Re: [Freesurfer] label a ROI

[Francesca Pentimalli]

External Email - Use Caution

Dear Bruce,

Thank you very much for answering!

We are doing a study on correlating dyslexia, at an early stage, with
various factors in children. Specifically, our goal is to look at how the
12 regions of the brain, that I mentioned in the previous email, play a
role in the study.

Up until now, I have done an mri_average of all the images and used the
qdec interface to see how cortical thickness and surface area vary with
parameters such as gender, age and maternal education. This produced
interesting results but they get affected when the Monte Carlo correction
is run on the same. Further, I want to run the analysis specifically inside
certain regions of interest. For that purpose, I thought about creating the
masks in freesurfer considering just the regions of interest and  run the
analysis in them. Is this a good way to go about this?

Thank you very much for your kind attention.

Best regards,

Francesca





Il giorno mer 5 giu 2019 alle ore 18:45 Bruce Fischl <
fis...@nmr.mgh.harvard.edu> ha scritto:

> Hi Francesca
>
> what analysis do you want to run?
>
> cheers
> Bruce
> On Wed, 5 Jun 2019, Francesca Pentimalli
> wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer experts,
> >
> >
> > I am trying to create a mask and run the analysis into it considering
> just the following anatomical
> > regions:
> >
> >
> >  (1) inferior frontal gyrus pars opercularis (IFGOp)
> >
> >  (2) inferior frontal gyrus pars orbitalis (IFGOr)
> >
> >  (3) inferior frontal gyrus pars triangularis (IFGTr)
> >
> >  (4) Heschl3s gyrus (HG)
> >
> >  (5) the superior temporal gyrus (STG)
> >
> >  (6) planum polare (PP)
> >
> >  (7) planum temporale (PT)
> >
> >  (8) supramarginal gyrus (SMAR)
> >
> >  (9) angular gyrus (AG)
> >
> > (10) fusiform gyrus (FFG)
> >
> > (11) inferior occipital gyrus (IOG)
> >
> > (12) insula
> >
> >
> > Which technique do you suggest? Is there a good tutorial for it?
> > Thank you very very much!!
> >
> > Best regards,
> >
> > Francesca  Francesca Pentimalli Biscaretti di Ruffia Via S. Eufemia 3,
> 35121 Padova (Italy)
> > Mobile: +39 3483862788
> > francesca.pentimallibiscarettidiruf...@studenti.unipd.it
> > fpentimalli...@gmail.com
> > fpe...@mit.edu
> > fp...@bu.edu
> >
> >___
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-- 
*Francesca Pentimalli Biscaretti di Ruffia *
Via S. Eufemia 3, 35121 Padova (Italy)
Mobile: +39 3483862788
francesca.pentimallibiscarettidiruf...@studenti.unipd.it
fpentimalli...@gmail.com
fpe...@mit.edu
fp...@bu.edu
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Re: [Freesurfer] label a ROI

[Bruce Fischl]

Hi Francesca

what analysis do you want to run?

cheers
Bruce
On Wed, 5 Jun 2019, Francesca Pentimalli 
wrote:




External Email - Use Caution

Dear Freesurfer experts,


I am trying to create a mask and run the analysis into it considering just the 
following anatomical
regions:


 (1) inferior frontal gyrus pars opercularis (IFGOp)

 (2) inferior frontal gyrus pars orbitalis (IFGOr)

 (3) inferior frontal gyrus pars triangularis (IFGTr)

 (4) Heschl3s gyrus (HG)

 (5) the superior temporal gyrus (STG)

 (6) planum polare (PP)

 (7) planum temporale (PT)

 (8) supramarginal gyrus (SMAR)

 (9) angular gyrus (AG)

(10) fusiform gyrus (FFG)

(11) inferior occipital gyrus (IOG)

(12) insula


Which technique do you suggest? Is there a good tutorial for it?
Thank you very very much!!

Best regards,

Francesca  Francesca Pentimalli Biscaretti di Ruffia Via S. Eufemia 3, 35121 
Padova (Italy)
Mobile: +39 3483862788
francesca.pentimallibiscarettidiruf...@studenti.unipd.it
fpentimalli...@gmail.com
fpe...@mit.edu
fp...@bu.edu

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[Freesurfer] error matlab segmentHA

[stdp82]

External Email - Use Caution

I have installed matlab 2018b and removed 2014b.

