Re: [Freesurfer] recon -all errors

[Jasmin Alves]

Hi Bruce,

Thanks for the reply, I attempted to direct Subjects_dir to the folder with
my data but I received the following error.

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ export
SUBJECTS_DIR=/Desktop/Brain_Child_subs

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd
/Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all &

[1] 13867

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ ERROR: Flag all
unrecognized.

-sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all

Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin Kernel Version 14.5.0: Tue
Sep  1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64

recon-all -s joya exited with ERRORS at Mon Jan 25 21:12:58 PST 2016

Thanks so much,

Jasmin

On Mon, Jan 25, 2016 at 6:33 AM, Bruce Fischl 
wrote:

> Hi Jasmin
>
> you  need to create a directory where you have write permission and room
> for the subject reconstruction to be written to, then set the SUBJECTS_DIR
> environment variable to point to it. At the moment you are trying to use
> the subject directory we distribute, which is in some system (and
> read-only) location. You can do this on the command line of recon-all via:
>
> recon-all -sd  ...
>
> cheers
> Bruce
>
>
>
> On Sun, 24 Jan 2016, Jasmin Alves wrote:
>
> Hello Freesurfer,
>>
>> I am trying to learn freesurfer and ran into the following issues below
>> running the recon -all command.
>>
>> FREESURFER_HOME: /Applications/freesurfer
>>
>> Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>>
>> Kernel info: Darwin 14.5.0 x86_64
>>
>>   1)
>>
>> joya
>>
>>  2)
>>
>>  Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i
>> T1_original_joya.nii
>> -subject joya -all &
>>
>>
>> 3)
>>
>> [1] 12300
>>
>> Jasmins-MacBook-Pro:subjects jasminalves$ mkdir:
>> /Applications/freesurfer/subjects/joya: Permission denied
>>
>> mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied
>>
>> mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied
>>
>> cp: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No
>> such
>> file or directory
>>
>> cat: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No
>> such
>> file or directory
>>
>> INFO: FreeSurfer build stamps do not match
>>
>> Subject Stamp:
>>
>> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>>
>> INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
>>
>> Actual FREESURFER_HOME /Applications/freesurfer
>>
>> /Applications/freesurfer/subjects/joya: No such file or directory.
>>
>>
>> [1]+  Exit 1  recon-all -i T1_original_joya.nii -subject
>> joya -a
>>
>> Thank you,Jasmin
>>
>> Jasmin AlvesPredoctoral Student
>> Medical Biology Graduate Program
>> University of Southern California
>> jal...@usc.edu
>>
>>
>>
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>
>
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> 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
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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[Freesurfer] Incomplete output

[maryam koochaki]

Dear experts,I am kind of new at working with freesurfer.recon-all process has 
completed without error, but when I look at brainmask volume on freeview, one 
of the issues is that lateral ventricle is completely excluded. I have tried to 
edit it with editing the white matter volume, but no success so far. I do not 
know how to correct it. Have anybody here had the same issue? Thanks,Maryam






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Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

[Erik Lindberg]

Dear Bruce and Freesurfers,


I probably then go about this in the wrong way. My aim is to create a
binary mask for regions that I found differences in - in a
group-comparison. I then want to export the mask so I can use it as
seed area in an fMRI analysis.


Can this be done


Thanks
Eric



Hi Erik


what is the dimensionality of sig.cluster.mgh? You can tell this with mri_info.
It is problaby a surface overlay (so nvertices in one dimension), and can't
be viewed in the volume but only on the surface.

cheers
Bruce
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Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

[Bruce Fischl]

yes, but do you want to do the fMRI analysis on the surface or in the 
volume? There are lots of advantages to doing it on the surface. If your 
sig.cluster.mgh was a surface overlay then the threholded.mgh might be 
exactly what you want. Load it on an inflated surface and take a look


cheers
Bruce


On Mon, 25 Jan 2016, Erik Lindberg wrote:



Dear Bruce and Freesurfers,

I probably then go about this in the wrong way. My aim is to create a binary
 mask for regions that I found differences in - in a group-comparison. I the
n want to export the mask so I can use it as seed area in an fMRI analysis.

