
>
> If this is not the good way to do it, please, could you explain more the 
> procedure? What do you mean by MT and PC?
>
> Thank you very much in advance,
>
> Best regards,
>
> Mohamed
>
>
> - Mail original -
> De: "Bruce Fischl" 
> À: "Freesurfer support list" 
> Envoyé: Vendredi 19 Janvier 2018 16:53:18
> Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
>
> Hi Mohamed
>
> how are you visualizing the MT or PC ROIs. Did you sample them into the
> volume? If so, can you tell me where the file ROIs are in the data you
> sent me?
>
> cheers
> Bruce
> On Fri, 19 Jan 2018, m.ba...@uliege.be wrote:
>
>> Dear Bruce,
>>
>> Many thanks for your kind help!
>>
>> I put the subject data on your ftp site (s8201.tar).
>>
>> Best regards,
>>
>> Mohamed
>>
>>
>>
>> - Mail original -
>> De: "Bruce Fischl" 
>> À: "Freesurfer support list" 
>> Envoyé: Jeudi 18 Janvier 2018 16:37:10
>> Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
>>
>> Hi Mohamed
>>
>> if you tar, gzip and ftp this subject to our ftp site we will take a look
>> cheers
>> Bruce
>> On
>> Thu, 18 Jan 2018, m.ba...@uliege.be wrote:
>>
>>> Dear Bruce,
>>>
>>> Attached is the screen shot of the results of the segmentation of the 
>>> perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented 
>>> Roi does not cover the entire cortical thickness of the region. Is there 
>>> any other alternative to get a better segmentation of this region?
>>>
>>> Many thanks in advance,
>>>
>>> Best regards,
>>>
>>> Mohamed
>>>
>>> - Mail original -
>>> De: "Bruce Fischl" 
>>> À: "Freesurfer support list" 
>>> Envoyé: Mardi 9 Janvier 2018 14:50:16
>>> Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
>>>
>>> Hi Mohamed
>>>
>>> I'm pretty sure this was an issue with the ribbon-filling in V5 that is
>>> better in V6. Try using it and see if it is fixed.
>>>
>>> cheers
>>> Bruce
>>> On Tue, 9 Jan 2018,
>>> m.ba...@uliege.be wrote:
>>>
 Dear Freesurfer experts,

 We would like to use volume and cortical thickness measures obtained for 
 the perirhinal cortex in Freesurfer 5. When checking the region that has 
 been segmented (using lh/rh.perirhinal.label), we noticed that the ROI 
 does not seem to cover the entire cortical thickness of the region. On the 
 coronal slice shown in example (attached file), one can see that there are 
 still a few voxels of gray matter between the external border of the ROI 
 and the external boundary of the cortex. How reliable is this 
 segmentation? Is there a reason why the ROI appears so thin?

 Many thanks in advance,

 Best regards,



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> 

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

[Iglesias Gonzalez, Eugenio]

I’ve never tried. Koen/Oula, what do you think?

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


From:  on behalf of Gabor Perlaki 

Reply-To: Freesurfer support list 
Date: Tuesday, 23 January 2018 at 06:37
To: freesurfer 
Subject: Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

Dear Iglesias,
Do you think that it is useful to also use a fieldmap for hippocampal subfield 
segmentation? Can Freesurfer's hippocampal subfield segmentation use it? I'm 
not sure that due to the limited resolution of the fieldmap and due to 
registration issues it is worth to acquire a fieldmap for hippocampal subfield 
segmentation. What do you think?

Best,
Gabor
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