Re: [Freesurfer] Projecting meta-analytic map on the surface

[Thomas Yeo]

External Email - Use Caution

Hi Srishti,

We recently wrote a paper on projecting data from Colin27/MNI152 to
fsaverage surface (https://www.biorxiv.org/content/early/2018/04/27/302794).
The paper is in press at HBM.

The code is available here:
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion

Regards,
Thomas

On Thu, May 10, 2018 at 9:03 AM, srishti goel <23srishtig...@gmail.com>
wrote:

> External Email - Use Caution
>
> Hello Freesurfers,
>
> I have a network based map that has been produced from a meta analysis
> using NeuroElf on the standard colins template. I want to project this map
> on the surface of an MNI template.
> Does anyone have thoughts about how that could be achieved?
>
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu
> skype: srishti.goel12
>
>
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[Freesurfer] Projecting meta-analytic map on the surface

[srishti goel]

External Email - Use Caution

Hello Freesurfers,

I have a network based map that has been produced from a meta analysis
using NeuroElf on the standard colins template. I want to project this map
on the surface of an MNI template.
Does anyone have thoughts about how that could be achieved?

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12
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[Freesurfer] Extract time-courses by ROI from preproc-sess preprocessed data

[Ben Smith]

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I have an event-related paradigm with variable length, and I would like to
get a functional activity parcellation ROI measurement for each trial
individually in order to enter into a reinforcement learning model at a
trial level.

Can I extract ROIs for parcellations directly from preprocessing output
(e.g., fmcpr.sm5.fsaverage.rh.nii.gz) created by preproc-sess? I would then
apply an HRF gamma function myself to each time series and then match each
trial to the activity at that time point.

I initially tried creating paradigm files for mkanalysis-sess where every
trial was essentially its own condition. But this seems clumsy and might
not work well because there's a differing number of 'conditions' (trials)
in different subjects and runs.

So now I'm wondering if there's a way to extract time courses associated
with each cortical parcellation? So, for instance with the Destrieux Atlas
there are 58 parcellation units, so for each session I would be ultimately
looking for a 58**t* matrix where *t* is the number of time points in that
session.

I've already run the anatomical parcellations, so I'd think the next step
is to match those to the preprocessed functional data
like fmcpr.sm5.fsaverage.rh.nii.gz, then extract across the time course.

I tried:

mri_segstats \
 --seg functional_preprocessed/sub261sess/bold/004/fmcpr.sm5.fsaverage.rh.nii.gz
\
 --annot $SUBJECTS_DIR/msm20171025T154741sub261/label/rh.aparc.annot \
 --avgwf testoutavgwf.dat --sum testoutsum.dat

This ran, but didn't create testoutavgwf.dat in the working directory,
though I did get a testoutsum.dat. But the time course is what I'm looking
for in this case.

Is it possible to do what I'm doing or should I be inputing a result from
vol2surf instead of from preprocessing output?

Thanks in advance for any help you can provide!

Best regards

Ben Smith
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Re: [Freesurfer] mri_vol2surf

[Martin Reuter]

Hi,Yes the longitudinal images after the long run are all aligned in the base space. You will find the map from each time point to the base in the base MRI transforms dir (maybe also in the long MRI transforms). Naming should make clear what reach one is.Best MartinAm 09.05.2018 21:11 schrieb "Douglas N. Greve" :There is a registration file that gets created by the longitudinal 

processing that can be used with mri_vol2vol. I don't know where the LTA 

file is, but maybe Martin can weigh in.





On 05/08/2018 12:31 PM, Abdullah Ishaque wrote:

>

>

> Hi,

>

> I figured that part out: I can't load surfaces as volumes in freeview, 

> but rather i need to load them as an overlay to the subject white, or 

> pial surfaces.

>

> I have another question for which I can't find an answer to. After 

> registering myelin maps to the individual subjects, how do I 

> register/transform them into the subjects' longitudinal T1s (obtained 

> after the recon-all long command)?

>

> The broad goal that I am trying to achieve is longitudinal myelin 

> analysis. Any feedback is appreciated. Thanks!