Can this be done

Thanks
Eric

Hi Erik

what is the dimensionality of sig.cluster.mgh? You can tell this
with mri_info. It is problaby a surface overlay (so nvertices in one
dimension), and can't be viewed in the volume but only on the surface.

cheers
Bruce


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Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

[Bruce Fischl]

Hi Erik

what is the dimensionality of sig.cluster.mgh? You can tell this with 
mri_info. It is problaby a surface overlay (so nvertices in one dimension), 
and can't be viewed in the volume but only on the surface.


cheers
Bruce


On Mon, 25 Jan 2016, Erik Lindberg wrote:



Dear Douglas and Freesufers,

 

You suggested:

mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 =
-log10(.05)

 

I tried this and was expecting that I would get a three-dimensional mask in
which the statistical significant part would be white and the rest black.

This seems not to be the case. While the program is telling me that it is
creating a mask in which x-number of voxels are included I cannot see
anything when I open the thresholded.mgh (in Freeview) Further when I look
at the dimensions of the generated image it seems to have 27307 “slices” in
one direction but only one and 6 slices in the other directions.



 

Is this the wrong approach for creating a 3-dimensional mask for the region
with the significant clusters?

 

Best

Eric


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Re: [Freesurfer] recon -all errors

[Bruce Fischl]

Hi Jasmin

you  need to create a directory where you have write permission and room 
for the subject reconstruction to be written to, then set the SUBJECTS_DIR 
environment variable to point to it. At the moment you are trying to use 
the subject directory we distribute, which is in some system (and 
read-only) location. You can do this on the command line of recon-all via:


recon-all -sd  ...

cheers
Bruce


On Sun, 24 Jan 2016, Jasmin Alves 
wrote:



Hello Freesurfer,

I am trying to learn freesurfer and ran into the following issues below
running the recon -all command. 

FREESURFER_HOME: /Applications/freesurfer

Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

Kernel info: Darwin 14.5.0 x86_64

  1) 

joya

 2) 

 Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i T1_original_joya.nii
-subject joya -all &


3)

[1] 12300 

Jasmins-MacBook-Pro:subjects jasminalves$ mkdir:
/Applications/freesurfer/subjects/joya: Permission denied

mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied

mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied

cp: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No such
file or directory

cat: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No such
file or directory

INFO: FreeSurfer build stamps do not match

Subject Stamp: 

Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects

Actual FREESURFER_HOME /Applications/freesurfer

/Applications/freesurfer/subjects/joya: No such file or directory.


[1]+  Exit 1                  recon-all -i T1_original_joya.nii -subject
joya -a

Thank you,Jasmin

Jasmin AlvesPredoctoral Student 
Medical Biology Graduate Program 
University of Southern California
jal...@usc.edu 


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[Freesurfer] R: Re: FDR map: hide very little cluster

[stdp82]

Please could you suggest me an example of command line.I'm trying from several 
day without results.Thank you very much.
Stefano




Messaggio originale

Da: Douglas Greve 

Data: 25-gen-2016 17.10

A: 

Ogg: Re: [Freesurfer] FDR map: hide very little cluster




  
  
Use the --minarea option to mri_surfcluster (not the CSD).



On 1/25/16 10:39 AM, std...@virgilio.it
  wrote:



  Hi list,
  please, could you help me because from several days I'm trying to have a 
solution.I have performed a seed-based fcMRI analysis by FAST.
  After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected 
results.I have corrected by FDR using the graphical interface provided in 
tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which 
I would like to hide in order to  present a more clear map. How is possible to 
do it?I have tried with  mri_surfcluster. To have vwsig.nii.gz I should have a 
CSD file. But this file 
  could be also produced when FDR correction is applied? I'm very confused.
  Thank you very much for your work.
  Kind regards.
Stefano
  

  
  

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Re: [Freesurfer] R: R: Re: FDR map: hide very little cluster

[Douglas N Greve]

