[Freesurfer] Cortical thickness (spc) extraction

[AKUDJEDU, THEOPHILUS]

External Email - Use Caution

Dear FreeSurfer,

I used QDEC for the longitudinal two‐stage model analyses, where temporal data 
within each subject was reduced to a symmetrised percent rate of change (spc) 
maps using the long_mris_slopes function for data acquired at two time-point. I 
observed an abnormal region with different spc in patients relative to controls 
over time. How do I extract the spc for this region in each individual? What 
scripts do I use?
Thanks
Theo

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[Freesurfer] Longitudinal QDEC

[AKUDJEDU, THEOPHILUS]

External Email - Use Caution

Dear All,

I am running a longitudinal (2-time points) group cortical analysis in 
Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a 
cross-sectional form, I added a text file containing the lines

MEASURE1 = long.thickness-avg
MEASURE2 = long.thickness-rate
MEASURE3 = long.thickness-pc1
MEASURE4 = long.thickness-spc

in the qdec directory to guide qdec to know about the newly created files (e.g. 
lh.long.thickness-spc...). However, it doesn't seem to be recognizing/picking 
up the new files or not reading the text file named Qdecrc.txt (which has the 
lines above.

Will be glad if you could offer any help.

Thanks

Theo



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[Freesurfer] Longitudinal QDEC

[AKUDJEDU, THEOPHILUS]

External Email - Use Caution

Dear All,

I am running a longitudinal (2-time points) group cortical analysis in 
Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a 
cross-sectional form, I added a text file containing the lines

MEASURE1 = long.thickness-avg
MEASURE2 = long.thickness-rate
MEASURE3 = long.thickness-pc1
MEASURE4 = long.thickness-spc

in the qdec directory to guide qdec to know about the newly created files (e.g. 
lh.long.thickness-spc...). However, it doesn't seem to be recognizing/picking 
up the new files or not reading the text file named Qdecrc.txt (which has the 
lines above.

Will be glad if you could offer any help.

Thanks

Theo

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[Freesurfer] FreeSurfer - Lateral Ventricle Definition

[AKUDJEDU, THEOPHILUS]

External Email - Use Caution

Dear FreeSurfer Experts,


Can you confirm whether, the volume of the choroid plexus has automatically 
been added to the laterel ventricle volume or not.


Thanks


Theo

___

Theophilus Akudjedu

BSc, MSc, PhD Candidate

Room 202 Comerford Suite,

Clinical Science Institute,

Department of Psychiatry,

National University of Ireland, Galway


Phone: +353 838329602

Email: t.akudje...@nuigalway.ie

   rasni...@gmail.com



[https://ci6.googleusercontent.com/proxy/b9-AoNc-V0v85TZ_pj6puJTgX7uWBNlZdohjQM11hVJywIAEwXEGsHgEnDPLCI7oFsH_DknZswzkpzUMsK1_yk3OwzRkUZZ73VRhQq1-TF2aFt-1u2fB2jnkmTrpvirljLd9ciRy-A_D1eiTBaS6Xak0JKNMiKL1sBIdRVKUiqrLEkqWzllvsRAPy9j9Ed1nWXu4-QUpob0nkuM=s0-d-e1-ft#https://docs.google.com/uc?export=download=0Bw-d1Byh7ldEU2czeGlfMjNVOTg=0Bw-d1Byh7ldENkZtSlhueGFHdTFhVVFSa25xSmNvNGs4QXdNPQ]

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Re: [Freesurfer] Freesurfer Digest, Vol 168, Issue 54

[AKUDJEDU, THEOPHILUS]

Hi Eugenio,


The folder scripts/ does not contain T1.log for hippocampal subfields. It only 
has the log files I sent earlier.


Thanks


Theo





From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of 
freesurfer-requ...@nmr.mgh.harvard.edu <freesurfer-requ...@nmr.mgh.harvard.edu>
Sent: 27 February 2018 17:00:01
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 168, Issue 54

Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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You can reach the person managing the list at
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

   1. Re: Hippocampal Subfield Error (Iglesias Gonzalez, Eugenio)
   2. Re: Invalid MEX file - FS dev-version error? (Hoopes, Andrew)
   3. Re: Creating ROI on the functional map (Sarah Cole)
   4. Freeview update on Mac (Sarah Cole)
   5. Re: Invalid MEX file - FS dev-version error? (Fereshte)
   6. Re: Antwort: Re: Quality issues when running recon-all
  (Bruce Fischl)