>

> On Tue, Apr 24, 2018 at 1:30 PM, Abdullah Ishaque 

> > wrote:

>

> I did: mri_vol2surf --src Myelin_conformed.mgz --out

> C01_myelin.mgz --regheader C01 --hemi lh --projfrac 0.5

>

> Now I'm just getting the error "freadFloat: fread failed" a whole

> bunch of times and the terminal gets stuck. Any suggestions?

>

> I checked Myelin_conformed.mgz and loaded it with orig.mgz in

> freeview and they look fine with great overlap and registration

>

> Thanks!

>

> On Tue, Apr 24, 2018 at 1:23 PM, Douglas Greve

> > wrote:

>

> Specify a file format for the output (eg, C01.mgz)

>

>

> On 4/24/18 3:17 PM, Abdullah Ishaque wrote:

>>

>>

>> Hi,

>>

>> Thank you for the prompt response.

>>

>> I used the following command:

>>

>> mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after

>> mri_vol2vol from the previous step) --out C01 --regheader C01

>> --hemi lh --projfrac 0.5

>>

>> This created two files called COR-.info and COR001. I tried

>> loaded the COR001 file into freeview and tksurfer, but I keep

>> the error "MRISalloc(8229512, 76): could allocated faces \

>> cannot allocate memory

>>

>> Am I making a mistake somewhere?

>>

>> Thanks,

>>

>> On Tue, Apr 24, 2018 at 11:34 AM, Douglas Greve

>> > wrote:

>>

>> That all looks correct. For the registration, just use

>> --regheader C01

>>

>>

>> On 4/24/18 11:12 AM, Abdullah Ishaque wrote:

>>>

>>>

>>> Hi,

>>>

>>> It's my first time using FreeSurfer and I'd like some

>>> guidance regarding some of my steps.

>>>

>>> I'm attempting to perform myelin mapping as outlined in

>>> the paper by Righart (2017) Ann Neurol. Overall, I want

>>> to calculate myelin maps from each subject, sample them

>>> from the mid-cortical level to create cortical myelin

>>> surface maps, and perform vertexwise and ROI based analyses.

>>>

>>> Here's what I've done so far:

>>>

>>> 1. recon-all for all the subjects

>>> 2. Used bbregister to register the native T2 scans to

>>> the conformed T1 scans using this command: bbregister

>>> --s C01 --mov C01_T2.nii --init-fsl --reg register.dat

>>> --t2 (my understanding here is that this generates the

>>> .dat file that has the transformation to register the T2

>>> image to the conformed orig.mgz file from subject C01)

>>> 3. Applied the register.dat file to the native T2 using

>>> mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz

>>> --fstarg --reg register.dat (this registers the T2 to

>>> the orig.mgz file in the conformed space)

>>>

>>> The next step for me is to perform mri_vol2surf. My

>>> question here is, which file should I select for the

>>> --srcreg flag and what should the --trgsubject input be?

>>> Secondly, am I on the right track to complete the

>>> analysis i.e., correct file types and my understanding

>>> of the steps? Clarifications regarding these questions

>>> and any suggestions for further directions will be very

>>> helpful!

>>>

>>> Let me know. Thanks!

>>>

>>>

>>> ___

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>>> Freesurfer@nmr.mgh.harvard.edu

>>> 

Re: [Freesurfer] inherent smoothing

[Glasser, Matthew]

External Email - Use Caution

You can do this in Connectome Workbench with wb_command
-metric-estimate-fwhm if you convert the thickness map and surface to
GIFTI with mris_convert.

Peace,

Matt.

On 5/9/18, 2:14 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N. Greve"  wrote:

>Not that I know of. I don''t know what it would mean
>
>
>
>On 05/09/2018 12:14 PM, Joost Janssen wrote:
>>
>>
>> Can it be done without (before) running a group analysis?
>> Thanks,
>> -joost
>> 
>>>4486> 
>>
>>
>>
>>
>> On Tue, May 8, 2018 at 6:07 PM, Douglas N. Greve
>> > wrote:
>>
>> If you run a group analysis, there will be a fwhm.dat file with the
>> estimate of the Gaussian full width half max. The smoothess is not
>> Gaussian, but it gives a measure. Does that work?
>>
>>
>> On 05/08/2018 04:20 AM, Joost Janssen wrote:
>> >
>> >
>> > Dear Doug,
>> >
>> > I'd like to determine the inherent smoothing of ?h.thickness in my
>> > sample. What is the best way to do this?
>> >
>> > Thanks,
>> > -joost
>> >
>> >
>> >
>> >
>> > ___
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>> 
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>>
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>>
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>> 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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Re: [Freesurfer] Errors are occurring after FreeSurfer Installation

[Dicamillo, Robert]

Hello Stefano,

It looks like you do not have permission to write to
/usr/local/freesurfer/subjects/bert

If multiple people will be using the data there at
the same time, then it is probably not a good idea
for everyone not to be writing to the same location.