use --o instead of --vwsig

On 01/25/2016 11:31 AM, std...@virgilio.it wrote:
>
> mri_surfcluster --in intercept/sig.nii.gz --hemi rh --sign abs 
> --no-adjust --fdr 0.05 --minarea 5 --sum summaryfile --subject 
> fsaverage --annot aparc
>
>
> produces only summary.txt
>
>
> mri_surfcluster --in intercept/sig.nii.gz --hemi rh --sign abs 
> --no-adjust --fdr 0.05 --minarea 5 --sum summaryfile --subject 
> fsaverage --annot aparc --vwsig vwsig.nii.gz
>
> ERROR: need csd with --vwsig
>
>
> How can I obtain/visualize the correspective map to summary.txt?
>
>
> Thanks,
>
>
>
> Stefano
>
>
>
> Messaggio originale
> Da: std...@virgilio.it
> Data: 25-gen-2016 17.25
> A: "Freesurfer support list"
> Ogg: [Freesurfer] R: Re: FDR map: hide very little cluster
>
> Please could you suggest me an example of command line.
> I'm trying from several day without results.
> Thank you very much.
>
> Stefano
>
> Messaggio originale
> Da: Douglas Greve 
> Data: 25-gen-2016 17.10
> A: 
> Ogg: Re: [Freesurfer] FDR map: hide very little cluster
>
> Use the --minarea option to mri_surfcluster (not the CSD).
>
> On 1/25/16 10:39 AM, std...@virgilio.it wrote:
>> Hi list,
>> please, could you help me because from several days I'm trying to 
>> have a solution.
>> I have performed a seed-based fcMRI analysis by FAST.
>> After mri_glmfit, I have obtained a sig.nii.gz which contains 
>> uncorrected results.I have corrected by FDR using the graphical interface 
>> provided in tksurfur. The FDR corrected contains some very small areas 
>> (<5-10 voxels) which I would like to hide in order to  present a more clear 
>> map. How is possible to do it?I have tried with  mri_surfcluster. To have 
>> vwsig.nii.gz I should have a CSD file. But this file
>> could be also produced when FDR correction is applied? I'm very 
>> confused.
>> Thank you very much for your work.
>> Kind regards.
>> Stefano
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>
>
> ___
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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/

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[Freesurfer] Brainstem segmentations (6.0)

[Cat Chong]

Hello Experts,
We used the brainstem segmentation that is built into FS 6.0, to interrogate 
midbrain volumes. My question was: the way FS segments the midbrain, does it 
include the cerebral peduncles? 
cheers,Cat___
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Re: [Freesurfer] Crashing with Fedora 23

[Barron, Daniel]

Hi Martin,
We’ve got the tcsh installed and seems to be working.  Can’t find a similar 
report on the list serve, so I’ve attached the bug report info below plus the 
orig_nu.log output, which is where the script is crashing. Please help!
Cheers,
Daniel

Output from buggr:
FREESURFER_HOME: /home/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
RedHat release: Fedora release 23 (Twenty Three)
Kernel info: Linux 4.3.3-300.fc23.x86_64 x86_64
Subject Name: 2_03T_N12_12_18441

Command I’m entering:
for subject in 2_03T_N12_12_18441; do
recon-all -subjid ${subject} -all -hippo-subfields
done

Error Message (from recon-all.error):
--
SUBJECT 2_03T_N12_12_18441
DATE Mon Jan 25 18:40:30 GMT 2016
USER dsbarron
HOST 
psyws26.psych.ox.ac.uk
PROCESSOR x86_64
OS Linux
Linux 
psyws26.psych.ox.ac.uk
 4.3.3-300.fc23.x86_64 #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 
GNU/Linux
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
/home/freesurfer/bin/recon-all
PWD /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri
CMD mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz

#
recon-all.log:

Mon Jan 25 18:43:18 GMT 2016
/home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441
/home/freesurfer/bin/recon-all
-subjid 2_03T_N12_12_18441 -all -hippo-subfields
subjid 2_03T_N12_12_18441
setenv SUBJECTS_DIR /home/dsbarron/Schmidt/Freesurfer
FREESURFER_HOME /home/freesurfer
Actual FREESURFER_HOME /home/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux 
psyws26.psych.ox.ac.uk
 4.3.3-300.fc23.x86_64 #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 
GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024
memorylocked 64 kbytes
maxproc  128183
maxlocks unlimited
maxsignal128183
maxmessage   819200
maxnice  0
maxrtprio0
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   32901484 2311624 1288116  1218962930174429874168
Swap:  16515068 134492415170144


program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2016/01/25-18:43:18-GMT  BuildTimeStamp: May 13 2013 
16:24:28  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ 
 User: dsbarron  Machine: 
psyws26.psych.ox.ac.uk
  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  
CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: 
$Name: stable5 $  TimeStamp: 2016/01/25-18:43:19-GMT  BuildTimeStamp: May 13 
2013 16:24:28  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve 
Exp $  User: dsbarron  Machine: 
psyws26.psych.ox.ac.uk
  Platform: Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC  
CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva 
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable5 $  TimeStamp: 2016/01/25-18:43:19-GMT  BuildTimeStamp: May 13 
2013 16:24:28  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ 
 User: dsbarron  Machine: 

Re: [Freesurfer] FDR map: hide very little cluster

[Douglas Greve]

Use the --minarea option to mri_surfcluster (not the CSD).