--

Message: 1
Date: Tue, 27 Feb 2018 16:13:30 +
From: "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk>
Subject: Re: [Freesurfer] Hippocampal Subfield Error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <cd18a07c-5fc8-4ec4-be83-d282314ff...@ucl.ac.uk>
Content-Type: text/plain; charset="utf-8"

Hi Theo,
Sorry for not being more clear; I meant hippocampal-subfields-T1.log, which 
should be in the directory ?scripts?.
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-boun...@nmr.mgh.harvard.edu> on behalf of "AKUDJEDU, 
THEOPHILUS" <t.akudje...@nuigalway.ie>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 27 February 2018 at 15:31
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal Subfield Error





Dear Eugenio,

Attached as requested.

Thanks

Theo
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Message: 2
Date: Tue, 27 Feb 2018 16:23:36 +
From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Invalid MEX file - FS dev-version error?
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>,
"Reetta-Liina   Armio" <rls...@utu.fi>
Message-ID: <etpan.5a958607.6e9d99d4@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Reetta, can you source freesurfer, run the ?bugr? command, and send the 
given buildstamp?

thanks
Andrew



On February 27, 2018 at 5:42:14 AM, Reetta-Liina Armio 
(rls...@utu.fi<mailto:rls...@utu.fi>) wrote:

Dear Freesurfer developers,

I have run basic segmentation (and hippocampal segmentation) with Freesurfer 
6.0. I have now tried to run amygdala segmentation with dev-version (downloaded 
from the FS-site today).

I have run the same amygdalasegmentation with same platform etc in October 2017 
and was able to get the volumes. I?m now trying to repeat the run with newer 
dev-version.

I get this Error
?invalid MEX file.?

So there is something wrong with the path?

Could you kindly help me with this?

Thank you in advance!

See log-file and Matlab-version attached.

Best,
Reetta-Liina Armio

L?hetetty iPhonesta
[cid:399A78D3-2E7E-4165-AFF6-773C57D612D7]



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Message: 3
Date: Tue, 27 Feb 2018 10:23:30 -0600
From: Sarah Cole <coleashle...@gmail.com>
Subject: Re: [Freesurfer] Creating ROI on the functional map
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<cajwstc22mc84bj-rfh2d32a

[Freesurfer] Hippocampal Subfield Error

[AKUDJEDU, THEOPHILUS]

Hi All,


I tried to run a subject through FreeSurfer 6.0 for hippocampal Subfield 
segmentation but exited with errors.


The content of the recon-all.error file is below.



SUBJECT CHRM2001
DATE Sun Feb 25 00:34:13 GMT 2018
USER 15233963
HOST psych-sl03
PROCESSOR x86_64
OS Linux
Linux psych-sl03 3.10.0-327.36.3.el7.x86_64 #1 SMP Mon Oct 24 16:09:20 UTC 2016 
x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
/opt/ohpc/pub/apps/freesurfer/6.0.0/bin/recon-all
PWD /home/15233963/freesurfer/SUBJECTS/CHRM2001/label
CMD mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a 
./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab CHRM2001 rh white




Will be glad if you can provide guidance.


Cheers


Theo


___

Theophilus Akudjedu

BSc, MSc, PhD Candidate

Room 202 Comerford Suite,

Clinical Science Institute,

Department of Psychiatry,

National University of Ireland, Galway


Phone: +353 838329602

Email: t.akudje...@nuigalway.ie

   rasni...@gmail.com



[https://ci6.googleusercontent.com/proxy/b9-AoNc-V0v85TZ_pj6puJTgX7uWBNlZdohjQM11hVJywIAEwXEGsHgEnDPLCI7oFsH_DknZswzkpzUMsK1_yk3OwzRkUZZ73VRhQq1-TF2aFt-1u2fB2jnkmTrpvirljLd9ciRy-A_D1eiTBaS6Xak0JKNMiKL1sBIdRVKUiqrLEkqWzllvsRAPy9j9Ed1nWXu4-QUpob0nkuM=s0-d-e1-ft#https://docs.google.com/uc?export=download=0Bw-d1Byh7ldEU2czeGlfMjNVOTg=0Bw-d1Byh7ldENkZtSlhueGFHdTFhVVFSa25xSmNvNGs4QXdNPQ]

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[Freesurfer] MNI Coordinates

[AKUDJEDU, THEOPHILUS]

Hi All,

I am trying to visualise nodes of a brain network reconstructed using 
FreeSurfer Desikan-Killiany Atlas parcellation scheme (aparc+aseg.mgz) on Brain 
Net Viewer and Network Based Statistics software.
In order to do so, I need to upload a .txt file listing Freesurfer labels 
coordinates in MNI space. Is there any way I can get a list of MNI coordinates 
for my set of labels?

