Re: [Freesurfer] Masking cortical thickness

[Bruce Fischl]

I think you could just load the cortex.label map onto the surface and 
edit those regions out. Then they will not contribute to smoothed maps, 
etc...  Doug: any reason this wouldn't work?

Bruce

On Tue, 13 Feb 2018, James Hobart wrote:

> Hi all,
> I am looking to mask out a small region of the GM when calculating the 
> cortical thickness of ROIs
> across the brain. Essentially I have a couple of cases with small GM lesions 
> where the cortical
> thickness is less likely to be meaningful for my analysis.
> 
> I have binary lesion masks and also full recon-all s for these cases. I was 
> thinking I would need to
> mask the cortical thickness map somehow (potentially mapping the mask volume 
> to a surface?) before
> using the mris_anatomical_stats to calculate cortical thickness.
> 
> Is this the best way to go about this?
> 
> Many thanks
> James
> 
>
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[Freesurfer] Masking cortical thickness

[James Hobart]

Hi all,

I am looking to mask out a small region of the GM when calculating the
cortical thickness of ROIs across the brain. Essentially I have a couple of
cases with small GM lesions where the cortical thickness is less likely to
be meaningful for my analysis.

I have binary lesion masks and also full recon-all s for these cases. I was
thinking I would need to mask the cortical thickness map somehow
(potentially mapping the mask volume to a surface?) before using the
mris_anatomical_stats to calculate cortical thickness.

Is this the best way to go about this?

Many thanks
James
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Re: [Freesurfer] map values to vertices {Disarmed}

[Frederick Barrett]

Thank you, Bruce.


I did reconstruct the surfaces from that subject. These are the steps that I've 
taken:


recon-all -s  -i  -all


mris_register /surf/.sphere fsaverag5/.?reg.template.tif 
/surf/.fsaverage5.sphere.reg


mri_surf2surf -s  -h  --sval-xyz .pial --trgsubject 
fsaverage5 --tval 


mri_surf2surf -s  --sval-xyz .pial --trgsubject 
fsaverage5 --tval .pial. --tval-xyz /mri/orig.mgz


mris_convert fsaverage5/surf/.pial. 
fsaverage5/surf/.pial..asc


this final file (fsaverage5/surf/.pial..asc) was read into MATLAB 
and MATLAB code generates a continuous value for each vertex (n=10242) for a 
given subject. I want to map these values back to the surface, but it sounds 
like if you're recommending mri_vol2surf, that you are saying I should 
represent these continuous values in a voxel in 3D space, is that correct? Is 
there an easy way to map the values for each vertex without having to go 
through a 3D representation?


Best,


Fred




Hi Fred



we usually use mri_vol2surf for this kind of thing. Did you reconstruct 
surfaces from that subject?

cheers
Bruce

On Tue, 13 Feb 2018, Frederick Barrett wrote:



Greetings all,


I apologize in advance for what may (or may not) be a basic question. I want to
map values from a continuous
variable (non-integer) to each vertex on a surface so that I can visualize
these values on the surface (or an
inflated brain), but I can't figure out how to do this.



I've projected the pial surface of fsaverage5 to native space within a
volunteer, then exported the xyz
coordinates of each vertex (10242 * 2, lh & rh) for that volunteer to an .asc
file using mris_convert. These
xyz coordinates (and the vertex #) and a 3D summary volume (NIfTI) for a BOLD
scan in native space for the
subject were read into MATLAB, and I've used a separate toolbox in Matlab to
generate weights from the BOLD
data that map to each vertex (a continuous variable, one weight per vertex per
subject), and these weights
can be written to a text file in the following format for each hemisphere:


x1 y1  z1 weight1

x2 y2 z2 weight2

...

x10242 y10242 z10242 weight10242


or


vertex1 weight1

vertex2 weight2

...

vertex10242 weight10242


or another format if that would be helpful.


