from:"Iglesias, Eugenio"

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

2016-06-09 Thread Iglesias, Eugenio

Hi Fernando,

Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code 
assumes that the T1 comes from FreeSurfer… For the paper, I hacked the code to 
take advantage of multiple images with higher resolution, but it hasn’t been 
thoroughly tested and it’s not publicly available at this point.
That said, there are different things you can do at this point:
1. Use the T1+T2 as is (disadvantage: T1 will be resampled to 1 mm).
2. Use only the T2.
3. Use only the T1. To do this, you would use the T1 as additional scan on its 
own (i.e., the main and additional scans are the same, but the additional one 
won’t be resampled).
4. There might be a way (hack) of using both scans at full resolution. If you 
change the header of the T1 scan and specify that the voxel size is 1mm, no 
resampling will happen; FreeSurfer will believe that you’re dealing with a 
subject with a very large head. If you do this, you’ll also have to enlarge the 
voxel size of the T2 by a factor 1/0.7. Also, the resulting volumes will have 
to be divided by (1/0.7)^3 in order to correct for the “wrong” voxel size.

I hope this helps!

Cheers,

Eugenio

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


On 9 Jun 2016, at 19:23, Fernando Pasquini Santos 
mailto:fernandop...@gmail.com>> wrote:

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal Subfield 
segmentation in Freesurfer 6.0 - 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the 
same standard 1mm T1 image with an additional scan. However, I want to use a 
0.7mm T1 image as input, with an additional T2 scan. When I run the program 
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel 
size. So, I don't know if this happens just because of the recon-all program or 
if the segmentation is being done in the downsampled T1 image or in the 
original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation 
using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation 
of in vivo MRI" I saw that, in the methods section, the algorithm is used to 
segment 0.6mm T1 images. But is this possible to do in the Freesurfer package? 
Obviously, doing the segmentation directly on 0.7mm data would be better than a 
downsampled version to 1mm...

Thanks,

Fernando Pasquini Santos
PhD student in Dynamic Systems
fernandosan...@pitt.edu
fernando.pasquini.san...@usp.br
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Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

2016-06-09 Thread Iglesias, Eugenio

Hi Matt,
you can use strategy 3 of my previous email ;-)
Cheers,
Eugenio

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


On 9 Jun 2016, at 19:31, Matt Glasser mailto:m...@ma-tea.com>> 
wrote:

I would be interested to know how well 0.7mm isotropic resolution data performs 
at hippocampal segmentation.  It would be better if folks could do this then 
needing to acquire specialized anisotropic scans for hippocampal segmentation.

Peace,

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fernando Pasquini Santos 
mailto:fernandop...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, June 9, 2016 at 1:23 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Hippocampal subfields segmentation - what is the voxel 
size of the input?

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal Subfield 
segmentation in Freesurfer 6.0 - 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the 
same standard 1mm T1 image with an additional scan. However, I want to use a 
0.7mm T1 image as input, with an additional T2 scan. When I run the program 
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel 
size. So, I don't know if this happens just because of the recon-all program or 
if the segmentation is being done in the downsampled T1 image or in the 
original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation 
using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation 
of in vivo MRI" I saw that, in the methods section, the algorithm is used to 
segment 0.6mm T1 images. But is this possible to do in the Freesurfer package? 
Obviously, doing the segmentation directly on 0.7mm data would be better than a 
downsampled version to 1mm...

Thanks,

Fernando Pasquini Santos
PhD student in Dynamic Systems
fernandosan...@pitt.edu
fernando.pasquini.san...@usp.br
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Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

2016-06-10 Thread Iglesias, Eugenio

Hi Matt,
Bruce actually mentioned this possibility yesterday. Good to hear it doesn’t 
crash when you run it! That said, I need to go through the code, and make sure 
that data are handled the way they are supposed to: the fact that it doesn’t 
crash doesn’t directly imply that it is working properly. Hopefully I’ll find 
time to do this next week…
Cheers,
Eugenio


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


On 9 Jun 2016, at 21:51, Hibert, Matthew Louis 
mailto:mhib...@mgh.harvard.edu>> wrote:

Hi Eugenio,
Would it also be possible to use the -hires flag in the initial recon-all 
command to prevent the T1 from being downsampled and maintain the voxel size 
that the T1 was acquired at, and use that resulting recon for the hippocampal 
subfield segmentation?  I've tested this with MEMPRAGE scans acquired at 0.75mm 
isotropic and coronal T2 anisotropic scans acquired at 0.33mm in plane with 1mm 
thick slices, and the results look reasonable.  The "1mm" label files are 
correctly downsampled to 0.75mm instead of 1mm, and the higher resolution label 
files remain at 0.33mm resolution.