On 1/25/16 10:39 AM, std...@virgilio.it wrote:

Hi list,
please, could you help me because from several days I'm trying to have a 
solution.
I have performed a seed-based fcMRI analysis by FAST.
After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected 
results.I have corrected by FDR using the graphical interface provided in 
tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which 
I would like to hide in order to  present a more clear map. How is possible to do 
it?I have tried with  mri_surfcluster. To have vwsig.nii.gz I should have a CSD 
file. But this file
could be also produced when FDR correction is applied? I'm very confused.
Thank you very much for your work.
Kind regards.
Stefano


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but does not contain patient information, please contact the sender and properly
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[Freesurfer] R: R: Re: FDR map: hide very little cluster

[stdp82]

mri_surfcluster --in intercept/sig.nii.gz --hemi rh --sign abs --no-adjust 
--fdr 0.05 --minarea 5 --sum summaryfile --subject fsaverage --annot aparc 
produces only summary.txt
mri_surfcluster --in intercept/sig.nii.gz --hemi rh --sign abs --no-adjust 
--fdr 0.05 --minarea 5 --sum summaryfile --subject fsaverage --annot aparc 
--vwsig vwsig.nii.gzERROR: need csd with --vwsig
How can I obtain/visualize the correspective map to summary.txt?
Thanks,

Stefano




Messaggio originale

Da: std...@virgilio.it

Data: 25-gen-2016 17.25

A: "Freesurfer support list"

Ogg: [Freesurfer] R: Re:  FDR map: hide very little cluster



Please could you suggest me an example of command line.I'm trying from several 
day without results.Thank you very much.
Stefano




Messaggio originale

Da: Douglas Greve 

Data: 25-gen-2016 17.10

A: 

Ogg: Re: [Freesurfer] FDR map: hide very little cluster




  
  
Use the --minarea option to mri_surfcluster (not the CSD).



On 1/25/16 10:39 AM, std...@virgilio.it
  wrote:



  Hi list,
  please, could you help me because from several days I'm trying to have a 
solution.I have performed a seed-based fcMRI analysis by FAST.
  After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected 
results.I have corrected by FDR using the graphical interface provided in 
tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which 
I would like to hide in order to  present a more clear map. How is possible to 
do it?I have tried with  mri_surfcluster. To have vwsig.nii.gz I should have a 
CSD file. But this file 
  could be also produced when FDR correction is applied? I'm very confused.
  Thank you very much for your work.
  Kind regards.
Stefano
  

  
  

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[Freesurfer] separate non-contiguous labels

[dgw]

Hi,

I want to separate each label in the Yeo parcellations into each of
their separate contiguous labels. Is there a command, which can do
this in Freesurfer?

Example lh.yeo7.annot
the network 7 label has 5 non-contiguous components

Is there a command to separate these into 5 separate labels?

Thank You,
Dan
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Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

[Douglas Greve]

please remember to include previous correspondences. We can't remember 
every post ...


On 1/25/16 3:39 AM, Erik Lindberg wrote:


Dear Douglas and Freesufers,

You suggested:

mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = 
-log10(.05)


I tried this and was expecting that I would get a three-dimensional 
mask in which the statistical significant part would be white and the 
rest black.


This seems not to be the case. While the program is telling me that it 
is creating a mask in which x-number of voxels are included I cannot 
see anything when I open the thresholded.mgh (in Freeview) Further 
when I look at the dimensions of the generated image it seems to have 
27307 “slices” in one direction but only one and 6 slices in the other 
directions.




Is this the wrong approach for creating a 3-dimensional mask for the 
region with the significant clusters?


Best

Eric



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[Freesurfer] R: Re: R: Re: FDR map: hide very little cluster

[stdp82]

Please give an example of the command line.
I have performed fdr correction by tksurfer. Should I save that map?

Thanks


Stefano

>Messaggio originale
>Da: Douglas N Greve 
>Data: 25-gen-2016 17.30
>A: 
>Ogg: Re: [Freesurfer] R: Re: FDR map: hide very little cluster
>
>just use the FDR thresholded input and set --thmin to 0.5
>
>On 01/25/2016 11:21 AM, std...@virgilio.it wrote:
>> Thanks. But I do not know how I can obtain a corrected sig.nii.gz.
>> In this way I have obtained only summary.txt.
>> If I add --vwsig vwsig cds file is request.
>>
>> Stefano
>>
>> Messaggio originale
>> Da: Douglas Greve 
>> Data: 25-gen-2016 17.10
>> A: 
>> Ogg: Re: [Freesurfer] FDR map: hide very little cluster
>>
>> Use the --minarea option to mri_surfcluster (not the CSD).
>>
>> On 1/25/16 10:39 AM, std...@virgilio.it wrote:
>>> Hi list,
>>> please, could you help me because from several days I'm trying to have 
a solution.
>>> I have performed a seed-based fcMRI analysis by FAST.
>>> After mri_glmfit, I have obtained a sig.nii.gz which contains 
uncorrected results.I have corrected by FDR using the graphical interface 
provided in tksurfur. The FDR corrected contains some very small areas (<5-10 
voxels) which I would like to hide in order to  present a more clear map. How 
is possible to do it?I have tried with  mri_surfcluster. To have vwsig.nii.gz I 
should have a CSD file. But this file
>>> could be also produced when FDR correction is applied? I'm very 
confused.
>>> Thank you very much for your work.
>>> Kind regards.
>>> Stefano
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>>
>>
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>
>-- 
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>MGH-NMR Center
>gr...@nmr.mgh.harvard.edu
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>Fax: 617-726-7422
>
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>
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[Freesurfer] FDR map: hide very little cluster

[stdp82]

Hi list,please, could you help me because from several days I'm trying to have 
a solution.I have performed a seed-based fcMRI analysis by FAST.After 
mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I 
have corrected by FDR using the graphical interface provided in tksurfur. The 
FDR corrected contains some very small areas (<5-10 voxels) which I would like 
to hide in order to  present a more clear map. How is possible to do it?I have 
tried with  mri_surfcluster. To have vwsig.nii.gz I should have a CSD file. But 
this file could be also produced when FDR correction is applied? I'm very 
confused.Thank you very much for your work.Kind regards.
Stefano___
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Re: [Freesurfer] R: Re: FDR map: hide very little cluster

[Douglas N Greve]

just use the FDR thresholded input and set --thmin to 0.5

On 01/25/2016 11:21 AM, std...@virgilio.it wrote:
> Thanks. But I do not know how I can obtain a corrected sig.nii.gz.
> In this way I have obtained only summary.txt.
> If I add --vwsig vwsig cds file is request.
>
> Stefano
>
> Messaggio originale
> Da: Douglas Greve 
> Data: 25-gen-2016 17.10
> A: 
> Ogg: Re: [Freesurfer] FDR map: hide very little cluster
>
> Use the --minarea option to mri_surfcluster (not the CSD).
>
> On 1/25/16 10:39 AM, std...@virgilio.it wrote:
>> Hi list,
>> please, could you help me because from several days I'm trying to have a 
>> solution.
>> I have performed a seed-based fcMRI analysis by FAST.
>> After mri_glmfit, I have obtained a sig.nii.gz which contains 
>> uncorrected results.I have corrected by FDR using the graphical interface 
>> provided in tksurfur. The FDR corrected contains some very small areas 
>> (<5-10 voxels) which I would like to hide in order to  present a more clear 
>> map. How is possible to do it?I have tried with  mri_surfcluster. To have 
>> vwsig.nii.gz I should have a CSD file. But this file
>> could be also produced when FDR correction is applied? I'm very confused.
>> Thank you very much for your work.
>> Kind regards.
>> Stefano
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
> ___
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] mri_convert and image orientation

[Yang, Daniel]

Dear FreeSurfer experts,

I find that mri_convert will convert DICOM of structural scan to neurological 
orientation by default.

For example, mri_convert --in_type dicom --out_type mii  

Thus, the NII may need to be swapped in x for use in FSL.

In this the case?

Many thanks,
Daniel

--
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Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu
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[Freesurfer] [All] position available immediately

[Bruce Fischl]

Research Coordinator Position in Psychiatric Neuroimaging at the
MGH-Martinos Center:
 
We are looking to hire a college graduate with at least one year of research
experience and strong organizational and interpersonal skills as a full time
research coordinator.  The position involves working on or several projects
investigating the neural basis and nature of cognitive deficits in
schizophrenia and autism spectrum disorder. The techniques employed include
polysomnography (sleep electroencephaolography), functional magnetic
resonance imaging (fMRI), magneto- and electroencephalography (MEG/EEG), and
diffusion tensor imaging (DTI).  Responsibilities are varied and will
include conducting overnight sleep studies at the MGH Clinical
Research Center. The coordinator will work closely with the Principal
Investigator, lab mates, and collaborators on all aspects of the research
projects. Training in data acquisition and analysis will be
provided.  Responsibilities include managing patient studies, recruitment,
screening and characterization of participants, maintaining accurate
records, and assisting with grant applications, human subject applications,
and publications.  Knowledge of Mac and/or Linux/UNIX operating systems as
well as some programming experience are an asset, as is a high level of
comfort with novel computer applications and environments.  We use Matlab
and/or unix scripting in many of our analyses. A background in psychology,
statistics, and neuroscience is an asset.  A mentored research project
is encouraged.  The candidate must be mature and responsible with excellent
organizational, interpersonal as well as oral and written communication
skills.  S/He must be able to work independently in a fast-paced
environment, juggle and prioritize multiple tasks, feel comfortable working
with clinical and non-clinical study populations, working as part of a team
and seek assistance when appropriate.  This is an excellent research
opportunity for someone bound for graduate school in psychology, cognitive
neuroscience, or medicine.  Position is available immediately.  A two-year
commitment is required.  Please submit a resume, writing sample,
college transcript (unofficial is fine) and contact information for three
references to Dara Manoach 
Dara S. Manoach, Ph.D.
Psychiatric Neuroimaging and
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Charlestown Navy Yard
149 13th Street, Room 1.111
Charlestown, MA 02129
email: d...@nmr.mgh.harvard.edu
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[Freesurfer] R: Re: FDR map: hide very little cluster

[stdp82]

Thanks. But I do not know how I can obtain a corrected sig.nii.gz.In this way I 
have obtained only summary.txt.If I add --vwsig vwsig cds file is request.
Stefano



Messaggio originale

Da: Douglas Greve 

Data: 25-gen-2016 17.10

A: 

Ogg: Re: [Freesurfer] FDR map: hide very little cluster




  
  
Use the --minarea option to mri_surfcluster (not the CSD).



On 1/25/16 10:39 AM, std...@virgilio.it
  wrote:



  Hi list,
  please, could you help me because from several days I'm trying to have a 
solution.I have performed a seed-based fcMRI analysis by FAST.
  After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected 
results.I have corrected by FDR using the graphical interface provided in 
tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which 
I would like to hide in order to  present a more clear map. How is possible to 
do it?I have tried with  mri_surfcluster. To have vwsig.nii.gz I should have a 
CSD file. But this file 
  could be also produced when FDR correction is applied? I'm very confused.
  Thank you very much for your work.
  Kind regards.
Stefano
  

  
  

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Re: [Freesurfer] mri_convert and image orientation

[Douglas N Greve]

not necessarily. For FSL, the determinant must be less than 0 (see 
mri_info output). Having said that, even if the det<0, it may still show 
up funny in fslview

On 01/25/2016 12:11 PM, Yang, Daniel wrote:
> Dear FreeSurfer experts,
>
> I find that mri_convert will convert DICOM of structural scan to 
> neurological orientation by default.
>
> For example, mri_convert --in_type dicom --out_type mii  the DICOM directory> 
>
> Thus, the NII may need to be swapped in x for use in FSL.
>
> In this the case?
>
> Many thanks,
> Daniel
>
> -- 
> Daniel Yang, Ph.D.
> Yale Child Study Center
> E-mail: daniel.yj.y...@yale.edu
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] separate non-contiguous labels

[Douglas N Greve]

No one command, but you could
mri_annotation2label choosing the --seg as the output
mri_binarize --i seg.mgz --match NN --o seg.NN.mgz  -- NN is the index 
of your chosen seg
mri_surfcluster --in seg.NN.mgz --thmin 0.5 --olab seg.NN

this should create a seg.NN-.label for each contiuous element

On 01/25/2016 03:36 PM, dgw wrote:
> Hi,
>
> I want to separate each label in the Yeo parcellations into each of
> their separate contiguous labels. Is there a command, which can do
> this in Freesurfer?
>
> Example lh.yeo7.annot
> the network 7 label has 5 non-contiguous components
>
> Is there a command to separate these into 5 separate labels?
>
> Thank You,
> Dan
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>

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Fax: 617-726-7422

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Re: [Freesurfer] Centroid of a binary volume question

[Bruce Fischl]

sure, but I think Doug wins this round (curse you Greve!)

Bruce

On Mon, 25 Jan 
2016, pfot...@nmr.mgh.harvard.edu wrote:

> Hi Bruce and Doug,
>
> Both methods sound great. Thank you both for your help!
>
> Best,
> Panos
>
>> I don't think there is a single command line to do it, but if you can
>> get the centroid voxel from somewhere else (eg, fsl), then you can run
>> mri_volsynth --template template.nii.gz --pdf delta -delta-crsf col row
>> slice 0
>> where col row and slice are the voxel coordinates
>>
>>
>> On 01/25/2016 03:49 PM, pfot...@nmr.mgh.harvard.edu wrote:
>>> Dear FS Community,
>>>
>>> I was wondering whether there is a way to create a binary volumetric
>>> file
>>> of just the centroid of a binary volume (represented maybe as a dot of
>>> 1x1x1 mm^3 voxel size).
>>> I know how to find the coordinates of the centroid (through either the
>>> fslstats command or MATLAB), but I didn't know whether there was a way
>>> to
>>> create a new binary volume of just the centroid through the terminal. (I
>>> would do it manually, but I have ~500 binary volumes that I would like
>>> to
>>> apply the same method to).
>>> Thank you in advance for your help!
>>>
>>> Best,
>>> Panos
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>>>
>>>
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>>
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>>
>>
>
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[Freesurfer] Centroid of a binary volume question

[pfotiad]

Dear FS Community,

I was wondering whether there is a way to create a binary volumetric file
of just the centroid of a binary volume (represented maybe as a dot of
1x1x1 mm^3 voxel size).
I know how to find the coordinates of the centroid (through either the
fslstats command or MATLAB), but I didn't know whether there was a way to
create a new binary volume of just the centroid through the terminal. (I
would do it manually, but I have ~500 binary volumes that I would like to
apply the same method to).
Thank you in advance for your help!

Best,
Panos
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Re: [Freesurfer] Centroid of a binary volume question

[Bruce Fischl]

Hi Panos

why not just write a matlab script to do it? It would be easy enough. I 
don't think we have a binary that will quite do what you want
Bruce
On Mon, 25 Jan 
2016, pfot...@nmr.mgh.harvard.edu wrote:

> Dear FS Community,
>
> I was wondering whether there is a way to create a binary volumetric file
> of just the centroid of a binary volume (represented maybe as a dot of
> 1x1x1 mm^3 voxel size).
> I know how to find the coordinates of the centroid (through either the
> fslstats command or MATLAB), but I didn't know whether there was a way to
> create a new binary volume of just the centroid through the terminal. (I
> would do it manually, but I have ~500 binary volumes that I would like to
> apply the same method to).
> Thank you in advance for your help!
>
> Best,
> Panos
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] Centroid of a binary volume question

[Douglas N Greve]

I don't think there is a single command line to do it, but if you can 
get the centroid voxel from somewhere else (eg, fsl), then you can run 
mri_volsynth --template template.nii.gz --pdf delta -delta-crsf col row 
slice 0
where col row and slice are the voxel coordinates


On 01/25/2016 03:49 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Dear FS Community,
>
> I was wondering whether there is a way to create a binary volumetric file
> of just the centroid of a binary volume (represented maybe as a dot of
> 1x1x1 mm^3 voxel size).
> I know how to find the coordinates of the centroid (through either the
> fslstats command or MATLAB), but I didn't know whether there was a way to
> create a new binary volume of just the centroid through the terminal. (I
> would do it manually, but I have ~500 binary volumes that I would like to
> apply the same method to).
> Thank you in advance for your help!
>
> Best,
> Panos
> ___
> 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
gr...@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/

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Re: [Freesurfer] Centroid of a binary volume question

[pfotiad]

Hi Bruce and Doug,

Both methods sound great. Thank you both for your help!

Best,
Panos

> I don't think there is a single command line to do it, but if you can
> get the centroid voxel from somewhere else (eg, fsl), then you can run
> mri_volsynth --template template.nii.gz --pdf delta -delta-crsf col row
> slice 0
> where col row and slice are the voxel coordinates
>
>
> On 01/25/2016 03:49 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Dear FS Community,
>>
>> I was wondering whether there is a way to create a binary volumetric
>> file
>> of just the centroid of a binary volume (represented maybe as a dot of
>> 1x1x1 mm^3 voxel size).
>> I know how to find the coordinates of the centroid (through either the
>> fslstats command or MATLAB), but I didn't know whether there was a way
>> to
>> create a new binary volume of just the centroid through the terminal. (I
>> would do it manually, but I have ~500 binary volumes that I would like
>> to
>> apply the same method to).
>> Thank you in advance for your help!
>>
>> Best,
>> Panos
>> ___
>> 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
> gr...@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/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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[Freesurfer] How YOU can help FreeSurfer

[Douglas N Greve]

We are in the process of preparing a grant to support FreeSurfer 
development and maintenance:
Title: FreeSurfer Development, Maintenance, and Hardening.
PIs: Greve and Fischl.

Grant reviewers need to know that FreeSurfer is useful to a lot of 
people, so we encourage you to do one of two things:

(1) fill out the form below (probably takes less than 1min) or
(2) write a letter of support on your institution's letterhead including 
the information requested on the form and send to gr...@nmr.mgh.harvard.edu

Feel free to forward this survey to others who might not be on the 
FreeSurfer mailing list (but use FS)
Please respond by Friday Jan 29.
Thanks!
doug

https://docs.google.com/forms/d/1FreWjajItomNlmq190TYl7IS3kPXrHViPJQfjAlg2A0/viewform?c=0=1=mail_form_link
 


-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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/

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Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

[Erik Lindberg]

Dear Douglas and Freesufers,



You suggested:

mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 =
-log10(.05)



I tried this and was expecting that I would get a three-dimensional mask in
which the statistical significant part would be white and the rest black.

This seems not to be the case. While the program is telling me that it is
creating a mask in which x-number of voxels are included I cannot see
anything when I open the thresholded.mgh (in Freeview) Further when I look
at the dimensions of the generated image it seems to have 27307 “slices” in
one direction but only one and 6 slices in the other directions.





Is this the wrong approach for creating a 3-dimensional mask for the region
with the significant clusters?



Best

Eric
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[Freesurfer] hippocampal subfields - multispectral segmentation with FLAIR

[Luigi Antelmi]

Dear members,

in our center we are  evaluating whether to introduce a T2 into a protocol
that, among others, already includes a T1 and a FLAIR sequences.

Our main concern is to to maximize the information-to-duration ratio of the
entire protocol.

In order to improve the subfields' segmentation we read that it is better
to add a T2 or "other" sequences.

Will the FLAIR alone (+T1)  can work well as the T2?

If instead the T2 is preferable, what is the coarsest-but-still-informative
resolution you suggest?

Thank you for sharing your experience!

Have a nice day,
Luigi.
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Re: [Freesurfer] hippocampal subfields - multispectral segmentation with FLAIR

[Eugenio Iglesias]

Ciao Luigi, 
I haven't tried FLAIR for images the subfields, but if you sent me a high-res 
FLAIR acquisition of the hippocampus, I could take a look. 
If you are doing T2, you could implement the procotol used in ADNI: coronal 
slices with 0.4x0.4 in plane resolution, with 2mm slice separation (ideally, 
you would position the box in an slightly oblique positions such that the 
coronal slices cut the hippocampus perpendicularly to it major axis). 
Cheers, 
Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Luigi Antelmi"  
To: "Freesurfer support list"  
Sent: Monday, January 25, 2016 9:43:29 AM 
Subject: [Freesurfer] hippocampal subfields - multispectral segmentation with 
FLAIR 

Dear members, 

in our center we are evaluating whether to introduce a T2 into a protocol that, 
among others, already includes a T1 and a FLAIR sequences. 

Our main concern is to to maximize the information-to-duration ratio of the 
entire protocol. 

In order to improve the subfields' segmentation we read that it is better to 
add a T2 or "other" sequences. 

Will the FLAIR alone (+T1) can work well as the T2? 

If instead the T2 is preferable, what is the coarsest-but-still-informative 
resolution you suggest? 

Thank you for sharing your experience! 

Have a nice day, 
Luigi. 

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properly 
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[Freesurfer] Qdec ROI Analysis

[Larissa McKetton]

Dear Freesurfer community,

I am working on an ROI analysis using qdec. I have created all aseg and
aparc stats files and would like to determine if there are any differences
in volume, surface area, and thickness for certain structures between two
groups. I was wondering with the analysis, would it be okay to use the
resulting aseg/aparc output stats from either the Desikan/Destrieux atlases
and run these values through SPSS or is it better to draw ROI labels on the
fsaverage brain, apply the label to each subject, and run the analyses this
way. I am asking because the following tutorial states:

*"Note*: If you want to use a pre-existing label and register it to
fsaverage, be aware that this might involve two instances of resampling and
the results might not be as accurate as they would be if you drew the label
on fsaverage. Please contact the FreeSurfer team to get more details on
this process if you have any concerns."

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI#TableoftheaveragethicknessofeachcorticalparcellationintheDestrieuxatlas

If drawing labels on the fsaverage brain and applying them to each subject
is the way to go- would I need to correct for multiple comparisons?

Many thanks,
Larissa
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