How can I map these weights back to a surface and visualize it? Please advise.
I began to think this fell
into the realm of annotation, but it seems that annotations are categorial
rather than continuous. Thank you
so much for your time.


Best,


Fred

--

Frederick Barrett, Ph.D

Assistant Professor of Psychiatry and Behavioral Sciences

Behavioral Pharmacology Research Unit

Johns Hopkins School of Medicine

5510 Nathan Shock Dr / Rm 3048

Baltimore, MD 21224


Voice/mail: (410) 550-9777

Email: fbarr...@jhmi.edu | frederick.barr...@gmail.com

NCBI: https://goo.gl/mUKEZm

Google Scholar: MailScanner has detected a possible fraud attempt from
"scholar.google.com" claiming to be
http://goo.gl/vjrrsl







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Re: [Freesurfer] map values to vertices {Disarmed}

[Bruce Fischl]

Hi Fred

we usually use mri_vol2surf for this kind of thing. Did you reconstruct 
surfaces from that subject?


cheers
Bruce
On Tue, 13 Feb 2018, Frederick Barrett wrote:



Greetings all,


I apologize in advance for what may (or may not) be a basic question. I want to 
map values from a continuous
variable (non-integer) to each vertex on a surface so that I can visualize 
these values on the surface (or an
inflated brain), but I can't figure out how to do this.

 

I've projected the pial surface of fsaverage5 to native space within a 
volunteer, then exported the xyz
coordinates of each vertex (10242 * 2, lh & rh) for that volunteer to an .asc 
file using mris_convert. These
xyz coordinates (and the vertex #) and a 3D summary volume (NIfTI) for a BOLD 
scan in native space for the
subject were read into MATLAB, and I've used a separate toolbox in Matlab to 
generate weights from the BOLD
data that map to each vertex (a continuous variable, one weight per vertex per 
subject), and these weights
can be written to a text file in the following format for each hemisphere:


x1 y1  z1 weight1

x2 y2 z2 weight2

...

x10242 y10242 z10242 weight10242


or 


vertex1 weight1

vertex2 weight2

...

vertex10242 weight10242


or another format if that would be helpful.


How can I map these weights back to a surface and visualize it? Please advise. 
I began to think this fell
into the realm of annotation, but it seems that annotations are categorial 
rather than continuous. Thank you
so much for your time.


Best,


Fred

--

Frederick Barrett, Ph.D

Assistant Professor of Psychiatry and Behavioral Sciences

Behavioral Pharmacology Research Unit

Johns Hopkins School of Medicine

5510 Nathan Shock Dr / Rm 3048

Baltimore, MD 21224


Voice/mail: (410) 550-9777

Email: fbarr...@jhmi.edu | frederick.barr...@gmail.com

NCBI: https://goo.gl/mUKEZm

Google Scholar: MailScanner has detected a possible fraud attempt from 
"scholar.google.com" claiming to be
http://goo.gl/vjrrsl





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Re: [Freesurfer] Problems running LGI {Disarmed}

[Dusan Hirjak]

Dear Andrew,


thank you very much! Yes, you were right! Now it works fine.


best regards


Dusan



From: Hoopes, Andrew 
Sent: Tuesday, February 13, 2018 12:23 PM
To: Freesurfer support list; Dusan Hirjak
Subject: Re: [Freesurfer] Problems running LGI

Hi Dusan, I just remembered that this is probably due to SIP being enabled on 
your mac, which blocks libraries stored in /usr. I would suggest disabling SIP 
and rerunning to see if that fixes things: 
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/

best,
Andrew



On February 12, 2018 at 10:28:09 AM, Hoopes, Andrew 
(ahoo...@mgh.harvard.edu) wrote:

Hi Dusan,

I’ll take a look at this and get back to you soon. I think this issue is 
related to the matlab version.

best
Andrew



On February 10, 2018 at 4:27:11 PM, Dusan Hirjak 
(dusanhir...@hotmail.com) wrote:

Dear Freesurfer Experts,


I am currently trying to run LGI. I have the 2017b Matlab version, Mac OS 
Sierra and I already set up the freesurfer PATH in Matlab. However, I am 
getting the following error after starting recon all -s localGI :


Dusans-MacBook-Pro:NSS_Analysis_01 dusan$ recon-all -s SP002 -localGI

Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/NSS_Analysis_01

Actual FREESURFER_HOME /Applications/freesurfer

-rw-rw-r--  1 dusan  wheel  508655 Jul 29  2017 
/Applications/freesurfer/subjects/NSS_Analysis_01/SP002/scripts/recon-all.log

Darwin Dusans-MBP 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 
2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64

/Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf

#

#@# Local Gyrification Index lh Sat Feb 10 21:59:13 CET 2018

\n mris_compute_lgi --i lh.pial \n

=

rm -Rf 
/Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial

=

=

mkdir -p 
/Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial

=

=

mris_fill -c -r 1 lh.pial 
/Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz

=

reading surface from lh.pial...

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib


dyld: Symbol not found: ___emutls_get_address

  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib


Abort

ERROR: mris_fill -c -r 1 lh.pial 
/Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 failed!

Darwin Dusans-MBP 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 
2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64



Any help would be greatly appreciated! Many thanks, Dusan

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[Freesurfer] map values to vertices {Disarmed}

[Frederick Barrett]

Greetings all,


I apologize in advance for what may (or may not) be a basic question. I want to 
map values from a continuous variable (non-integer) to each vertex on a surface 
so that I can visualize these values on the surface (or an inflated brain), but 
I can't figure out how to do this.



I've projected the pial surface of fsaverage5 to native space within a 
volunteer, then exported the xyz coordinates of each vertex (10242 * 2, lh & 
rh) for that volunteer to an .asc file using mris_convert. These xyz 
coordinates (and the vertex #) and a 3D summary volume (NIfTI) for a BOLD scan 
in native space for the subject were read into MATLAB, and I've used a separate 
toolbox in Matlab to generate weights from the BOLD data that map to each 
vertex (a continuous variable, one weight per vertex per subject), and these 
weights can be written to a text file in the following format for each 
hemisphere:


x1 y1  z1 weight1

x2 y2 z2 weight2

...

x10242 y10242 z10242 weight10242


or


vertex1 weight1

vertex2 weight2

...

vertex10242 weight10242


or another format if that would be helpful.


How can I map these weights back to a surface and visualize it? Please advise. 
I began to think this fell into the realm of annotation, but it seems that 
annotations are categorial rather than continuous. Thank you so much for your 
time.


Best,


Fred

--

Frederick Barrett, Ph.D

Assistant Professor of Psychiatry and Behavioral Sciences

Behavioral Pharmacology Research Unit

Johns Hopkins School of Medicine

5510 Nathan Shock Dr / Rm 3048

Baltimore, MD 21224


Voice/mail: (410) 550-9777

Email: fbarr...@jhmi.edu | 
frederick.barr...@gmail.com

NCBI: https://goo.gl/mUKEZm

Google Scholar: 
http://goo.gl/vjrrsl



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Re: [Freesurfer] Problems running LGI

[Hoopes, Andrew]

Hi Dusan, I just remembered that this is probably due to SIP being enabled on 
your mac, which blocks libraries stored in /usr. I would suggest disabling SIP 
and rerunning to see if that fixes things: 
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/

best,
Andrew



On February 12, 2018 at 10:28:09 AM, Hoopes, Andrew 
(ahoo...@mgh.harvard.edu) wrote:

Hi Dusan,

I’ll take a look at this and get back to you soon. I think this issue is 
related to the matlab version.

best
Andrew



On February 10, 2018 at 4:27:11 PM, Dusan Hirjak 
(dusanhir...@hotmail.com) wrote:

Dear Freesurfer Experts,


I am currently trying to run LGI. I have the 2017b Matlab version, Mac OS 
Sierra and I already set up the freesurfer PATH in Matlab. However, I am 
getting the following error after starting recon all -s localGI :