An alternative is to set the environment variable
SUBJECTS_DIR to point to a copy of the ./bert
subdirectory under a path you can both read from and write to.

I think the ./bert subdir is about 400M, so you could
try copying it somewhere, e.g., to your $HOME
directory.  So if you ended up with $HOME/bert
as the path to the data, then you would set
SUBJECTS_DIR to $HOME in your shell.

- rob

On May 9, 2018, at 1:20 PM, std...@virgilio.it wrote:


External Email - Use Caution


This errors are occurring when we test FreeSurfer Installation on our server:

1) ubuntu01:/usr/local/freesurfer/subjects> mri_convert sample-001.mgz 
sample-001.nii.gz
mri_convert.bin sample-001.mgz sample-001.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from sample-001.mgz...
TR=7.25, TE=3.22, TI=600.00, flip angle=7.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to sample-001.nii.gz...
niiWrite(): error opening file sample-001.nii.gz
ERROR: failure writing sample-001.nii.gz

2) ubuntu01:/usr/local/freesurfer/subjects> recon-all -i sample-001.nii.gz -s 
bert -all
mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': 
Permission denied
mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': 
Permission denied
mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': 
Permission denied
cp: cannot create regular file 
'/usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt': No such file or 
directory
cat: /usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt: No such file 
or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
/usr/local/freesurfer/subjects/bert/scripts/patchdir.txt: No such file or 
directory.

3) ubuntu01:/usr/local/freesurfer/subjects> freeview -v sample-001.mgz
freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open 
shared object file: No such file or directory


Thanks

Stefano

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Re: [Freesurfer] inherent smoothing

[Douglas N. Greve]

Not that I know of. I don''t know what it would mean



On 05/09/2018 12:14 PM, Joost Janssen wrote:
>
>
> Can it be done without (before) running a group analysis?
> Thanks,
> -joost
> 
>  
>
>
>
>
> On Tue, May 8, 2018 at 6:07 PM, Douglas N. Greve 
> > wrote:
>
> If you run a group analysis, there will be a fwhm.dat file with the
> estimate of the Gaussian full width half max. The smoothess is not
> Gaussian, but it gives a measure. Does that work?
>
>
> On 05/08/2018 04:20 AM, Joost Janssen wrote:
> >
> >
> > Dear Doug,
> >
> > I'd like to determine the inherent smoothing of ?h.thickness in my
> > sample. What is the best way to do this?
> >
> > Thanks,
> > -joost
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
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> 
>
>
> 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
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> to you in error
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Re: [Freesurfer] recon-all(about Installation' command) error

[Douglas N. Greve]