Many thanks,


Theo



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[Freesurfer] How to obtain MNI coordinates

[AKUDJEDU, THEOPHILUS]

Hi All,

I am trying to visualise nodes of a brain network reconstructed using 
FreeSurfer Desikan-Killiany Atlas parcellation scheme (aparc+aseg.mgz) on Brain 
Net Viewer and Network Based Statistics software.
In order to do so, I need to upload a .txt file listing Freesurfer labels 
coordinates in MNI space. Is there any way I can get a list of MNI coordinates 
for my set of labels?

Many thanks,
Theo




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[Freesurfer] Subcortical Segmentation

[AKUDJEDU, THEOPHILUS]

Hi FreeSurfers,


Are we able to correct the anatomical boundaries of subcortical structures 
delineated with FreeSurfer? On which output file do we do this if it's possible?


Thank you


Theo

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[Freesurfer] Longitudinal Pipeline

[AKUDJEDU, THEOPHILUS]

Hi All,

Is it standard practice to conduct  test when corrections are made in 
freesurfer for subcortical structure volumes?

Also, are you able to analyse data acquired (1.5T - time point one) with 
time-point two (3T) in the longitudinal pipeline?


Thanks


Theo


From: AKUDJEDU, THEOPHILUS
Sent: Tuesday, June 13, 2017 3:19:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Longitudinal Pipeline


Hi All,


Is it standard practice to conduct reliability when corrections are made in 
freesurfer for subcortical structure volumes?


Also, are you able to analyse data acquired (1.5T - time point one) with 
time-point two (3T) in the longitudinal pipeline?



Thanks



Theo





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[Freesurfer] Longitudinal Pipeline

[AKUDJEDU, THEOPHILUS]

Hi All,


Is it standard practice to conduct reliability when corrections are made in 
freesurfer for subcortical structure volumes?


Also, are you able to analyse data acquired (1.5T - time point one) with 
time-point two (3T) in the longitudinal pipeline?



Thanks



Theo





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Re: [Freesurfer] Freesurfer Digest, Vol 152, Issue 22

[AKUDJEDU, THEOPHILUS]

Dear All,


I want to know the freesurfer anatomical definition for the caudate and the 
hippocampus.


Thank you.


Theo



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 
freesurfer-requ...@nmr.mgh.harvard.edu 
Sent: 16 October 2016 17:00:01
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 152, Issue 22

Send Freesurfer mailing list submissions to
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To subscribe or unsubscribe via the World Wide Web, visit
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You can reach the person managing the list at
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

   1. Using "for" to run multiple subjects (Farzaneh keyvanfard)
   2. Problem in upload file through ftp (Cong)


--

Message: 1
Date: Sat, 15 Oct 2016 18:52:12 + (UTC)
From: Farzaneh keyvanfard 
Subject: [Freesurfer] Using "for" to run multiple subjects
To: Freesurfer Support List 
Message-ID: <941247766.328043.1476557532...@mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Dear expert,
I want to run recon-all for 100 subject simultaneously. I found the following 
link about it, but as I'm a beginner in this field, I don't understand how to 
use it. Would you please kindly give an example with a subject names, directory 
, etc. what should be written instead of * , or how could I define the number 
of subjects, ...? Thank you very much.
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts/Two
Best Regards


F.Keyvanfard
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Message: 2
Date: Sun, 16 Oct 2016 11:17:36 +0800
From: Cong <3110103...@zju.edu.cn>
Subject: [Freesurfer] Problem in upload file through ftp
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <194f90e6-0f88-4bda-8e6e-48ee30621...@zju.edu.cn>
Content-Type: text/plain; charset="gb2312"

Dear freesurfer experts
When I use command "put path/to/my/file?, it?s always appear an error "229 
Entering Extended Passive Mode (|||37867|).
553 Could not create file?, if I use epsv command before put, then comes an 
error "227 Entering Passive Mode (132,183,202,158,147,237). 553 Could not 
create file?. Could you give me some advices?

Best Wishes
Cong Chen
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[Freesurfer] FreeSurfer Atlas

[AKUDJEDU, THEOPHILUS]

Hi All,


Which default atlas does FreeSurfer 5.3 use for the segmentation of subcortical 
structures?


Thanks


Theo

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