Dusans-MacBook-Pro:NSS_Analysis_01 dusan$ recon-all -s SP002 -localGI

Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/NSS_Analysis_01

Actual FREESURFER_HOME /Applications/freesurfer

-rw-rw-r--  1 dusan  wheel  508655 Jul 29  2017 
/Applications/freesurfer/subjects/NSS_Analysis_01/SP002/scripts/recon-all.log

Darwin Dusans-MBP 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 
2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64

/Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf

#

#@# Local Gyrification Index lh Sat Feb 10 21:59:13 CET 2018

\n mris_compute_lgi --i lh.pial \n

=

rm -Rf 
/Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial

=

=

mkdir -p 
/Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial

=

=

mris_fill -c -r 1 lh.pial 
/Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz

=

reading surface from lh.pial...

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib


dyld: Symbol not found: ___emutls_get_address

  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib


Abort

ERROR: mris_fill -c -r 1 lh.pial 
/Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 failed!

Darwin Dusans-MBP 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 
2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64



Any help would be greatly appreciated! Many thanks, Dusan

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[Freesurfer] inter-hemisphere registration on customised template

[Ting Qi]

Dear Freesurfer experts,

I am writing to ask how to do the surface-based inter-hemispheric registration 
based on the customised template, instead of fsaverage. 

I am planning to calculate the lateralisation index for each vertex, which 
means I should to use the symmetry template, for example, fsaverage_sym. 
However, the current issue is my participants are children. Therefore it would 
be better to put the individual data to the customised average template, which 
is already created by ANTS in my case. So I was wondering how to perform the 
symmetry registration on this created template?

Thank you in advance. 

Cheers,
Ting 
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Re: [Freesurfer] IndexError: list index out of range

[Makaretz, Sara Johanna]

*I also got this error when I ran w/ python 2:


python2 $FREESURFER_HOME/bin/asegstats2table --common-segs -t 
aparc.a2009s+aseg.max.table -i aparc.a2009s+aseg.lst -m max

Parsing the .stats files
Traceback (most recent call last):
  File "/usr/local/freesurfer/stable6/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)
  File "/autofs/cluster/freesurfer/centos7_x86_64/stable6/bin/fsutils.py", line 
115, in parse
seg = strlst[1] # segmentation id is in the 2nd field
IndexError: list index out of range




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Makaretz, Sara Johanna 

Sent: Tuesday, February 13, 2018 10:12:07 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] IndexError: list index out of range


Hi Doug,


I am also getting the error "IndexError: list index out of range" - I got the 
same error using FS6.0/FS5.3/dev. This is what I'm running for asegstats2table:


asegstats2table --common-segs -t aparc.a2009s+aseg.max.table -i 
aparc.a2009s+aseg.lst -m max

Parsing the .stats files
Traceback (most recent call last):
  File "/usr/local/freesurfer/stable6/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)
  File "/autofs/cluster/freesurfer/centos7_x86_64/stable6/bin/fsutils.py", line 
115, in parse
seg = strlst[1] # segmentation id is in the 2nd field
IndexError: list index out of range

This is what I ran to make my stats files, which look fine:
mri_label2vol --seg aparc.a2009s+aseg.nii --temp pet.nii --o 
ns_aparc.a2009s+aseg.nii --reg anat2pet.lta
mri_segstats --seg ns_aparc.a2009s+aseg.nii --i pet.nii --sum 
aparc.a2009s+aseg.stats


Do you have any tips on getting this working?


Thanks in advance for any help!