Thanks,
Matt

Stufflebeam Lab
Athinoula A. Martinos Center
Massachusetts General Hospital
149 13th Street, Room 1115S
Charlestown, MA 02129

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Iglesias, Eugenio 
[e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>]
Sent: Thursday, June 09, 2016 2:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the 
voxel size of the input?

Hi Fernando,

Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code 
assumes that the T1 comes from FreeSurfer… For the paper, I hacked the code to 
take advantage of multiple images with higher resolution, but it hasn’t been 
thoroughly tested and it’s not publicly available at this point.
That said, there are different things you can do at this point:
1. Use the T1+T2 as is (disadvantage: T1 will be resampled to 1 mm).
2. Use only the T2.
3. Use only the T1. To do this, you would use the T1 as additional scan on its 
own (i.e., the main and additional scans are the same, but the additional one 
won’t be resampled).
4. There might be a way (hack) of using both scans at full resolution. If you 
change the header of the T1 scan and specify that the voxel size is 1mm, no 
resampling will happen; FreeSurfer will believe that you’re dealing with a 
subject with a very large head. If you do this, you’ll also have to enlarge the 
voxel size of the T2 by a factor 1/0.7. Also, the resulting volumes will have 
to be divided by (1/0.7)^3 in order to correct for the “wrong” voxel size.

I hope this helps!

Cheers,

Eugenio

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


On 9 Jun 2016, at 19:23, Fernando Pasquini Santos 
mailto:fernandop...@gmail.com>> wrote:

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal Subfield 
segmentation in Freesurfer 6.0 - 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the 
same standard 1mm T1 image with an additional scan. However, I want to use a 
0.7mm T1 image as input, with an additional T2 scan. When I run the program 
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel 
size. So, I don't know if this happens just because of the recon-all program or 
if the segmentation is being done in the downsampled T1 image or in the 
original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation 
using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation 
of in vivo MRI" I saw that, in the methods section, the algorithm is used to 
segment 0.6mm T1 images. But is this possible to do in the Freesurfer package? 
Obviously, doing the segmentation directly on 0.7mm data would be better than a 
downsampled version to 1mm...

Thanks,

Fernando Pasquini Santos
PhD student in Dynamic Systems
fernandosan...@pitt.edu<mailto:fernandosan...@pitt.edu>
fernando.pasquini.san...@usp.br<mailto:fernando.pasquini.san...@usp.br>
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Re: [Freesurfer] Brainstem Substructures does not work.

2016-06-10 Thread Iglesias, Eugenio

FreeSurfer 6.0 is not available yet, but you can download the development 
version to take advantage of this functionality.
Cheers,
Eugenio

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


On 10 Jun 2016, at 18:10, shi yao wang 
mailto:wangshiyao2...@gmail.com>> wrote:

Dear FSL expert:
Firstly, I would like to thank for the reply from Douglas. Thank you for your 
suggestion! aparcstats2table is working!.

Then, I have another question about the brainstem substructures.
According to the guideline, 
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
I download the environment and successfully installed. However, when I running 
command
" recon-all -s subject -brainstem-structures"

it shows wrong message

"ERROR: Flag -brainstem-structures unrecognized.
-s 201 -brainstem-structures"

So how can I fix it? Is that due to FSL version problem? If yes, how can I 
update to freesurfer 6.0?


thanks!
Lawrence
Emory.

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Re: [Freesurfer] using both T1/T2 and resolutions

2016-06-10 Thread Iglesias, Eugenio

Hi!
I actually sent out an email yesterday regarding this. The way that the 
subfield module is set up, you cannot take advantage of your full res T1 and 
your T1. We are working on a solution.
Cheers,
Eugenio

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


On 10 Jun 2016, at 17:04, Matt Glasser 
mailto:m...@ma-tea.com>> wrote:

Hi Jim,

I would just use the HCP Pipelines for that: 
https://github.com/Washington-University/Pipelines, as they take care of all of 
those things re FreeSurfer.  I would set to using the 0.8mm templates so that 
nothing is down sampled.

Peace,

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Alexopoulos, Dimitrios" 
mailto:alexopoulo...@kids.wustl.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, June 10, 2016 at 10:56 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] using both T1/T2 and resolutions

Hi,

We’d like to process pediatric data through the complete FS 5.3 pipeline. The 
T1/T2 data are acquired with a 3T Siemens as follows:
T1 mpr sag - 0.82x0.82x0.85
T2 Space - 1x1x1

We’d like to process using both the T1 and T2 (for better dura removal and 
possible myelin analysis).
Is it possible to use the hires T1 and have data not downsampled to 1x1x1? 
Ifpossible, can this be done in tandem with the lower resolution T2-space?