Your cp command failed. You'll need somethin glike

cp $FREESURFER_HOME/subjects/sample-001.mgz sample-001.mgz


On 05/09/2018 12:45 AM, subin oh wrote:
>
> Hello, Freesurfer Developer
> when I run the 'Test your FreeSurfer Installation' command 
> (Example1~Example3)(https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>  
> )
>
>
> I got the following errors pop up like this:
> Sorry for I'm a beginner..
> Thanks very much for any suggestions!
> Best Regards,
> Subin Oh
> -[Example1~Example2]-
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer/
> FSFAST_HOME   /Applications/freesurfer//fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Applications/freesurfer//subjects
> MNI_DIR   /Applications/freesurfer//mni
> FSL_DIR   /usr/local/fsl
> bash-3.2$ export c
> bash-3.2$ export SUBJECTS_DIR=/Application/freesurfer/subjects/subj01
> bash-3.2$ cp $FREESURFER_HOME/subjects/sample-001.mgz
> usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file
> cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... 
> target_directoy
> bash-3.2$ mri_convert sample-001.mgz sample-001.nii.gz
> mri_convert sample-001.mgz sample-001.nii.gz
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from sample-001.mgz...
> mghRead(/Users/chan/sample-001.mgz, -1): could not open file
> bash-3.2$ mri_convert sample-001.mgz fsample-001.nii.gz
> mri_convert sample-001.mgz fsample-001.nii.gz
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from sample-001.mgz...
> mghRead(/Users/chan/sample-001.mgz, -1): could not open file
> bash-3.2$ mri_convert sample-001.mgz fsample-001.nii.gz
> mri_convert sample-001.mgz fsample-001.nii.gz
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from sample-001.mgz...
> mghRead(/Users/chan/sample-001.mgz, -1): could not open file
> bash-3.2$ export SUBJECTS_DIR=/Applications/freesurfer/subjects/subj01
> bash-3.2$ recon-all -i sample-001.nii.gz -s subj01 -all
> ERROR: cannot find sample-001.nii.gz
> Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 
> 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64
>
> recon-all -s  exited with ERRORS at Wed May  9 12:43:41 KST 2018
>
> For more details, see the log file
> To report a problem, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
> 
>
> bash-3.2$ recon-all -i fsample-001.nii.gz -s subj01 -all
> ERROR: cannot find fsample-001.nii.gz
> Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 
> 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64
>
> recon-all -s  exited with ERRORS at Wed May  9 12:43:50 KST 2018
>
> For more details, see the log file
> To report a problem, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
> 
> -
> ---[Example3]
> bash-3.2$ export SUBJECTS_DIR=/Applications/freesurfer/subjects/
> bash-3.2$ recon-all -s subj01 -all
> Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
> Actual FREESURFER_HOME /Applications/freesurfer
> Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 
> 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64
> #
> #@# MotionCor Wed May  9 12:56:55 KST 2018
> ERROR: no run data found in /Applications/freesurfer/subjects/subj01/mri. 
> Make sure to
> have a volume called 001.mgz in  
> /Applications/freesurfer/subjects/subj01/mri/orig.
> If you have a second run of data call it 002.mgz, etc.
> See also:http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion 
> 
> Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 
> 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64
>
> recon-all -s subj01 exited with ERRORS at Wed May  9 12:56:55 KST 2018
>
> For more details, see the log file 
> /Applications/freesurfer/subjects/subj01/scripts/recon-all.log
> To report a problem, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
> 
>
> 
>
>
>
>
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Re: [Freesurfer] mri_vol2surf

[Douglas N. Greve]

There is a registration file that gets created by the longitudinal 
processing that can be used with mri_vol2vol. I don't know where the LTA 
file is, but maybe Martin can weigh in.