Sara


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maksimovskiy, Arkadiy 

Sent: Monday, January 8, 2018 11:50:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] IndexError: list index out of range


Hi Doug,



I sent you the tar files, but just wanted to update you that I tried running 
this with just one subjects and am still getting an error but a different one. 
The two inputs and output errors in the terminal are pasted below:



[arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits]
 amaksimovskiy% asegstats2table --subjects SILVA030  --meas volume --stats 
aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt

SUBJECTS_DIR : 
/Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits

Parsing the .stats files

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)

  File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse

seg = strlst[1] # segmentation id is in the 2nd field

IndexError: list index out of range

[arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits]
 amaksimovskiy% asegstats2table --subjects SILVA040  --meas volume --stats 
aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt

SUBJECTS_DIR : 
/Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits

Parsing the .stats files

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)

  File "/Applications/freesurfer/bin/fsutils.py", line 122, in parse

self.measurelist.append( float(strlst[self.measure_column_map[measure]] ))

ValueError: could not convert string to float: Left-Cerebellum-Cortex





Let me know if any further info is needed to troubleshoot. Thank you for 
helping with this.

-arkadiy



--

Arkadiy L. Maksimovskiy, Ph.D.

Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School
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Re: [Freesurfer] IndexError: list index out of range

[Makaretz, Sara Johanna]

Hi Doug,


I am also getting the error "IndexError: list index out of range" - I got the 
same error using FS6.0/FS5.3/dev. This is what I'm running for asegstats2table:


asegstats2table --common-segs -t aparc.a2009s+aseg.max.table -i 
aparc.a2009s+aseg.lst -m max

Parsing the .stats files
Traceback (most recent call last):
  File "/usr/local/freesurfer/stable6/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)
  File "/autofs/cluster/freesurfer/centos7_x86_64/stable6/bin/fsutils.py", line 
115, in parse
seg = strlst[1] # segmentation id is in the 2nd field
IndexError: list index out of range

This is what I ran to make my stats files, which look fine:
mri_label2vol --seg aparc.a2009s+aseg.nii --temp pet.nii --o 
ns_aparc.a2009s+aseg.nii --reg anat2pet.lta
mri_segstats --seg ns_aparc.a2009s+aseg.nii --i pet.nii --sum 
aparc.a2009s+aseg.stats


Do you have any tips on getting this working?


Thanks in advance for any help!

Sara


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maksimovskiy, Arkadiy 

Sent: Monday, January 8, 2018 11:50:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] IndexError: list index out of range


Hi Doug,



I sent you the tar files, but just wanted to update you that I tried running 
this with just one subjects and am still getting an error but a different one. 
The two inputs and output errors in the terminal are pasted below:



[arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits]
 amaksimovskiy% asegstats2table --subjects SILVA030  --meas volume --stats 
aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt

SUBJECTS_DIR : 
/Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits

Parsing the .stats files

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)

  File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse

seg = strlst[1] # segmentation id is in the 2nd field

IndexError: list index out of range

[arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits]
 amaksimovskiy% asegstats2table --subjects SILVA040  --meas volume --stats 
aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt

SUBJECTS_DIR : 
/Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits

Parsing the .stats files

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)

  File "/Applications/freesurfer/bin/fsutils.py", line 122, in parse

self.measurelist.append( float(strlst[self.measure_column_map[measure]] ))

ValueError: could not convert string to float: Left-Cerebellum-Cortex





Let me know if any further info is needed to troubleshoot. Thank you for 
helping with this.

-arkadiy



--

Arkadiy L. Maksimovskiy, Ph.D.

Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School
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[Freesurfer] quantifyHAsubregions.sh , HBT/FS60/CA

[Eva Hilland]

Hi Eugenio,

Is it possible to use *quantifyHAsubregions.sh*  to write out the three
different hippocampal subfield outputs ?


- HBT: the hippocampus is subdivided into head, body and tail.
-

FS60: it mimics the FreeSurfer 6.0 hippocampal module, i.e., no head/body
subdivision for the hippocampal subregions.
- CA: the "internal" labels (GC-ML-DG and molecular layer) are absorbed by
the CA subfields: GC-ML-DG is absorbed by CA4, and the voxels in the
molecular layer are assigned the label of the closest voxel that is neither
molecular layer nor background

Best
Eva
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