What recon-all command would be best for this process?

Jim


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unauthorized use, disclosure, copying, distribution or the taking of any action 
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Re: [Freesurfer] using both T1/T2 and resolutions

2016-06-10 Thread Iglesias, Eugenio

Oh gosh, you’re right Matt.
Sorry about this!

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


On 10 Jun 2016, at 18:54, Matt Glasser 
mailto:m...@ma-tea.com>> wrote:

Hi Eugenio,

I think he is just after cortical surfaces.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Iglesias, Eugenio" 
mailto:e.igles...@ucl.ac.uk>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, June 10, 2016 at 12:30 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] using both T1/T2 and resolutions

Hi!
I actually sent out an email yesterday regarding this. The way that the 
subfield module is set up, you cannot take advantage of your full res T1 and 
your T1. We are working on a solution.
Cheers,
Eugenio

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


On 10 Jun 2016, at 17:04, Matt Glasser 
mailto:m...@ma-tea.com>> wrote:

Hi Jim,

I would just use the HCP Pipelines for that: 
https://github.com/Washington-University/Pipelines, as they take care of all of 
those things re FreeSurfer.  I would set to using the 0.8mm templates so that 
nothing is down sampled.

Peace,

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Alexopoulos, Dimitrios" 
mailto:alexopoulo...@kids.wustl.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, June 10, 2016 at 10:56 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] using both T1/T2 and resolutions

Hi,

We’d like to process pediatric data through the complete FS 5.3 pipeline. The 
T1/T2 data are acquired with a 3T Siemens as follows:
T1 mpr sag - 0.82x0.82x0.85
T2 Space - 1x1x1

We’d like to process using both the T1 and T2 (for better dura removal and 
possible myelin analysis).
Is it possible to use the hires T1 and have data not downsampled to 1x1x1? 
Ifpossible, can this be done in tandem with the lower resolution T2-space?

What recon-all command would be best for this process?

Jim


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Information. If you are not the intended recipient, be advised that any 
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Re: [Freesurfer] unit for hippocampus segmentation results

2016-06-16 Thread Iglesias, Eugenio

If you mean the new subfield module, then the answer is: cubic mm.


Juan Eugenio Iglesias

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fengji Geng 

Sent: Wednesday, June 15, 2016 8:34:09 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] unit for hippocampus segmentation results

Hi freesurfer experts,

We used the development version of freesurfer 6.0 to segment hippocampus. We 
are wondering what the unit is for the segmentation results.

Thanks,

--
Fengji Geng
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Re: [Freesurfer] Hippocampal Subfields Segmentation

2016-06-27 Thread Iglesias, Eugenio

Hi everyone,
you need to install the Matlab 2012b runtime as explained in the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
Cheers,
Eugenio

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

On 27 Jun 2016, at 15:16, pierre deman
mailto:deman.pie...@gmail.com>> wrote:

Hello,

I have similar problem. "
"Error:Cannot find CTF archive
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
the file is here but when I try to execute it, it's always missing some library
(libmwi18n.so for example, it was missing others before that I added on my
computer, but it never ends)
I am on ubuntu 14.04.
I thought that the problem is linked to the matlab runtime. I installed the
2012b. I tried newer version. installed again the 2012b.

Regards,
Pierre

On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon
mailto:permesh.dhil...@nottingham.ac.uk>>
wrote:
Hello FreeSurfer Developers,

I’m having issues with the hippocampal subfields segmentation using OS X
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer Subject Stamp:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Current Stamp:
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting
an error message : Error:CTF file
'/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf'
failed to open for 'Read' access. Error message: 'Open a zip file for
read/modify failed.’

The segmented hippocampal files as described on free surfer wiki cannot be
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh

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Re: [Freesurfer] Hippocampal Subfields Segmentation

2016-06-27 Thread Iglesias, Eugenio

Hi Pierre,
Due to some technical problems, it might take me a couple of days to figure out
what’s going on. But it definitely sounds funny that it is asking for the CTF,
since this is supposed to be embedded in the executable… I’ll get back to you
as soon as possible.
Cheers,
Eugenio

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

On 27 Jun 2016, at 15:32, pierre deman
mailto:deman.pie...@gmail.com>> wrote:

I tried that. but didn't work.