On 05/08/2018 12:31 PM, Abdullah Ishaque wrote:
>
>
> Hi,
>
> I figured that part out: I can't load surfaces as volumes in freeview, 
> but rather i need to load them as an overlay to the subject white, or 
> pial surfaces.
>
> I have another question for which I can't find an answer to. After 
> registering myelin maps to the individual subjects, how do I 
> register/transform them into the subjects' longitudinal T1s (obtained 
> after the recon-all long command)?
>
> The broad goal that I am trying to achieve is longitudinal myelin 
> analysis. Any feedback is appreciated. Thanks!
>
> On Tue, Apr 24, 2018 at 1:30 PM, Abdullah Ishaque 
> > wrote:
>
> I did: mri_vol2surf --src Myelin_conformed.mgz --out
> C01_myelin.mgz --regheader C01 --hemi lh --projfrac 0.5
>
> Now I'm just getting the error "freadFloat: fread failed" a whole
> bunch of times and the terminal gets stuck. Any suggestions?
>
> I checked Myelin_conformed.mgz and loaded it with orig.mgz in
> freeview and they look fine with great overlap and registration
>
> Thanks!
>
> On Tue, Apr 24, 2018 at 1:23 PM, Douglas Greve
> > wrote:
>
> Specify a file format for the output (eg, C01.mgz)
>
>
> On 4/24/18 3:17 PM, Abdullah Ishaque wrote:
>>
>>
>> Hi,
>>
>> Thank you for the prompt response.
>>
>> I used the following command:
>>
>> mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after
>> mri_vol2vol from the previous step) --out C01 --regheader C01
>> --hemi lh --projfrac 0.5
>>
>> This created two files called COR-.info and COR001. I tried
>> loaded the COR001 file into freeview and tksurfer, but I keep
>> the error "MRISalloc(8229512, 76): could allocated faces \
>> cannot allocate memory
>>
>> Am I making a mistake somewhere?
>>
>> Thanks,
>>
>> On Tue, Apr 24, 2018 at 11:34 AM, Douglas Greve
>> > wrote:
>>
>> That all looks correct. For the registration, just use
>> --regheader C01
>>
>>
>> On 4/24/18 11:12 AM, Abdullah Ishaque wrote:
>>>
>>>
>>> Hi,
>>>
>>> It's my first time using FreeSurfer and I'd like some
>>> guidance regarding some of my steps.
>>>
>>> I'm attempting to perform myelin mapping as outlined in
>>> the paper by Righart (2017) Ann Neurol. Overall, I want
>>> to calculate myelin maps from each subject, sample them
>>> from the mid-cortical level to create cortical myelin
>>> surface maps, and perform vertexwise and ROI based analyses.
>>>
>>> Here's what I've done so far:
>>>
>>> 1. recon-all for all the subjects
>>> 2. Used bbregister to register the native T2 scans to
>>> the conformed T1 scans using this command: bbregister
>>> --s C01 --mov C01_T2.nii --init-fsl --reg register.dat
>>> --t2 (my understanding here is that this generates the
>>> .dat file that has the transformation to register the T2
>>> image to the conformed orig.mgz file from subject C01)
>>> 3. Applied the register.dat file to the native T2 using
>>> mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz
>>> --fstarg --reg register.dat (this registers the T2 to
>>> the orig.mgz file in the conformed space)
>>>
>>> The next step for me is to perform mri_vol2surf. My
>>> question here is, which file should I select for the
>>> --srcreg flag and what should the --trgsubject input be?
>>> Secondly, am I on the right track to complete the
>>> analysis i.e., correct file types and my understanding
>>> of the steps? Clarifications regarding these questions
>>> and any suggestions for further directions will be very
>>> helpful!
>>>
>>> Let me know. Thanks!
>>>
>>>
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>>> Freesurfer@nmr.mgh.harvard.edu
>>> 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>
>>
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>> 
>> 

[Freesurfer] Errors are occurring after FreeSurfer Installation

[stdp82]

External Email - Use Caution

This errors are occurring when we test FreeSurfer Installation on our server:

1) ubuntu01:/usr/local/freesurfer/subjects> mri_convert sample-001.mgz 
sample-001.nii.gz
mri_convert.bin sample-001.mgz sample-001.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from sample-001.mgz...
TR=7.25, TE=3.22, TI=600.00, flip angle=7.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to sample-001.nii.gz...
niiWrite(): error opening file sample-001.nii.gz
ERROR: failure writing sample-001.nii.gz

2) ubuntu01:/usr/local/freesurfer/subjects> recon-all -i sample-001.nii.gz -s 
bert -all
mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': 
Permission denied
mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': 
Permission denied
mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': 
Permission denied
cp: cannot create regular file 
'/usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt': No such file or 
directory
cat: /usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt: No such file 
or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
/usr/local/freesurfer/subjects/bert/scripts/patchdir.txt: No such file or 
directory.

3) ubuntu01:/usr/local/freesurfer/subjects> freeview -v sample-001.mgz
freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open 
shared object file: No such file or directory


Thanks


Stefano
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Re: [Freesurfer] inherent smoothing

[Joost Janssen]

External Email - Use Caution

Can it be done without (before) running a group analysis?
Thanks,
-joost




On Tue, May 8, 2018 at 6:07 PM, Douglas N. Greve 
wrote:

> If you run a group analysis, there will be a fwhm.dat file with the
> estimate of the Gaussian full width half max. The smoothess is not
> Gaussian, but it gives a measure. Does that work?
>
>
> On 05/08/2018 04:20 AM, Joost Janssen wrote:
> >
> >
> > Dear Doug,
> >
> > I'd like to determine the inherent smoothing of ?h.thickness in my
> > sample. What is the best way to do this?
> >
> > Thanks,
> > -joost
> >
> >
> >
> >
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> 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
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