On Tue, Sep 26, 2017 at 9:30 PM, <freesurfer-request@nmr.mgh.harvard.edu> wrote:

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Today's Topics:

1. generating automatic functional label (Yagmur Ozdemir 19)
2. Re: Error in segmentHA_T1 (Iglesias Gonzalez, Eugenio)
3. Re: Problem with New Hippocampus/Amygdala Segmentation
(Iglesias Gonzalez, Eugenio)
4. Fwd: longtitudinal pipeline (miracle ozzoude)
5. mne_surf2bem error persists after editing file in freeview
(Anna Kasdan)
6. Re: mne_surf2bem error persists after editing file in
freeview (Bruce Fischl)
7. Re: generating automatic functional label (Douglas N Greve)
8. Re: Fw: sim-sign abs/ cluster summary results confirmation
(Douglas N Greve)
9. Re: Automatic Topology Correction (Fereshte)
10. Volume Version of ?h.sphere.reg and method to read it
(Daniel van de Velden)
11. Re: Automatic Topology Correction (Bruce Fischl)
12. Re: bad midline cut (Gabor Perlaki)
13. Re: Volume Version of ?h.sphere.reg and method to read it
(Bruce Fischl)
14. Re: bad midline cut (Bruce Fischl)
15. freesurfer longitudinal pipeline (miracle ozzoude)

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

Message: 1
Date: Mon, 25 Sep 2017 19:21:03 +0000
From: Yagmur Ozdemir 19 <yozdemir19@amherst.edu>
Subject: [Freesurfer] generating automatic functional label
To: Freesurfer support list ?[freesurfer@nmr.mgh.harvard.edu]?
<freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<4C60F8ADC8518344A2F46EEE28EA3380D4DF554E@EX10-MC1-NODE01.amherst.edu>
Content-Type: text/plain; charset="windows-1256"

Hello FreeSurfer developers,

This is a piece of code I came across for producing a functional label with using time course estimates from MEG/EEG data, for freesurfer use. I am wondering if something similar is available to estimate a functional label/region from fMRI data with similar tresholding.

https://martinos.org/mne/stable/auto_examples/inverse/plot_label_from_stc.html#generate-a-functional-label-from-source-estimates

Best,
Idil
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Message: 2
Date: Mon, 25 Sep 2017 19:22:08 +0000
From: "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.uk>
Subject: Re: [Freesurfer] Error in segmentHA_T1
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <5730952C-DDE7-4058-AC31-F5275B35F5C2@ucl.ac.uk>
Content-Type: text/plain; charset="utf-8"

Dear Tiril,
Were you pointed to downloading a version of Java when you first tried to run the subfields? If so, did you follow the instructions?
Cheers,
/Eugenio

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

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Tiril Pedersen Gurholt <t.p.gurholt@medisin.uio.no>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 22 September 2017 at 20:47
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Error in segmentHA_T1

Dear Experts,

I recently installed Freesurfer development version (dated Sept. 16, 2017) on a Mac Sierra (10.12.6).

When trying to run segmentHA_T1.sh I encounter a java problem: "JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib?.

See full error message below. The java.opts file in MCRv80/bin/maci64 is dated Nov. 5, 2014. There also appears to be a problem with a Matlab app (?), although matlab runtime has been installed.

Any ideas as to how to fix these problems?

Best regards,

Tiril

Error message:

#--------------------------------------------
#@# Hippocampal Subfields processing (T1) left Fri Sep 22 20:17:14 CEST 2017
------------------------------------------
Setting up environment variables
---
DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80//runtime/maci64:/Applications/freesurfer/MCRv80//bin/maci64:/Applications/freesurfer/MCRv80//sys/os/maci64:
Warning: application is running on a locale different from the original platform locale.
JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib
JavaVM FATAL: Failed to load the jvm library.
2017-09-22 20:17:16.597 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2017-09-22 20:17:16.599 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2017-09-22 20:17:16.599 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2017-09-22 20:17:16.600 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2017-09-22 20:17:16.600 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2017-09-22 20:17:16.601 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2017-09-22 20:17:16.601 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2017-09-22 20:17:16.602 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2017-09-22 20:17:16.602 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib
JavaVM FATAL: Failed to load the jvm library.
Fatal Error on startup: Unable to start the JVM because of a bad Java option or unknown error.
Please check your java.opts file.

#--------------------------------------------
#@# Hippocampal Subfields processing (T1) right Fri Sep 22 20:17:16 CEST 2017
------------------------------------------
Setting up environment variables
---
DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80//runtime/maci64:/Applications/freesurfer/MCRv80//bin/maci64:/Applications/freesurfer/MCRv80//sys/os/maci64:
Warning: application is running on a locale different from the original platform locale.
JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib
JavaVM FATAL: Failed to load the jvm library.
2017-09-22 20:17:18.151 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2017-09-22 20:17:18.151 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2017-09-22 20:17:18.152 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2017-09-22 20:17:18.152 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2017-09-22 20:17:18.154 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2017-09-22 20:17:18.154 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib
JavaVM FATAL: Failed to load the jvm library.
Fatal Error on startup: Unable to start the JVM because of a bad Java option or unknown error.
Please check your java.opts file.

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Message: 3
Date: Mon, 25 Sep 2017 19:23:19 +0000
From: "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.uk>
Subject: Re: [Freesurfer] Problem with New Hippocampus/Amygdala
Segmentation
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <E4E120AF-FB1D-45E6-B750-CCA48B2A7771@ucl.ac.uk>
Content-Type: text/plain; charset="utf-8"

Dear Max,
It seems that a basic call to mri_robust_register is failing. Can you please try running this command, to make sure that there isn?t a problem with the license?
Cheers,
/Eugenio

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

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Max Owens <owensmax03@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 22 September 2017 at 22:21
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Problem with New Hippocampus/Amygdala Segmentation

Hi Freesurfer Experts,

I'm trying to run the new version 6.0 hippocampus/amygdala segmentation procedure (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) on data from subjects with whom I have already completed recon-all. I have downloaded the newest development version (and license), as well as the required matlab runtime. However, I am getting the following error:

?LD_LIBRARY_PATH is .:freesurfer/MCRv80//runtime/glnxa64:freesurfer/MCRv80//bin/glnxa64:freesurfer/MCRv80//sys/os/glnxa64:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/server:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/client:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64:

Registering imageDump.mgz to hippocampal mask from ASEG

cp: cannot stat ?freesurfer/average/HippoSF/atlas/AtlasDump.mgz?: No such file or directory

Error using myMRIread (line 16)

Error in myMRIread: temporary directory does not exist

Error in segmentSubjectT1_autoEstimateAlveusML (line 134)

Command exited with non-zero status 255

@#@FSTIME 2017:09:22:15:55:53 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 2.85 S 0.11 U 2.85 P 103% M 205292 F 1 R 22759 W 0 c 2477 w 641 I 0 O 63584 L 0.41 0.56 0.64

@#@FSLOADPOST 2017:09:22:15:55:56 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.41 0.56 0.64

All done! ?

Have you ever seen this error before? If not, can you provide any suggestions for ways that I might troubleshoot it? I have attached the command I used and the error log if this is of help.

Thanks very much for your time,

Max

--
Max Owens, M.S.
Graduate Student in Psychology
Clinical Neuroscience Lab
University of Georgia
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Message: 4
Date: Mon, 25 Sep 2017 15:24:11 -0400
From: miracle ozzoude <miracooloz@gmail.com>
Subject: [Freesurfer] Fwd: longtitudinal pipeline
To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CANfOk0iA9GPr8rd8SCutaTuJ4H+7a9dAO8J1uV_K=ZFpz2yYXA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

---------- Forwarded message ----------
From: miracle ozzoude <miracooloz@gmail.com>
Date: Fri, Sep 22, 2017 at 2:17 PM
Subject: longtitudinal pipeline
To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu>

Hello Freesurfer,

For the longitudinal pipeline, the website/ recon-all -help suggested that
I calculate the different on the results from the longitudinal command
(e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were
named 0001a.long.0001.longbase and 0001b.long.0001.longbase. is there a
command i can use to preform this?

Second question, i want to extract the output of the longitudinal pipeline
using asegstats2table and aparcstats2table commands. what flag/s should i
include in the original command to perform this?

Thanks.
Paul
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Message: 5
Date: Mon, 25 Sep 2017 16:03:15 -0400
From: Anna Kasdan <anna.kasdan@nyu.edu>
Subject: [Freesurfer] mne_surf2bem error persists after editing file
in freeview
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAERmW5aBa5TTT2a_xz8grny0goRpiqAn14vwERVg=Z2dZrfX=g@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

I am trying to create a high-resolution image to use with mne in
mne_analyze. I first ran mkheadsurf -subjid s and this did not result in
any errors.

I then ran mne_surf2bem --surf ../surf/lh.seghead --id 4 --check --fif
s-head.fif
and ran into an error about vertices for a few of my subjects.

input file # 1 : ../surf/lh.seghead / id = 4 / sigma N/A

output file : EVO07-head.fif

New quad file : nvert = 288077 nquad = 294014

Triangle and vertex normals and neighboring triangles...[done]

Vertex neighbors...Too many neighbors for vertex 92055.

I tried editing the seghead.mgz file in freeview, and filled in the voxels
that were missing at the neck. I then reran the mkheadusrf command
(mkheadusrf -subjid s --noseghead), still with no errors, but got the same
error as before again when I ran the mne_surf2bem command.

Suggestions? Many thanks!

Anna
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Message: 6
Date: Mon, 25 Sep 2017 17:01:32 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mne_surf2bem error persists after editing
file in freeview
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Matti Hamalainen <msh@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1709251700390.20962@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Anna

perhaps this is a question for Matti (ccd)?

cheers
Bruce
On Mon, 25 Sep 2017, Anna Kasdan
wrote:

> I am trying to create a high-resolution image to use with mne in mne_analyze. I first ran mkheadsurf
> -subjid s and this did not result in any errors.
> I then ran mne_surf2bem --surf ../surf/lh.seghead --id 4 --check --fif s-head.fif
> and ran into an error about vertices for a few of my subjects.?
>
> input? file # ? 1 : ../surf/lh.seghead / id = 4 / sigma N/A
>
> output file ? ? ? : EVO07-head.fif
>
>
> New quad file : nvert = 288077 nquad = 294014
>
> Triangle and vertex normals and neighboring triangles...[done]
>
> Vertex neighbors...Too many neighbors for vertex 92055.
>
>
> I tried editing the seghead.mgz file in freeview, and filled in the voxels that were missing at the
> neck. I then reran the mkheadusrf command (mkheadusrf -subjid s --noseghead), still with no errors,
> but got the same error as before again when I ran the mne_surf2bem command.
>
> Suggestions? Many thanks!
>
> Anna
>
>
>

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

Message: 7
Date: Mon, 25 Sep 2017 17:53:55 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] generating automatic functional label
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <668a13ab-794d-8081-ff8a-f27cf90b87e0@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1256; format=flowed

Hi Idil, I'm not going to plow through someone else's code:) If you want
to summarize what it does, I might be able to figure out if we have
something that does it.

On 09/25/2017 03:21 PM, Yagmur Ozdemir 19 wrote:
> Hello FreeSurfer developers,
>
> This is a piece of code I came across for producing a functional label
> with using time course estimates from MEG/EEG data, for freesurfer
> use. I am wondering if something similar is available to estimate a
> functional label/region from fMRI data with similar tresholding.
>
> https://martinos.org/mne/stable/auto_examples/inverse/plot_label_from_stc.html#generate-a-functional-label-from-source-estimates
>
> Best,
> Idil
>
>
> _______________________________________________
> 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
greve@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/

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

Message: 8
Date: Mon, 25 Sep 2017 18:01:38 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Fw: sim-sign abs/ cluster summary results
confirmation
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <c6497fc6-f321-f84c-3300-a0ce73ee6ed1@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=utf-8; format=flowed

On 09/24/2017 02:17 PM, miracle ozzoude wrote:
>
>
> Sent from my BlackBerry 10 smartphone.
> *From: *miracle ozzoude <miracooloz@gmail.com>
> *Sent: *Friday, September 22, 2017 9:37 PM
> *To: *Douglas N Greve
> *Subject: *sim-sign abs/ cluster summary results confirmation
>
>
> Hello,
>
> I ran cortical thickness analyses using the following contrast and
> fsgd. After that, I corrected for multiple comparison using monte
> carlo 5000 with cluster forming threshold of 2 and unsigned/2-tailed
> t-test (abs). I wanted to confirm my interpretation of the results.
>
> 1) Since my contrast is (-1 1 0 0 representing control>stroke), it
> should be red/yellow and if blue, it should be control<stroke.
> However, I see clusters with colors different from the aformentioned
> (see attached screenshot). How should I interpret them?
That is a parcellation/segmentation of the clusters, and the colors
don't have inherent value. Eg, when you look at the aparc, you see
precentral and postcentral are red and blue, but those colors don't mean
anything, they are just a way to distinguish between areas. You have
chosen abs, so it is not possible to interpret the sign.
>
> 2) I want to view the uncorrected p-values, which of the columns in
> the summary text file should I concentrate, and should the p < or > 0.05?
The uncorrected p-values are the voxel-wise values. The stats file will
have the maximum uncorrected p-value (actually, -log10(p)).
>
> 3) Looking at the CWP column in the summary text file, can I conclude
> that the obtained regions/clusters are significant? This is because
> non of the cluster-wise p-values are below 0.05 (--cwp 0.05).
Not sure which column you are talking about. All the CWP values are
close to 1, so nothing is significant
>
> 4) Which of the columns represent the sign of my contrast i.e. where
> Control>Stroke and Control<Stroke because i used abs? Max?
if you used abs, then you can't interpret sign. Having said that, the
"Max" column will indicate the sign of the vertex with the maximum
-log10(p), and that will probably be the sign of the entire cluster
>
> FSGD file
> GroupDescriptorFile
> Title StrokevsControl
> Class1 Stroke
> Class2 Control
> Variable bmi
> Input 6001 Stroke 20
> Input 8001 Control 30
>
> Contrast:
> -1 1 0 0 (Control>Stroke removing the effects of bmi)
>
> Thank you,
> Paul
>
>
>
>
> _______________________________________________
> 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
greve@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/

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

Message: 9
Date: Tue, 26 Sep 2017 07:28:49 +0000
From: Fereshte <fereshte.ramezani@gmail.com>
Subject: Re: [Freesurfer] Automatic Topology Correction
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAAdxBZpS14zdC3FX7BT78rAJaGdT1Ei7vWbifw0t=M32YVXQDw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Experts,
I checked the topology corrected surfaces in recon-all pipeline however i
found it didn't do well as still there are many topology defects in the
pial surfaces. I know how to correct them manually in freeview but are
there any commands to recorrect these topological defects with for example
variables ? ( shall i use mris_fix_topology or? )
Thank you.

On Sat, Sep 23, 2017 at 7:16 PM Fereshte <fereshte.ramezani@gmail.com>
wrote:

> Thank you.
> Cheers
>
> On Sat, Sep 23, 2017 at 7:13 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> wrote:
>
>> Segonne, F., Pacheco, J., Fischl, B., 2007. Geometrically accurate
>> topology-correction of cortical surfaces using nonseparating loops. IEEE
>> Trans Med Imaging 26, 518-529.
>>
>> Fischl, B., Liu, A., Dale, A.M., 2001. Automated manifold surgery:
>> constructing geometrically accurate and topologically correct models of
>> the human cerebral cortex. IEEE Trans Med Imaging 20, 70-80.
>>
>> Florent S?gonne,Eric GrimsonBruce Fischl, 2003. Topological Correction of
>> Subcortical Segmentation
>> MICCAI 2003: Medical Image Computing and Computer-Assisted Intervention -
>> MICCAI 2003 pp 695-702
>>
>> On Sat, 23 Sep
>> 2017, Fereshte wrote:
>>
>> > Where can i find the details?
>> > Thank you.
>> >
>> > On Sat, Sep 23, 2017 at 6:59 PM Bruce Fischl <
>> fischl@nmr.mgh.harvard.edu> wrote:
>> > Yes, that is part of the recon-all pipeline (actually we have 3
>> separate
>> > topology correction procedures, two for the surface and one for
>> the
>> > volume)
>> >
>> > cheers
>> > Bruce
>> > On Sat, 23 Sep 2017, Fereshte wrote:
>> >
>> > > Dear FreeSurfer Developers Is it possible to correct
>> topological defects automatically
>> > in
>> > > FreeSurfer? ( not correcting manually with Recon Edit)
>> > > Thank you.
>> > >
>> > >_______________________________________________
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> > The information in this e-mail is intended only for the person to
>> whom it is
>> > addressed. If you believe this e-mail was sent to you in error
>> and the e-mail
>> > contains patient information, please contact the Partners
>> Compliance HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent
>> to you in error
>> > but does not contain patient information, please contact the
>> sender and properly
>> > dispose of the e-mail.
>> >
>> >
>> >_______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>
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Message: 10
Date: Tue, 26 Sep 2017 09:52:46 +0200
From: Daniel van de Velden <daniel.vandevelden@yahoo.de>
Subject: [Freesurfer] Volume Version of ?h.sphere.reg and method to
read it
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <e44c3b44-542f-1b39-a6fe-fed511600813@yahoo.de>
Content-Type: text/plain; charset=utf-8; format=flowed

Dear Freesurfer Team,

I am using your reconstruction pipeline for my study. Since I need to
morph all my subjects to an average subject (using mne-python for this)
for upcoming a Volume Source Analysis I deeply looked into the whole
source-code of both software packages. Narowing down the problem, I
think I will need a volume version of the ?h-sphere.reg files, which are
created during the whole reconstruction process.

Mne-python reads the subject specific 'sphere_tris' from this file. If I
would have a similiar file for the volume edges that would be helpful.

Do you agree with my conclusion and see where I am going?

Thanks in advance for any kind of help.

Yours sincerely,

??? Daniel van de Velden

.

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

Message: 11
Date: Tue, 26 Sep 2017 09:59:42 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Automatic Topology Correction
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1709260959000.20962@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

why do you think there are defects? If you have run recon-all there are
pretty much guaranteed not wo be any. You can't really see this visually,
but mris_euler_number will tell you if there are any

cheers
Bruce
On Tue, 26 Sep 2017,
Fereshte wrote:

> Dear Experts,
> I checked the topology corrected surfaces in recon-all pipeline however i found it didn't do well as
> still there are many topology defects in the pial surfaces. I know how to correct them manually in
> freeview but are there any commands to recorrect these topological defects with for example
> variables ? ( shall i use mris_fix_topology or? )?
> Thank you.?
>
> On Sat, Sep 23, 2017 at 7:16 PM Fereshte <fereshte.ramezani@gmail.com> wrote:
> Thank you.?
> Cheers?
>
> On Sat, Sep 23, 2017 at 7:13 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> Segonne, F., Pacheco, J., Fischl, B., 2007. Geometrically accurate
> topology-correction of cortical surfaces using nonseparating loops. IEEE
> Trans Med Imaging 26, 518-529.
>
> Fischl, B., Liu, A., Dale, A.M., 2001. Automated manifold surgery:
> constructing geometrically accurate and topologically correct models of
> the human cerebral cortex. IEEE Trans Med Imaging 20, 70-80.
>
> Florent S?gonne,Eric GrimsonBruce Fischl, 2003. Topological Correction of
> Subcortical Segmentation
> MICCAI 2003: Medical Image Computing and Computer-Assisted Intervention -
> MICCAI 2003 pp 695-702
>
> On Sat, 23 Sep
> 2017, Fereshte wrote:
>
> > Where can i find the details??
> > Thank you.
> >
> > On Sat, Sep 23, 2017 at 6:59 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> >? ? ? ?Yes, that is part of the recon-all pipeline (actually we have 3 separate
> >? ? ? ?topology correction procedures, two for the surface and one for the
> >? ? ? ?volume)
> >
> >? ? ? ?cheers
> >? ? ? ?Bruce
> >? ? ? ?On Sat, 23 Sep 2017, Fereshte wrote:
> >
> >? ? ? ?> Dear FreeSurfer Developers?Is it possible to correct topological defects
> automatically
> >? ? ? ?in
> >? ? ? ?> FreeSurfer? ( not correcting manually with Recon Edit)
> >? ? ? ?> Thank you.
> >? ? ? ?>
> >? ? ? ?>_______________________________________________
> >? ? ? ?Freesurfer mailing list
> >? ? ? ?Freesurfer@nmr.mgh.harvard.edu
> >? ? ? ?https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >? ? ? ?The information in this e-mail is intended only for the person to whom it
> is
> >? ? ? ?addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> >? ? ? ?contains patient information, please contact the Partners Compliance
> HelpLine at
> >? ? ? ?http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> >? ? ? ?but does not contain patient information, please contact the sender and
> properly
> >? ? ? ?dispose of the e-mail.
> >
> >
> >_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.
>
>
>

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

Message: 12
Date: Tue, 26 Sep 2017 16:00:32 +0200
From: Gabor Perlaki <petzinger.gabor@gmail.com>
Subject: Re: [Freesurfer] bad midline cut
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CA+f2votN=H0b0VN6ghO_HLyw2ECHgU9PM8Ea6AgwBCbh8GP3Eg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Bruce,

I've corrected the lateral ventricles in the aseg.presurf.mgz and ran
"recon-all -autorecon2-noaseg -autorecon3 -subjid". Although the labels in
aseg.mgz is fine the surfaces (and midline cut) remained bad. Any other
idea how to correct this type of error?

Best Regards,
Gabor
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Message: 13
Date: Tue, 26 Sep 2017 10:00:47 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Volume Version of ?h.sphere.reg and method
to read it
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1709261000130.20962@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Daniel

you might try asking the MNE developers about this, but I don't think
this is correct. What would a volume version of the sphere.reg be? A filled
in sphere?

cheers
Bruce

On Tue, 26 Sep 2017, Daniel van de Velden wrote:

> Dear Freesurfer Team,
>
> I am using your reconstruction pipeline for my study. Since I need to
> morph all my subjects to an average subject (using mne-python for this)
> for upcoming a Volume Source Analysis I deeply looked into the whole
> source-code of both software packages. Narowing down the problem, I
> think I will need a volume version of the ?h-sphere.reg files, which are
> created during the whole reconstruction process.
>
> Mne-python reads the subject specific 'sphere_tris' from this file. If I
> would have a similiar file for the volume edges that would be helpful.
>
> Do you agree with my conclusion and see where I am going?
>
> Thanks in advance for any kind of help.
>
> Yours sincerely,
>
> ??? Daniel van de Velden
>
>
> .
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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

Message: 14
Date: Tue, 26 Sep 2017 10:04:51 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] bad midline cut
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1709261004250.20962@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed

Hi Gabor

you don't want to specify -noaseg. That tells recon-all not to use the
aseg. I think autorecon2-cp and autorecon3 should do the trick

cheers
Bruce
On Tue, 26 Sep 2017, Gabor Perlaki wrote:

> Dear Bruce,
>
> I've corrected the lateral ventricles in the aseg.presurf.mgz and ran "recon-all -autorecon2-noaseg
> -autorecon3 -subjid". Although the labels in aseg.mgz is fine the surfaces (and midline cut)
> remained bad. Any other idea how to correct this type of error?
>
> Best Regards,
> Gabor
>
>

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

Message: 15
Date: Tue, 26 Sep 2017 11:50:19 -0400
From: miracle ozzoude <miracooloz@gmail.com>
Subject: [Freesurfer] freesurfer longitudinal pipeline
To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CANfOk0gmXTj=V=wM_d-OQ0ePjiYzyAt0SHtOxPBFefX6i6OmNw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hello Freesurfer,

For the longitudinal pipeline, the website/ recon-all -help suggested that
I calculate the different on the results from the longitudinal command
(e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were
named 1001_Baseline.long.longbase and 1001_Followup.long.longbase; is there
a command i can use to preform this?

Second question, i want to extract the output of the longitudinal pipeline
using asegstats2table and aparcstats2table commands. what flag/s should i
include in the original command to perform this?

Thanks.
Paul
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