Cheers,
Pierre

On Mon, Jun 27, 2016 at 4:32 PM, Iglesias, Eugenio
mailto:e.igles...@ucl.ac.uk>> wrote:
Hi everyone,
you need to install the Matlab 2012b runtime as explained in the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
Cheers,
Eugenio

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

On 27 Jun 2016, at 15:16, pierre deman
mailto:deman.pie...@gmail.com>> wrote:

Hello,

Regards,
Pierre

On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon
mailto:permesh.dhil...@nottingham.ac.uk>>
wrote:
Hello FreeSurfer Developers,

The segmented hippocampal files as described on free surfer wiki cannot be
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh

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Mobile : +33 7 82 57 80 94
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Re: [Freesurfer] Hippocampal Subfields Segmentation

2016-06-29 Thread Iglesias, Eugenio

I could finally look into this. It is indeed weird. The CTF is indeed embedded
in the executable…
Zeke/Nick, can you shed some light on this?
Cheers,
Eugenio

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

On 27 Jun 2016, at 15:43, Iglesias, Eugenio
mailto:e.igles...@ucl.ac.uk>> wrote:

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

On 27 Jun 2016, at 15:32, pierre deman
mailto:deman.pie...@gmail.com>> wrote:

I tried that. but didn't work.

Cheers,
Pierre

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

On 27 Jun 2016, at 15:16, pierre deman
mailto:deman.pie...@gmail.com>> wrote:

Hello,

Regards,
Pierre

On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon
mailto:permesh.dhil...@nottingham.ac.uk>>
wrote:
Hello FreeSurfer Developers,

The segmented hippocampal files as described on free surfer wiki cannot be
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh

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Re: [Freesurfer] Hippocampal Subfields Segmentation

2016-07-06 Thread Iglesias, Eugenio

Dear all,

We are working on this; I'll write again when the problem is solved (hopefully 
soon!)

Cheers

Eugenio


Juan Eugenio Iglesias

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of pierre deman 

Sent: Tuesday, July 5, 2016 7:04:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation


Hi,
I still have a problem as well with the subfields segmentation (ubuntu 14.04, 
with the files .ctf)

Cheers,
Pierre

Hello FreeSurfer Experts,

I'm having issues with the hippocampal subfields segmentation using OS X 
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp: 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp: 
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting 
an error message : Error:CTF file 
'/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' 
failed to open for 'Read' access. Error message: 'Open a zip file for 
read/modify failed.'

The segmented hippocampal files as described on free surfer wiki cannot be 
found under the subject 'mri' folder.
I understand other users have complained of a similar issue within the last 
week.

I'd ve grateful if you could assist me with the issue above.

Many thanks
Permesh




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Re: [Freesurfer] hippocampal subfields command

2016-07-06 Thread Iglesias, Eugenio

Hi Jim,
the latter command uses a new, higher resolution atlas based on ex vivo scans.
Cheers,
Eugenio

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


On 6 Jul 2016, at 15:39, Alexopoulos, Dimitrios 
mailto:alexopoulo...@kids.wustl.edu>> wrote:

A quick question re: hippocampal segmentation.

I have processed 1mm isotropic T1 data with 5.3 using the following command:
recon-all  -qcache -all  -hippo-subfields

How is this this different than using the following command I have found here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
-hippocampal-subfields-T1


Thanks.
Jim


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Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

2016-07-06 Thread Iglesias, Eugenio

Not yet, sorry. But it’s on my todo list.


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


On 6 Jul 2016, at 14:39, Hibert, Matthew Louis 
mailto:mhib...@mgh.harvard.edu>> wrote:

Hi Eugenio,
Have you had a chance to look into the possibility of combining the -hires flag 
with the hippocampal subfield segmentation?

Thanks,
Matt

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Iglesias, Eugenio 
[e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>]
Sent: Friday, June 10, 2016 3:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the 
voxel size of the input?

Hi Matt,
Bruce actually mentioned this possibility yesterday. Good to hear it doesn’t 
crash when you run it! That said, I need to go through the code, and make sure 
that data are handled the way they are supposed to: the fact that it doesn’t 
crash doesn’t directly imply that it is working properly. Hopefully I’ll find 
time to do this next week…
Cheers,
Eugenio


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


On 9 Jun 2016, at 21:51, Hibert, Matthew Louis 
mailto:mhib...@mgh.harvard.edu>> wrote:

Hi Eugenio,
Would it also be possible to use the -hires flag in the initial recon-all 
command to prevent the T1 from being downsampled and maintain the voxel size 
that the T1 was acquired at, and use that resulting recon for the hippocampal 
subfield segmentation?  I've tested this with MEMPRAGE scans acquired at 0.75mm 
isotropic and coronal T2 anisotropic scans acquired at 0.33mm in plane with 1mm 
thick slices, and the results look reasonable.  The "1mm" label files are 
correctly downsampled to 0.75mm instead of 1mm, and the higher resolution label 
files remain at 0.33mm resolution.