When I run segmentHA_T1.sh the error reported below occurs:

MATLAB is exiting because of fatal error

/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 
37:3955 Killed: 9 
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 $args

Darwin iMac-di-Stefano.local 17.7.0 Darwin Kernel Version 17.7.0: Wed Apr 24 
21:17:24 PDT 2019; root:xnu-4570.71.45~1/RELEASE_X86_64 x86_64

T1 hippocampal subfields exited with ERRORS at Tue Jun4 00:55:25 CEST 2019

For more details, see the log file 
/Applications/freesurfer/subjects/subj/scripts/hippocampal-subfields-T1.log

Please also take in account

segmentation violation detected at Tue Jun4 00:57:53 2019



Configuration:

Crash Decoding : Disabled

Current Visual : Quartz

Default Encoding : ISO-8859-1

MATLAB Architecture: maci64

MATLAB Root: /Applications/freesurfer/MCRv84

MATLAB Version : 8.4.0.150421 (R2014b)

MATLAB Version : 8.4.0.150421 (R2014b) 

Why it does not find 2018 version?

I have follow the guidelines at 
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime 

Thanks

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[Freesurfer] label a ROI

[Francesca Pentimalli]

External Email - Use Caution

Dear Freesurfer experts,


I am trying to create a mask and run the analysis into it considering just
the following anatomical regions:


 (1) inferior frontal gyrus pars opercularis (IFGOp)

 (2) inferior frontal gyrus pars orbitalis (IFGOr)

 (3) inferior frontal gyrus pars triangularis (IFGTr)

 (4) Heschl3s gyrus (HG)

 (5) the superior temporal gyrus (STG)

 (6) planum polare (PP)

 (7) planum temporale (PT)

 (8) supramarginal gyrus (SMAR)

 (9) angular gyrus (AG)

(10) fusiform gyrus (FFG)

(11) inferior occipital gyrus (IOG)

(12) insula


Which technique do you suggest? Is there a good tutorial for it?

Thank you very very much!!

Best regards,

Francesca
*Francesca Pentimalli Biscaretti di Ruffia *
Via S. Eufemia 3, 35121 Padova (Italy)
Mobile: +39 3483862788
francesca.pentimallibiscarettidiruf...@studenti.unipd.it
fpentimalli...@gmail.com
fpe...@mit.edu
fp...@bu.edu
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Re: [Freesurfer] How to get a circle mask on surface

[Zhi Li]

External Email - Use Caution

Hi Bruce,

Thanks. I found a command from a previous post which seems capable of
generating a surface data file in which all the vertices = 0 except the
peak vertex:

mri_volsynth --temp $SUBJECTS_DIR/yoursubject/surf/lh.curv --pdf delta
--delta-crsf vertexno 0 0 0 --o delta.mgh

I could run this command but I am not clear how to change the vertexno,
what the three zeros denotes? If the index of my vertex is 1500 in
fsaverage, how should I change above command accordingly? In addition, what
are the meanings of flag "--pdf" and "delta"? I did not found the
description in the "mri_volsynthn".

Best regards,

Lizhi
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Re: [Freesurfer] running recon -all and trac -all from different FreeSurfer home

[Yendiki, Anastasia]

Hi Costanza - When you use "\" in a shell script to continue a command onto the 
next line, make sure that the "\" is the very last character of the line (see 
second to last entry in your bvec list.


On a separate note, you'll have to specify the bval file(s).


Best,

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Costanza Gianni' 

Sent: Wednesday, June 5, 2019 9:27:12 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] running recon -all and trac -all from different 
FreeSurfer home


External Email - Use Caution

Hi Anastasia,

I've attached the configuration file.

Best,
Costanza

Il giorno mer 5 giu 2019 alle ore 15:07 Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> ha scritto:
Hi Costanza - can you please attach your configuration file?

Best,
a.y

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Costanza Gianni' 
mailto:costanza.gia...@uniroma1.it>>
Sent: Wednesday, June 5, 2019 6:49:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] running recon -all and trac -all from different 
FreeSurfer home


External Email - Use Caution

Hello, FreeSurfer Developers,

I'm trying to run trac -all (I prepared the configuration file following the 
instructions from v. 5.3) on a set of subjects already processed with recon 
-all in another computer with a different FREESURFER HOME, and I'm getting this 
error:

Too many ('s.
INFO: SUBJECTS_DIR is /home/costanza/extra/PET/PET
INFO: Diffusion root is /home/costanza/extra/PET/PET
Actual FREESURFER_HOME /home/costanza/freesurfer
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
/home/costanza/freesurfer/bin/dmri_motion: Command not found.
/home/costanza/freesurfer/bin/dmri_group: error while loading shared libraries: 
libnetcdf.so.6: cannot open shared object file: No such file or directory
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /home/costanza/freesurfer
Previous: 
/autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013
dcmlist: Subscript out of range.

I've searched the list and I couldn't find any similar error. Do you think the 
main problem is running commands from different FREESURFER HOME?

1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
2) Ubuntu 14.04.5 LTS
3) umane -a Linux wks4 3.13.0-166-generic #216-Ubuntu SMP Thu Feb 7 14:07:53 
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

Thanks a lot for your help,

Costanza

--
Costanza Giannì, MD
Radiologist
PhD student
Sapienza University, Rome
+39 348 711 8987



___
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Fai crescere la tua università
Dona il 5 per mille alla Sapienza
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--
Costanza Giannì, MD
Radiologist
PhD student
Sapienza University, Rome
+39 348 711 8987



___
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Fai crescere la tua università
Dona il 5 per mille alla Sapienza
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Re: [Freesurfer] How to get a circle mask on surface

[Bruce Fischl]

Hi Lizhi

you could do it once on fsaverage then map the resulting label to all 
your subjects. They won't be circular in the individuals though (or really 
in fsaverage, but at least closer to circular). Or if you can find the peak 
vertex in each subject and create a label from it you can use 
mri_label2label which has a --dilate N option


cheers
Bruce




On Wed, 5 Jun 2019, Zhi Li wrote:



External Email - Use Caution

Hi Bruce,

Thank you very much for your kind reply. We have dozens of ROIs and hundreds of 
individuals, we need
to draw the mask for each individual. May I know If I could do it in command 
lines? If it is
applicable, which commands/functions should I refer to?

In addition, whether it is possible to use the index (16k+ for each surface) of 
this peak vertex in
a annotation file to draw the mask? I am not clear how the index of each vertex 
ranked in a surface,
could I found the index-vector of all the vertices in the circle mask centred 
the peak vertex? If
circle is not applicable, how about square?

Best regards,

Lizhi



On Wed, 5 Jun 2019 at 11:51, Bruce Fischl  wrote:
  Hi Lizhi

  the easiest way to approximate this is to generate a label that is just
  the peak vertex, then use the label editing tools in the current dev
  version of freeview to dilate it 4-5 times.

  cheers
  Bruce

  On Wed, 5 Jun 2019, Zhi Li
  wrote:

  >
  > External Email - Use Caution
  >
  > Dear Freesurfer experts,
  >
  > Now I would like to find the peak vertex showed significant group 
effect in a given
  ROI (e.g. left
  > insula), then draw a 5-mm-radius circle mask centred this peak point. 
May I know
  whether it is
  > applicable and how should I do it with command line? Any suggestions 
would be much
  appreciated.
  >
  > Best regards,
  >
  > Lizhi
  >
  >___
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Re: [Freesurfer] How to get a circle mask on surface

[Zhi Li]

External Email - Use Caution

Hi Bruce,

Thank you very much for your kind reply. We have dozens of ROIs and
hundreds of individuals, we need to draw the mask for each individual. May
I know If I could do it in command lines? If it is applicable, which
commands/functions should I refer to?

In addition, whether it is possible to use the index (16k+ for each
surface) of this peak vertex in a annotation file to draw the mask? I am
not clear how the index of each vertex ranked in a surface, could I found
the index-vector of all the vertices in the circle mask centred the peak
vertex? If circle is not applicable, how about square?

Best regards,

Lizhi



On Wed, 5 Jun 2019 at 11:51, Bruce Fischl 
wrote:

> Hi Lizhi
>
> the easiest way to approximate this is to generate a label that is just
> the peak vertex, then use the label editing tools in the current dev
> version of freeview to dilate it 4-5 times.
>
> cheers
> Bruce
>
> On Wed, 5 Jun 2019, Zhi Li
> wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer experts,
> >
> > Now I would like to find the peak vertex showed significant group effect
> in a given ROI (e.g. left
> > insula), then draw a 5-mm-radius circle mask centred this peak point.
> May I know whether it is
> > applicable and how should I do it with command line? Any suggestions
> would be much appreciated.
> >
> > Best regards,
> >
> > Lizhi
> >
> >___
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Re: [Freesurfer] How to get a circle mask on surface

[Bruce Fischl]

Hi Lizhi

the easiest way to approximate this is to generate a label that is just 
the peak vertex, then use the label editing tools in the current dev 
version of freeview to dilate it 4-5 times.


cheers
Bruce

On Wed, 5 Jun 2019, Zhi Li 
wrote:




External Email - Use Caution

Dear Freesurfer experts,

Now I would like to find the peak vertex showed significant group effect in a 
given ROI (e.g. left
insula), then draw a 5-mm-radius circle mask centred this peak point. May I 
know whether it is
applicable and how should I do it with command line? Any suggestions would be 
much appreciated.

Best regards,

Lizhi

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[Freesurfer] How to get a circle mask on surface

[Zhi Li]

External Email - Use Caution

Dear Freesurfer experts,

Now I would like to find the peak vertex showed significant group effect in
a given ROI (e.g. left insula), then draw a 5-mm-radius circle mask centred
this peak point. May I know whether it is applicable and how should I do it
with command line? Any suggestions would be much appreciated.

Best regards,

Lizhi
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Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Yes! The changes will probably be tiny, though.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Boris Rauchmann 

Reply-To: Freesurfer support list 
Date: Wednesday, 5 June 2019 at 15:12
To: Freesurfer support list 
Subject: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the 
amygdala


External Email - Use Caution
Dear all,

depends the Segmentation of hippocampal subfields and nuclei of the amygdala 
pipeline on the fs-recon all pipeline? I made some changes mainly by defining 
control points to fix intensity normalization in my dataset and rerun recon 
all. I´m not sure if I also have to rerun the subfields pipeline now?

Thanks,
Boris

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Re: [Freesurfer] Fwd: freesurfer picture

[Abby tang]

External Email - Use Caution

*Hi Bruce*
*I have tried freeview, but I don't know what file should be loaded in
freeview.  After qdec processing, what file format should be selected to
load freeview?*
*best wish*
*Abby*

Bruce Fischl  于2019年6月5日周三 下午9:53写道：

> Hi Abby
>
> have you tried using freeview? It is a lot more flexible than qdec and
> supports a bunch of different color maps
> cheers
> Bruce
>
>
> On Wed, 5 Jun 2019, Abby tang wrote:
>
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer Developers,
> >
> > I'm attempting to get some pictures about my results , so QDEC was used.
> However I can't adjust thos
> > e pictures which QDEC produced, such as picture1.
> >
> > When I read other's paper, they provided different pictures just like
> picture2. If there any other m
> > ethods to produce statistic pictures of brain? Can you give me some
> advices?
> >
> > Thank you for your help.
> >
> > Best regards
> >
> > Abby
> >
> >___
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[Freesurfer] CSF mask

[Marina Fernández]

External Email - Use Caution

Dear Freesurfer experts,

Is there any way to obtain a CSF mask in Freesurfer similar to that
obtained with the SPM segmentation (see attached)?

Thank you in advance.

Best regards,
Marina.
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Re: [Freesurfer] Fwd: freesurfer picture

[Bruce Fischl]

Hi Abby

have you tried using freeview? It is a lot more flexible than qdec and 
supports a bunch of different color maps

cheers
Bruce


On Wed, 5 Jun 2019, Abby tang wrote:



External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to get some pictures about my results , so QDEC was used. 
However I can't adjust thos
e pictures which QDEC produced, such as picture1.

When I read other's paper, they provided different pictures just like picture2. 
If there any other m
ethods to produce statistic pictures of brain? Can you give me some advices? 


Thank you for your help.

Best regards

Abby

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Re: [Freesurfer] running recon -all and trac -all from different FreeSurfer home

[Costanza Gianni']

External Email - Use Caution

Hi Anastasia,

I've attached the configuration file.

Best,
Costanza

Il giorno mer 5 giu 2019 alle ore 15:07 Yendiki, Anastasia <
ayend...@mgh.harvard.edu> ha scritto:

> Hi Costanza - can you please attach your configuration file?
>
> Best,
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Costanza Gianni' <
> costanza.gia...@uniroma1.it>
> *Sent:* Wednesday, June 5, 2019 6:49:02 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] running recon -all and trac -all from different
> FreeSurfer home
>
>
> External Email - Use Caution
>
> Hello, FreeSurfer Developers,
>
> I'm trying to run trac -all (I prepared the configuration file following
> the instructions from v. 5.3) on a set of subjects already processed with
> recon -all in another computer with a different FREESURFER HOME, and I'm
> getting this error:
>
> Too many ('s.
> INFO: SUBJECTS_DIR is /home/costanza/extra/PET/PET
> INFO: Diffusion root is /home/costanza/extra/PET/PET
> Actual FREESURFER_HOME /home/costanza/freesurfer
> INFO: FreeSurfer build stamps do not match
> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
> /home/costanza/freesurfer/bin/dmri_motion: Command not found.
> /home/costanza/freesurfer/bin/dmri_group: error while loading shared
> libraries: libnetcdf.so.6: cannot open shared object file: No such file or
> directory
> INFO: current FREESURFER_HOME does not match that of previous processing.
> Current: /home/costanza/freesurfer
> Previous:
> /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013
> dcmlist: Subscript out of range.
>
> I've searched the list and I couldn't find any similar error. Do you think
> the main problem is running commands from different FREESURFER HOME?
>
> 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
> 2) Ubuntu 14.04.5 LTS
> 3) umane -a Linux wks4 3.13.0-166-generic #216-Ubuntu SMP Thu Feb 7
> 14:07:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>
> Thanks a lot for your help,
>
> Costanza
>
> --
> Costanza Giannì, MD
> Radiologist
> PhD student
> Sapienza University, Rome
> +39 348 711 8987
>
>
>
> ___
> *Il tuo 5 diventa 1000*
> Fai crescere la tua università
> Dona il 5 per mille alla Sapienza
> Codice fiscale: *80209930587*
>
> https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cinque-mille
>
> ___
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-- 
Costanza Giannì, MD
Radiologist
PhD student
Sapienza University, Rome
+39 348 711 8987

-- 
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*Il tuo 5 diventa 1000*
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crescere la tua università
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# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
# 
setenv SUBJECTS_DIR /home/costanza/extra/PET/PET

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /home/costanza/extra/PET/PET

# Subject IDs
#
set subjlist = ( DOD_C01_recon \
 DOD_MS01_recon \
 DOD_MS03_recon \
 DOD_MS06_recon \
 DOD_MS07_recon \
 DOD_MS08_recon \
 DOD_MS09_recon \
 DOD_MS10_recon \
 DOD_MS12_recon \
 DOD_MS14_recon \
 DOD_MS16_recon \
 DOD_MS18_recon \
 Marco_CTRL002_recon \
 Marco_CTRL003_recon \
 Marco_CTRL009_recon \
 Marco_CTRL018_recon \
 Marco_CTRL021_recon \
 Marco_CTRL022_scan2_recon \
 Marco_CTRL033_scan1_recon \
 Marco_CTRL035_recon \
 MSPET08_recon \
 MSPET09_recon \
 MSPET10_recon \
 MSPET12_recon \
 MSPET13_recon_skullfixed \
 MSPET14_recon \
 MSPET15_recon \
 MSPET16_recon \
 MSPET17_recon \
 MSPET19_recon \
 MSPET20_recon \
 MSPET_C01_recon \
 MSPET_C02_recon \
 MSPET_C04_recon \
 MSPET_C06_recon \
 MSPET_C09_recon \
 MSPET_C11_recon \
 MSPET_C13_recon )

# In case you want to analyze only Huey and Louie
# Default: Run analysis on all subjects
#
#set runlist = (1 3)

# Input diffusion 

Re: [Freesurfer] running recon -all and trac -all from different FreeSurfer home

[Yendiki, Anastasia]

Hi Costanza - can you please attach your configuration file?

Best,
a.y

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Costanza Gianni' 

Sent: Wednesday, June 5, 2019 6:49:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] running recon -all and trac -all from different 
FreeSurfer home


External Email - Use Caution

Hello, FreeSurfer Developers,

I'm trying to run trac -all (I prepared the configuration file following the 
instructions from v. 5.3) on a set of subjects already processed with recon 
-all in another computer with a different FREESURFER HOME, and I'm getting this 
error:

Too many ('s.
INFO: SUBJECTS_DIR is /home/costanza/extra/PET/PET
INFO: Diffusion root is /home/costanza/extra/PET/PET
Actual FREESURFER_HOME /home/costanza/freesurfer
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
/home/costanza/freesurfer/bin/dmri_motion: Command not found.
/home/costanza/freesurfer/bin/dmri_group: error while loading shared libraries: 
libnetcdf.so.6: cannot open shared object file: No such file or directory
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /home/costanza/freesurfer
Previous: 
/autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013
dcmlist: Subscript out of range.

I've searched the list and I couldn't find any similar error. Do you think the 
main problem is running commands from different FREESURFER HOME?

1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
2) Ubuntu 14.04.5 LTS
3) umane -a Linux wks4 3.13.0-166-generic #216-Ubuntu SMP Thu Feb 7 14:07:53 
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

Thanks a lot for your help,

Costanza

--
Costanza Giannì, MD
Radiologist
PhD student
Sapienza University, Rome
+39 348 711 8987



___
Il tuo 5 diventa 1000
Fai crescere la tua università
Dona il 5 per mille alla Sapienza
Codice fiscale: 80209930587
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[Freesurfer] How to transfer previous FS edits to the new runs?

[Reetta-Liina Armio]

External Email - Use Caution

Dear Freesurfer experts,

I have run subcortical segmentation with FS development version 6.0. I did 
manual edits to these runs. Now I’m running the same data with FS stable 
version 6.0.

I tried to run the data with stable version from the same location so that the 
earlier brainmask file with the previous edits would be used. This did not 
happen and the previous edits were not transfered to the new runs.

How can I preseve the previous edits in these new runs?

Thank you for the help!

Best, Reetta-Liina Armio

Lähetetty iPhonesta

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[Freesurfer] running recon -all and trac -all from different FreeSurfer home

[Costanza Gianni']

External Email - Use Caution

Hello, FreeSurfer Developers,

I'm trying to run trac -all (I prepared the configuration file following
the instructions from v. 5.3) on a set of subjects already processed with
recon -all in another computer with a different FREESURFER HOME, and I'm
getting this error:

Too many ('s.
INFO: SUBJECTS_DIR is /home/costanza/extra/PET/PET
INFO: Diffusion root is /home/costanza/extra/PET/PET
Actual FREESURFER_HOME /home/costanza/freesurfer
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
/home/costanza/freesurfer/bin/dmri_motion: Command not found.
/home/costanza/freesurfer/bin/dmri_group: error while loading shared
libraries: libnetcdf.so.6: cannot open shared object file: No such file or
directory
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /home/costanza/freesurfer
Previous:
/autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013
dcmlist: Subscript out of range.

I've searched the list and I couldn't find any similar error. Do you think
the main problem is running commands from different FREESURFER HOME?

1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
2) Ubuntu 14.04.5 LTS
3) umane -a Linux wks4 3.13.0-166-generic #216-Ubuntu SMP Thu Feb 7
14:07:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

Thanks a lot for your help,

Costanza

-- 
Costanza Giannì, MD
Radiologist
PhD student
Sapienza University, Rome
+39 348 711 8987

-- 
___
*Il tuo 5 diventa 1000*
Fai 
crescere la tua università
Dona il 5 per mille alla Sapienza
Codice 
fiscale: *80209930587*

https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cinque-mille
 


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[Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

[Boris Rauchmann]

External Email - Use Caution

Dear all,

depends the Segmentation of hippocampal subfields and nuclei of the amygdala 
pipeline on the fs-recon all pipeline? I made some changes mainly by defining 
control points to fix intensity normalization in my dataset and rerun recon 
all. I´m not sure if I also have to rerun the subfields pipeline now?

Thanks, 
Boris

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[Freesurfer] Error in matlab with segmentHA_T1.sh

[stdp82]

External Email - Use Caution

I have installed matlab 2018b and removed 2014b.

When I run segmentHA_T1.sh the error reported below occurs:

MATLAB is exiting because of fatal error

/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 
37:3955 Killed: 9 
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 $args

Darwin iMac-di-Stefano.local 17.7.0 Darwin Kernel Version 17.7.0: Wed Apr 24 
21:17:24 PDT 2019; root:xnu-4570.71.45~1/RELEASE_X86_64 x86_64

T1 hippocampal subfields exited with ERRORS at Tue Jun4 00:55:25 CEST 2019

For more details, see the log file 
/Applications/freesurfer/subjects/subj/scripts/hippocampal-subfields-T1.log


Please also take in account

segmentation violation detected at Tue Jun4 00:57:53 2019



Configuration:

Crash Decoding : Disabled

Current Visual : Quartz

Default Encoding : ISO-8859-1

MATLAB Architecture: maci64

MATLAB Root: /Applications/freesurfer/MCRv84

MATLAB Version : 8.4.0.150421 (R2014b)

MATLAB Version : 8.4.0.150421 (R2014b) 

Why it does not find 2018 version?

I have follow the guidelines at 
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime 


Thanks

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