Thanks,
Matt

Stufflebeam Lab
Athinoula A. Martinos Center
Massachusetts General Hospital
149 13th Street, Room 1115S
Charlestown, MA 02129

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Iglesias, Eugenio 
[e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>]
Sent: Thursday, June 09, 2016 2:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the 
voxel size of the input?

Hi Fernando,

Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code 
assumes that the T1 comes from FreeSurfer… For the paper, I hacked the code to 
take advantage of multiple images with higher resolution, but it hasn’t been 
thoroughly tested and it’s not publicly available at this point.
That said, there are different things you can do at this point:
1. Use the T1+T2 as is (disadvantage: T1 will be resampled to 1 mm).
2. Use only the T2.
3. Use only the T1. To do this, you would use the T1 as additional scan on its 
own (i.e., the main and additional scans are the same, but the additional one 
won’t be resampled).
4. There might be a way (hack) of using both scans at full resolution. If you 
change the header of the T1 scan and specify that the voxel size is 1mm, no 
resampling will happen; FreeSurfer will believe that you’re dealing with a 
subject with a very large head. If you do this, you’ll also have to enlarge the 
voxel size of the T2 by a factor 1/0.7. Also, the resulting volumes will have 
to be divided by (1/0.7)^3 in order to correct for the “wrong” voxel size.

I hope this helps!

Cheers,

Eugenio

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


On 9 Jun 2016, at 19:23, Fernando Pasquini Santos 
mailto:fernandop...@gmail.com>> wrote:

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal Subfield 
segmentation in Freesurfer 6.0 - 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the 
same standard 1mm T1 image with an additional scan. However, I want to use a 
0.7mm T1 image as input, with an additional T2 scan. When I run the program 
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel 
size. So, I don't know if this happens just because of the recon-all program or 
if the segmentation is being done in the downsampled T1 image or in the 
original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation 
using ex vivo, ultra-high resolution MRI: Ap

Re: [Freesurfer] {Filename?} Hippocampal subfields --> Can't find a *ctf file?

2016-07-08 Thread Iglesias, Eugenio

I think I identified the problem; hopefully this will be sorted out very soon.
Cheers,
Eugenio

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

On 7 Jul 2016, at 19:23, Perea Camargo, Rodrigo Dennis
mailto:rpereacama...@mgh.harvard.edu>> wrote:

Warning: This message has had one or more attachments removed (recon-all.cmd).
Please read the "UCL-Attachment-Warning.txt" attachment(s) for more information.

Hi all,
I am currently trying to run hippocampal subfields in a couple of my
participants using FreeSurfer6.0 (located at
*nmr*:/usr/local/freesurfer/stable6).

It did run successfully for many of my subjects earlier in the year but some of
them only had a let hemisphere segmentation. So I decided to re-run them using
launchpad and also my local nmr computer.

Now, none of the hippocampal sufields segmentations appear (no
rh/lh.hippoSfLabels-T1-T2.*.mgz appears). I looked at
/scripts/scripts/hippocampal-subfields-T1T2.log and the error I get
is:

Error:Cannot find CTF archive
/autofs/cluster/freesurfer/centos6_x86_64/stable6/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf

Could a missing *.ctf cause the error? (btw, the re-run happened after the
major hardware crash).

Thanks in advance for your help,
Rodrigo

PS: I am attaching the *log files as suggested in the bug reporting page.

---
Rodrigo Dennis Perea
Research Fellow
Department of Radiology
Athinoula A. Martinos Center
Massachusetts General Hospital
rpereacama...@mgh.harvard.edu

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Re: [Freesurfer] Hippocampal subfields --> Can't find a *ctf file?

2016-07-13 Thread Iglesias, Eugenio

Dear all,
our expert developer Zeke Kaufman figured out what the problem was. We have now
fixed the Linux version; the MAC version will hopefully be ready as well in a
couple of days. I have also fixed other bugs (including the problem that caused
the code to get stuck every once in a while).
You can downloaded the latest development version from our website.
Thanks everyone for your feedback.
Cheers,
Eugenio

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

On 8 Jul 2016, at 12:14, Iglesias, Eugenio
mailto:e.igles...@ucl.ac.uk>> wrote: