Re: [Freesurfer] help

[Dilip Puri]

Hi everyone,

when I used following command:

mri_binarize --i myfile.img --match 17 --binval -1 --o your.lefthippo.nii.gz

then I got output your.lefthippo.nii.gz file when I read this file using
FREEVIEW then it completly different from original mask.



Thanks

Dilip​

On Thu, Apr 6, 2017 at 11:08 PM, Bruce Fischl 
wrote:

> Hi Dilip
>
> yes, freesurfer will do this for you, although the labels will be 17 for
> left hippocampus and 53 for right.
>
> cheers
> Bruce
> On Thu, 6 Apr 2017, Dilip Puri wrote:
>
> > Hi everyone,
> >
> > I am working on Hippocampus segmentation using Neural Networks for that
> I need labeled images of Hippocampus corresponding to original images.
> >
> > I am using OASIS Dataset for this. I want to generate labeled images
> using FREESURFER. Is there any way to label each 3D co-ordinate
> > HippoCampus -1
> > Otherwise - 0
> >
> > Here are sample files link
> >
> > Kindly help me!
> >
> >
> > Dilip Puri
> > IIIT Vadodara
> >
> >
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Re: [Freesurfer] long mri_ca_register error

[Chris Adamson]

Just the standard pipeline.

recon-all -s cross1 -all -bigventricles
recon-all -base cross -tp cross1 ... -all -bigventricles
recon-all -long cross1 cross -all -bigventricles

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Friday, 7 April 2017 3:37 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] long mri_ca_register error

Hi Chris

it's possible we never looked at -bigventricle in the long stage. What was your 
recon-all command line?

cheers
Bruce
On Thu, 6 Apr 2017, Chris Adamson wrote:

> 
> It happens when I use -bigventricles.
> 
>  
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris 
> Adamson
> Sent: Thursday, 6 April 2017 12:27 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] long mri_ca_register error
> 
>  
> 
> Freesurfer devs,
> 
>  
> 
> In freesurfer 6 stable I’m having a problem at the careg stage of the 
> long. The relevant recon-all log is pasted below. Could you point me to where 
> to debug this problem?
> 
>  
> 
> Cheers,
> 
>  
> 
> Chris.
> 
>  
> 
> mri_ca_register -rusage 
> 136_S_0426_20070604.long.136_S_0426/touch/rusage.mri_ca_register.dat 
> -bigventricles -smoothness 0.5 -levels 2 -A 1 -l 
> *base*/transforms/talairach.m3z identity.nofile -align-after -mask 
> brainmask.mgz norm.mgz 
> /usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
> transforms/talairach.m3z
> 
>  
> 
> handling expanded ventricles...
> 
> l_smoothness = 0.50
> 
> levels = 2
> 
> smoothing gradient with 1 averages...
> 
> reading previously computed atlas xform 
> /isilon/data/addo/ADNI3T/freesurfer6/136_S_0426/mri/transforms/talaira
> ch.m3z and applying inverse registration identity.nofile
> 
> renormalizing sequences with structure alignment, equivalent to:
> 
>     -renormalize
> 
>     -regularize_mean 0.500
> 
>     -regularize 0.500
> 
> using MR volume brainmask.mgz to mask input volume...
> 
>  
> 
> == Number of threads available to mri_ca_register for OpenMP = 2 ==
> 
> reading 1 input volumes...
> 
> logging results to talairach.log
> 
> reading input volume 'norm.mgz'...
> 
> reading GCA 
> '/usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
> 
> label assignment complete, 0 changed (0.00%)
> 
> TransformSample: gcam has not been inverted!
> 
> freeing gibbs priors...done.
> 
> average std[0] = 5.0
> 
> setting orig areas to linear transform determinant scaled 8.40
> 
> writing talairach.invalid.mgz
> 
> writing talairach.status.mgz
> 
> registering ventricular system...
> 
> using threshold 45.0 from atlas ventricle (20.1 +- 5.0) and caudate 
> (70.0 +- 5.0) distributions for initial ventricular estimate
> 
> No such file or directory
> 
> TransformSample: gcam has not been inverted!
> 
> No such file or directory
> 
> TransformSample: gcam has not been inverted!
> 
> No such file or directory
> 
> TransformSample: gcam has not been inverted!
> 
> No such file or directory
> 
> TransformSample: gcam has not been inverted!
> 
> No such file or directory
> 
> TransformSample: gcam has not been inverted!
> 
> No such file or directory
> 
> TransformSample: gcam has not been inverted!
> 
> No such file or directory
> 
> TransformSample: gcam has not been inverted!
> 
> No such file or directory
> 
> TransformSample: gcam has not been inverted!
> 
> No such file or directory
> 
> TransformSample: gcam has not been inverted!
> 
> No such file or directory
> 
> TransformSample: gcam has not been inverted!
> 
> No such file or directory
> 
> TransformSample: gcam has not been inverted!
> 
> No such file or directory
> 
>  
> 
> Dr Chris Adamson
> 
> Senior Research Officer
> 
> Developmental Imaging, Clinical Sciences
> 
>  
> 
> Murdoch Childrens Research Institute
> 
> The Royal Children’s Hospital
> 
> Flemington Road, Parkville, VIC 3052 Australia
> 
> E chris.adam...@mcri.edu.au
> 
> www.mcri.edu.au
> 
>  
> 
>  
> 
> This e-mail and any attachments to it (the "Communication") are, 
> unless otherwise stated, confidential, may contain copyright material 
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> 
>  
> 
> P Please consider the environment before printing this email
> 
>  
> 
> 
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Re: [Freesurfer] MRIread (load_nifti)- Out of memory

[Ilaria Sani]

Hi Doug,

Thanks for the tip. I can load the volume now!

I'm getting different types of errors when I proceed with my analyses though.

Can you help me to understand why it works when data are decompressed and in 
what way data are different now.


Thanks a lot,
Ilaria

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Thursday, April 6, 2017 3:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory

is it a compressed nifti (nii.gz)? If so, try uncompressing it first


On 04/06/2017 02:53 PM, Ilaria Sani wrote:
> Hi Bruce,
>
> Not sure this answer your question...
>
> In matlab workspace, I am able to load data in two halves:
>
> H1=MRIread(half1)
> H2=MRIread(half2)
>
> And then concatenate the volumes
> concatenate them var=cat(4,H1,H2).
>
> So, somehow matlab can handle...
>
> However, when those operations are embedded inside a function (like in the 
> case of load_nifti and MRIread) I get the error.
>
>
> Thanks,
> Ilaria
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
> Fischl
> Sent: Thursday, April 6, 2017 1:36 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
>
> Hi Ilaria
>
> do you have any reason to believe that it isn't just out of memory? If 
> so, there's not much to do other than get more RAM or use a different 
> machine
>
> cheers
> Bruce
>
>
> On Thu,
> 6 Apr 2017, Ilaria Sani wrote:
>
>> Dear All,
>>
>>   
>>
>> I’m trying to load a pretty big diffusion MRI dataset (320x320x260x122).
>>
>> I’m running matlab 2015a 64bit on a linux machine.
>>
>>   
>>
>> I’m using MRIread, which in turn calls load_nifti.
>>
>> I’m getting the following error:
>>
>>   
>>
>> Error using  +
>>
>> Out of memory. Type HELP MEMORY for your options.
>>
>>   
>>
>> Error in load_nifti (line 158)
>>
>>hdr.vol = hdr.vol * hdr.scl_slope  + hdr.scl_inter;
>>
>>   
>>
>> Error in MRIread (line 158)
>>
>> hdr = load_nifti(fspec,headeronly);
>>
>>   
>>
>> When I load half dataset (320x320x260x61) it works ok.
>>
>> I tried to increase the Maximum array size in Matalb (default 1,000 - now 
>> 10,000), but I’m still getting the error.
>>
>> I tried to change machine (which runs matlab 2013a on linux) and it worked 
>> fine.
>>
>>   
>>
>> I think this is due to some matlab settings.
>>
>> Can anyone help?
>>
>>   
>>
>> Thanks a lot,
>>
>> Ilaria
>>
>>   
>>
>>   
>>
>> ---
>> Ilaria Sani, PhD
>> Postdoctoral Fellow, Freiwald Lab
>> The Rockefeller University
>> 1230 York Ave., New York, NY 10065.
>> Phone: (212) 327 7699
>> Fax: (212) 327 7698
>> Email: isan...@rockefeller.edu
>>
>>   
>>
>>
>>
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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

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Re: [Freesurfer] Ventricle-to-Brain Ratio

[Gullickson, James]

Doug,

Thanks for your reply.

Difference between the two TVV methods ranges between 1-6%
Difference between the two TBV methods ranges between 2-4%

Basically, my question is two-fold:

a) what is the most accurate representation of total ventricular volume
b) what is the most accurate representation of total brain volume (all
parenchyma)

Best,

James

On Thu, Apr 6, 2017 at 3:17 PM, Douglas N Greve 
wrote:

> that looks right. how different are the values?
>
>
> On 04/05/2017 10:58 AM, Gullickson, James wrote:
> > Hello all,
> >
> > I want to calculate a Ventricle-to-Brain ratio (VBR) as a measure of
> > parenchymal atrophy using Freesurfer version 5.3.0. I have tried to go
> > about this using the aseg.stats output (using asegstats2table), but am
> > running into inconsistencies.
> >
> > The basic calculation for VBR is:
> >
> > (Total Ventricular Volume/Total Brain Volume) * 100
> >
> > i.e. Bigler, E. D. (2013). Traumatic brain injury, neuroimaging, and
> > neurodegeneration. /Frontiers in human neuroscience/, /7/, 395.
> >
> >
> > What is the best way to get Total Ventricular Volume (TVV) and Total
> > Brain Volume (TBV) for this calculation? I have tried several ways,
> > which lead to different values:
> >
> > TVV = left lateral ventricle + left inf lateral ventricle + right
> > lateral ventricle + right inf lateral ventricle + 3rd ventricle + 4th
> > ventricle + 5th ventricle + choroid plexus
> >
> > which gives me a different result than
> >
> > TVV = BrainSegVol - BrainSegVolNotVent
> >
> >
> > and for TBV
> >
> > TBV = TotalGrayVol + CorticalWhiteMatterVol
> >
> > which differs from
> >
> > TBV = BrainSegVolNotVent
> >
> >
> > Thank you for your help,
> >
> > James Gullickson
> >
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
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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
>
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Re: [Freesurfer] Custom registration template

[Linda Zhang]

Hi Douglas,

Thanks, good to know!  That was the full terminal output after I ran
mris_preproc, though.

Cheers,
Linda


On Thu, 6 Apr 2017 at 22:07 Douglas N Greve 
wrote:

> 1. The "..." means to include the other options needed for the command
> to run. Looks like you figured it out. Using -f as you have is correct.
>
> 2. can you send the full terminal output?
>
>
> On 04/06/2017 08:55 AM, Linda Zhang wrote:
> > Dear all,
> >
> > I've been following the instructions for building a custom
> > registration template as written here
> > (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) and
> > here
> > (
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018345.html
> ).
> >
> >
> > I'm now at the mris_preproc stage and according to the instructions,
> > the command should be:
> >
> > # Get thickness values in the newtemplate space for GLM analysis
> > mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s
> > subj3 ...
> >
> > I put my subject list into a text file and replaced --s with --f
> > [subjlist] but kept everything else the same.  I got two errors for no
> > source hemi specified and no output specified, so I added --hemi lh
> > and --out lh.surfreg.newtemplate.thick --meas thickness.  Am I
> > supposed to do this, and will the output file be used for anything
> > else down the line, i.e., should it be named something more specific?
> > I see that the next step is to rerun the make_average_subject, but I
> > don't see where the output from the mris_preproc step would figure in.
> >
> > On a (maybe) separate issue, when I finally ran my command line:
> >
> > mris_preproc --surfreg sphere.reg.newtemplate --f subjlist --hemi lh
> > --out lh.surfreg.newtemplate.thick --meas thickness
> >
> > I got the following error:
> >
> > nsubjects=100
> > tmpdir is ./tmp.mris_preproc.25619
> > /home/fsuser/data
> > set: Variable name must contain alphanumeric characters.
> >
> > I'm not sure where the problem might be here.  I'm running FreeSurfer
> > v.5.3 in Virtualbox, and I haven't had any problems while running
> > recon-all on the subjects previously.
> >
> > Any insight would be greatly appreciated, thank you!
> >
> > Cheers,
> > Linda
> >
> >
> >
> > ___
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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
>
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[Freesurfer] QDEC-Cortical Thickness

[Limachia, Gaurang (NIH/NINDS) [F]]

Hello Freesurfer Experts,

I want to compare the cortical thickness between the groups (HC & Patients), 
and wanted to know where qdec shows this information. Once the design tab is 
loaded, I am seeing the question in the analysis results – does the correlation 
between thickness and Age differ from zero?   Do I need to a run the command 
for GLM in order to see if there is a cortical difference between the two 
populations? I would greatly appreciate your help.

Thanks,

Gaurang
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Re: [Freesurfer] R: Re: R: R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis

[Douglas N Greve]

depends on your analysis but probably so


On 04/06/2017 05:26 PM, std...@virgilio.it wrote:
> Thanks.
> The file could not be open by fslview.
> I presume that it is inflated.
> How can I do to transform it?
> Stefano
>
> Messaggio originale
> Da: "Douglas Greve" 
> Data: 6-apr-2017 17.56
> A: 
> Ogg: Re: [Freesurfer] R: R: Re: R: Re: Whole preprocessing with
> FAST without to perform a seed based analysis
>
> It will be in the space that you analyzed it in. If you want the
> native space, then use -native when running preproc-sess and
> mkanalysis
>
>
> On 4/6/17 2:34 AM, std...@virgilio.it wrote:
>> Furthermore, the res-001.nii which is produce in produced in the
>> res folder in not the same dimension of f.nii.
>> I would do the whole FAST preprocessing on f.nii., maintaining
>> the same dimension and open it with FSL.
>> Thanks
>> Stefano
>>
>> Messaggio originale
>> Da: std...@virgilio.it
>> Data: 5-apr-2017 23.39
>> A: "Freesurfer support list"
>> Ogg: [Freesurfer] R: Re: R: Re: Whole preprocessing with FAST
>> without to perform a seed based analysis
>>
>> Hi,
>>
>> as you advise I have run selxavg3-sess with the -svres option.
>> I found a folder called "res" which contain "res-001.nii". Is
>> it the f.nii fully processed?
>> Thanks
>> Stefano
>>
>> Messaggio originale
>> Da: "Douglas Greve" 
>> Data: 14-mar-2017 17.38
>> A: 
>> Ogg: Re: [Freesurfer] R: Re: Whole preprocessing with
>> FAST without to perform a seed based analysis
>>
>> You can't  on either occasion just using preproc-sess.
>> You can create an analysis with those components, then
>> run selxavg3-sess with the -svres option. This will
>> create a folder called eres with volumes that have had
>> all the nuisance variables and low freqeuncies regressed out
>>
>>
>> On 3/14/17 12:32 PM, std...@virgilio.it wrote:
>>> Thanks.
>>> 1- By using only preproc-sess, how can I perform "band
>>> pass filtering"?
>>> 2- And how can I take in account the nuisance variables:
>>> the CSF from which the top 5 principle components, the
>>> white matter from which the top 5 principle components,
>>> motion correction parameters (-mcextreg), 5th order
>>> polynomial. How can I eliminate the first 4 time points?
>>> Regards
>>> Stefano
>>>
>>> Messaggio originale
>>> Da: "Douglas Greve" 
>>> Data: 14-mar-2017 16.14
>>> A: 
>>> Ogg: Re: [Freesurfer] Whole preprocessing with FAST
>>> without to perform a seed based analysis
>>>
>>> just use preproc-sess
>>>
>>>
>>> On 3/14/17 10:45 AM, std...@virgilio.it wrote:
 Hi list,
 in FS-FAST, on rs-fMRI data, is possible to run
 selxavg3-sess without -a option?
 I would use whole the FS-FAST to preprocess my
 data. I would include the mkanalysis-sess step but
 I would not perform a seed-based analysis.
 Thanks
 Stefano


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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>>>
>>>
>>>
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>>
>>
>>
>>
>>
>>
>>
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[Freesurfer] R: Re: R: R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis

[stdp82]

Thanks.The file could not be open by fslview.I presume that it is inflated.How 
can I do to transform it?Stefano 




Messaggio originale

Da: "Douglas Greve" 

Data: 6-apr-2017 17.56

A: 

Ogg: Re: [Freesurfer] R: R: Re: R: Re: Whole preprocessing with FAST without to 
perform a seed based analysis




  
  

It will be in the space that you analyzed it in. If you want the
  native space, then use -native when running preproc-sess and
  mkanalysis




On 4/6/17 2:34 AM, std...@virgilio.it
  wrote:


Furthermore, the res-001.nii which is produce in
  produced in the res folder in not the same dimension of f.nii.
  I would do the whole FAST preprocessing on f.nii.,
maintaining the same dimension and open it with FSL.
  Thanks
  Stefano




  Messaggio originale

  Da: std...@virgilio.it

  Data: 5-apr-2017 23.39

  A: "Freesurfer support
  list"

  Ogg: [Freesurfer] R: Re: R: Re: Whole preprocessing with FAST
  without to perform a seed based analysis

  

  Hi, 
  

  
  as you advise I have run selxavg3-sess with the -svres
option.
  I found a folder called "res" which contain
"res-001.nii". Is it the f.nii fully processed?
  Thanks
  Stefano
  



  Messaggio originale

  Da: "Douglas Greve" 

  Data: 14-mar-2017 17.38

  A: 

  Ogg: Re: [Freesurfer] R: Re: Whole preprocessing with FAST
  without to perform a seed based analysis

  

  
  
You can't  on either occasion just using preproc-sess.
You can create an analysis with those components, then
run selxavg3-sess with the -svres option. This will
create a folder called eres with volumes that have had
all the nuisance variables and low freqeuncies regressed
out

  
  

  On 3/14/17 12:32 PM, std...@virgilio.it
wrote:

  
  
Thanks.
1- By using only preproc-sess, how can I perform
  "band pass filtering"?
2- And how can I take in account the nuisance
  variables: the CSF from which the top 5 principle
  components, the white matter from which the top 5
  principle components, motion correction parameters
  (-mcextreg), 5th order polynomial. How can I eliminate
  the first 4 time points?
Regards
Stefano

   Messaggio originale

Da: "Douglas Greve" 

Data: 14-mar-2017 16.14

A: 

Ogg: Re: [Freesurfer] Whole preprocessing with FAST
without to perform a seed based analysis





just use preproc-sess




On 3/14/17 10:45 AM, std...@virgilio.it
  wrote:



  
Hi list,
in FS-FAST, on rs-fMRI data, is possible to
  run selxavg3-sess without -a option?
I would use whole the FS-FAST to preprocess
  my data. I would include the mkanalysis-sess
  step but I would not perform a seed-based
  analysis. 
Thanks
Stefano
  
  

  
  

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Re: [Freesurfer] QDEC-volume, thickness and area

[Douglas N Greve]

probably so. It is up to you whether you want to fight the reviewer or not.


On 04/06/2017 05:08 PM, Lim, Lena wrote:
>
> Thanks, Doug.
>
>
> There is no significant interaction and I merged the males and females 
> within each group, but the reviewer wants me to include gender as a 
> covariate. Do we always need to control for gender esp. when the group 
> x gender is insignificant? Will that be "over-controlled"?
>
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> *Sent:* 06 April 2017 20:45
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] QDEC-volume, thickness and area
> what do you mean they do not differ in gender ratio? Just that the
> relative number of M/F is the same in each group? If there is not a
> significant interaction between gender and group, then you can usually
> merge the genders.
>
>
> On 04/05/2017 05:13 PM, Lim, Lena wrote:
> >
> > Dear Freesurfer Experts,
> >
> > 1) I have 2 groups (A & B), which do not differ in terms of gender
> > ratio. If there were no significant regions for Group-Gender
> > interaction in mean cortical thickness in the QDEC analysis, can I
> > conclude that gender does not influence the effect of group on
> > thickness? The differences between A and B on mean thickness is not
> > affected by Gender? Is this valid or do I need to add Gender as a
> > covariate even though the group do not differ on gender ratio?
> >
> > 2) A reviewer pointed that it is not right to test for group
> > differences in volume once I have tested for thickness and area,
> > especially when there is a cluster where A and B do not differ
> > significantly in thickness and area but they differ significantly in
> > volume…Is this right?
> >
> > Please kindly advise.
> >
> > Many thanks,
> >
> > Lena
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > 
> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Clena.lim%40kcl.ac.uk%7C1a7a3062e8634c0e8d1c08d47d2577ca%7C8370cf1416f34c16b83c724071654356%7C0&sdata=PhNkIdT%2Fj8FHEIG2Wo1UjfG65ns90Ao7ajxUX7ErJus%3D&reserved=0
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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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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Re: [Freesurfer] QDEC-volume, thickness and area

[Lim, Lena]

Thanks, Doug.


There is no significant interaction and I merged the males and females within 
each group, but the reviewer wants me to include gender as a covariate. Do we 
always need to control for gender esp. when the group x gender is 
insignificant? Will that be "over-controlled"?



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N Greve 

Sent: 06 April 2017 20:45
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] QDEC-volume, thickness and area

what do you mean they do not differ in gender ratio? Just that the
relative number of M/F is the same in each group? If there is not a
significant interaction between gender and group, then you can usually
merge the genders.


On 04/05/2017 05:13 PM, Lim, Lena wrote:
>
> Dear Freesurfer Experts,
>
> 1) I have 2 groups (A & B), which do not differ in terms of gender
> ratio. If there were no significant regions for Group-Gender
> interaction in mean cortical thickness in the QDEC analysis, can I
> conclude that gender does not influence the effect of group on
> thickness? The differences between A and B on mean thickness is not
> affected by Gender? Is this valid or do I need to add Gender as a
> covariate even though the group do not differ on gender ratio?
>
> 2) A reviewer pointed that it is not right to test for group
> differences in volume once I have tested for thickness and area,
> especially when there is a cluster where A and B do not differ
> significantly in thickness and area but they differ significantly in
> volume…Is this right?
>
> Please kindly advise.
>
> Many thanks,
>
> Lena
>
>
>
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Re: [Freesurfer] QDEC and ROI drawing

[Douglas N Greve]

what is your label2label command line?


On 04/06/2017 04:52 PM, Arnaud Boré wrote:
> Dear Freesurfer's experts,
> I draw a specific region on fsaverage using QDEC, then I mapped this 
> label on each subject using mri_label2label. I looked at these 
> registered labels using freeview. Most of them are perfect but for 
> some of them I would like to correct the segmentation. I would like to 
> modify it using QDEC but when I overlay this label on the surface of 
> my subject it has been shifted. I think this shift is because QDEC is 
> using fsaverage as the standard space. I try opening QDEC using the 
> "average" option and use the subject I want but I still get this 
> shift. am I missing something ?
> Thank you in advance for your help.
> Arnaud Bore
>
>
>
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[Freesurfer] QDEC and ROI drawing

[Arnaud Boré]

Dear Freesurfer's experts,
I draw a specific region on fsaverage using QDEC, then I mapped this label
on each subject using mri_label2label. I looked at these registered labels
using freeview. Most of them are perfect but for some of them I would like
to correct the segmentation. I would like to modify it using QDEC but when
I overlay this label on the surface of my subject it has been shifted. I
think this shift is because QDEC is using fsaverage as the standard space.
I try opening QDEC using the "average" option and use the subject I want
but I still get this shift. am I missing something ?
Thank you in advance for your help.
Arnaud Bore
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Re: [Freesurfer] General QDEC clarification queastions

[Douglas N Greve]

On 04/03/2017 01:45 PM, Veggeberg, Rosanna wrote:
> Hello,
> I am using QDEC to analyze cortical structural data and am looking for 
> some clarification on some questions that have come up.
>
> 1. _Design tab_: In the "Measure" drop-down selection, I understand 
> what we are getting when looking at thickness but the other 
> measurements I am unclear on. Is there information or publications on 
> the other 12 possible measures (how they are measured, what they mean, 
> applications for using them). In particular, I am interested in 
> learning more about area, area.pial, volume, sulc, and curv but would 
> like to understand what the others mean as well to determine if they 
> would be applicable to our study questions.
There is not a specific pub on this. The area is the area of a vertex 
(the average of the triangles around it), same interpreation for the 
volume. These are kind of like VBM analysis. area.pial is the area of 
the pial surface whereas simple area is the area of the white. curv is 
the curvature; sulc is the sulcal depth. These are used for registration 
and generally not that interesting.
>
> 2. _Design tab_: I am a little unclear on why the model factors are 
> labeled the way they are and wanted to see if I am using them correctly.
> -Discrete (Fixed Factors): this is pretty straight forward to be used 
> as independent categorical variables, correct?
yes
> -Continuous (Covariate): even though it says covariate, should these 
> variables just be treated as independent continuous varaibles?
correct
> -Nuisance Factors: should these just be treated as the covariates we 
> wish to control for?
yes. it allows you to have more continuous variable, but you won't get 
tests that include them
>
> 3. _Results_: When I am doing a group comparison (i.e. disease vs. 
> control), does QDEC run the comparison based off of which order the 
> labels appear in the table: disease vs. control, or does it run the 
> comparison based off of which label comes first alphabetically: 
> control vs. disease?
The order in your levels file
>
> 4. _Results_: When viewing the results in freeview, if I click on a 
> significant cluster, in the bottom panel, does a negative value next 
> to the mc-z.abs.th13.sig.cluster.mgh label indicate a decrease in 
> cortical thickness (i.e. disease vs. control: negative value indicates 
> control is greater than disease)?
It depends on the order above. It will be contrast = first - second.
>
> 5. Finally, once you have closed QDEC, is it possible to reopen the 
> files again in the Gui? Or would you have to rerun the analysis?
sorry, not sure
>
> Thank you for help and please let me know if you need any further 
> clarification.
>
>
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Re: [Freesurfer] Custom color maps

[Senften, Peter]

Thanks, I'll take a look at it and let you know how it goes. 

Peter

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, April 06, 2017 1:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Custom color maps

See if annotval2surfoverlay.m does what you want. It is in v6. If you
have v5.x, I can send you the mfile separtely


On 04/06/2017 01:00 PM, Senften, Peter wrote:
> hi,
>
> I've read through the list, and searched over the last few days, and can't 
> quite seem to find what I'm looking for. My first message wasn't clear at all 
> either (my apologies), it was one of those days where your brain ends up in a 
> bit of a fog.
>
> I am trying to get a heat map style visual output based on the destrieux 72 
> region map using cortical thickness as our measure. I'm using FS 6.0 and the 
> edits and outputs have all gone great. We are doing the analysis of the 
> cortical thickness outside of FS and would like to create a heat-map style 
> visual output of the areas that show a large effect size. My original idea 
> was to create a custom color map and somehow load that in place of the 
> default destrieux color map but I couldn't get that to work. Tried replacing 
> the FS LUT table as well and when loaded the colors remained the same as well.
>
> Hope that clarifies what I'm trying to do.
>
> Thanks,
>
> Peter
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dg wakeman 
> [dgwake...@gmail.com]
> Sent: Tuesday, April 04, 2017 12:11 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Custom color maps
>
> Hi Peter,
>
> We will need a lot more details to help. I suggest you look through
> the e-mail list a bit. I spent a lot of time helping a user or two
> with a similar issue. The key details are what are you trying to show
> (an annotation, a single label, or values)?
>
> hth
> d
>
> On Wed, Mar 29, 2017 at 11:15 AM, Senften, Peter  wrote:
>> Hello,
>>
>> I am wondering if it is possible to create a custom color map that will be
>> visible in freeview using the 3D viewer - not the coronal, axial, or sagital
>> views. I created a copy of the LUT file and then replaced the RGB values the
>> ones I wanted but haven't been able to get it to load at all.
>>
>> In the end I am trying to make pretty 3D pictures to see our regions of
>> interest better for our data. I am open to other ways of doing this.
>>
>> Thanks,
>>
>> Peter
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
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>
>

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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] correlation coefficient R

[Douglas N Greve]

I guess you could average it over space (eg, over a cluster). Let me 
know if you want instructions. Otherwise, I'm not sure what to say.


On 04/04/2017 06:49 AM, tom parker wrote:
> Hi Doug,
> Thanks! I realize now I didn't explain myself properly.
> I need one single R value for the correlation analysis I made, 
> similarly to when I correlate two variables with Pearson's R in a 
> statistical package. I have a referee asking me to put it on a table 
> with the freesurfer results. Is there a way to get a single average R 
> value from the pcc.mgh file?
> Thank you so much!
>
> Douglas Greve 
> 
>  
> Mon, 03 Apr 2017 18:46:46 -0700 
> 
>  
>
>
> Each vertex is a correlation value.
>
> 2017-04-04 1:09 GMT+01:00 tom parker  >:
>
> Thanks Doug!
>
> I have version 6 and got a pcc.mgh file.
>
> How can I get a correlation R value from this file?
>
> Thanks again
>
> Douglas N Greve
> 
> 
> Mon, 03 Apr 2017 09:41:41 -0700
> 
> 
>
>
> if you are using version 6, then it should have produced a file called
> pcc.mgh. This the partial pearson correlation coef.
>
>
>
> 2017-04-03 15:40 GMT+01:00 tom parker  >:
>
> Dear Freesurfers,
>
> I made some correlations between cortical thickness and age in
> qdec.
>
> Is it possible to get the correlation coefficient value of
> this analysis?
>
> I just need to put it in a table with the significant results.
>
> Thank you so much!
>
>
>
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] ROI seed size

[Douglas N Greve]

these are good questions without good answers. It is hard to compare 
surface-based vs volume-based. The surface-based may be smaller, but it 
will only include gray matter whereas a volume-based sphere will be 
bigger but will include WM and CSF. If you're voxel size is small, then 
3mm radius might not get more than one or two of them


On 04/03/2017 09:53 PM, ERIK JAHNER wrote:
> What is the appropriate size for a surface based seed?
>
> I am referencing a study with volumetric based seeds with spheres with a 
> radius of 3mm (in fMRI data). I would like to do a similar study using 
> surface based representations. In a volumetric based analysis folding may 
> actually increase the amount of cortical surface represented in a sphere. 
> Using a circle on the surface with a 3 mm radius therefore would not be the 
> same. But…. is the difference so minimal and variable across the cortex that 
> it is not worth considering especially since the seeds are derived from 
> published work and not using a localizer?
>
> Do you know of any published guidelines on generating seed sizes in surface 
> based models, not based on a localizer.
> Or is this the completely wrong approach? Should I be using the tal 
> coordinates to locate which parcellation of the available atlases that the 
> seed was located in? (for example i have a fusiform face area seed which I 
> have set as a circle 3mm radius)
>
> many thanks for your continued help
> Erik
>
>
>
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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

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Re: [Freesurfer] Ventricle-to-Brain Ratio

[Douglas N Greve]

that looks right. how different are the values?


On 04/05/2017 10:58 AM, Gullickson, James wrote:
> Hello all,
>
> I want to calculate a Ventricle-to-Brain ratio (VBR) as a measure of 
> parenchymal atrophy using Freesurfer version 5.3.0. I have tried to go 
> about this using the aseg.stats output (using asegstats2table), but am 
> running into inconsistencies.
>
> The basic calculation for VBR is:
>
> (Total Ventricular Volume/Total Brain Volume) * 100
>
> i.e. Bigler, E. D. (2013). Traumatic brain injury, neuroimaging, and 
> neurodegeneration. /Frontiers in human neuroscience/, /7/, 395.
>
>
> What is the best way to get Total Ventricular Volume (TVV) and Total 
> Brain Volume (TBV) for this calculation? I have tried several ways, 
> which lead to different values:
>
> TVV = left lateral ventricle + left inf lateral ventricle + right 
> lateral ventricle + right inf lateral ventricle + 3rd ventricle + 4th 
> ventricle + 5th ventricle + choroid plexus
>
> which gives me a different result than
>
> TVV = BrainSegVol - BrainSegVolNotVent
>
>
> and for TBV
>
> TBV = TotalGrayVol + CorticalWhiteMatterVol
>
> which differs from
>
> TBV = BrainSegVolNotVent
>
>
> Thank you for your help,
>
> James Gullickson
>
>
>
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Selxavg3-sess Looking for (and can't find) "fmc.sm0"

[Douglas N Greve]

can you send the full terminal output?


On 04/05/2017 04:02 PM, Taylor, Johnmark wrote:
> Hello,
>
> I am getting an odd bug on selxavg3-sess. I am getting the error message,
>
> *ERROR: cannot find [rest of file path]/fmc.sm0*
>
> I am indicating zero smoothing in mkanalysis-sess ("-fwhm 0"). I am 
> confused because the output of preproc-sess for no smoothing is 
> fmc.nii.gz, *NOT *fmc.sm0.nii.gz when doing analyses in native volume 
> space, so I am not sure why selxavg-sess is looking for the wrong file 
> path. For reference, here is my call to mkanalysis-sess:
>
> mkanalysis-sess -analysis analysis_name -fsd bold -runlistfile runlist.txt
> -native -nuisreg mcextreg 3 -fwhm 0 -event-related -nconditions 8
> -paradigm spiralpara.par -spmhrf 0 -refeventdur 12 -TR 1.5
> -polyfit 2 -nskip 8
>
> I am using Freesurfer 5.3, if that helps. The analysis works fine when 
> I apply 3mm smoothing (I've done preprocessing for both the 0mm and 
> 3mm options).
>
> Thank you very much, and cheers,
>
> JohnMark
>
>
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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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Re: [Freesurfer] Custom registration template

[Douglas N Greve]

1. The "..." means to include the other options needed for the command 
to run. Looks like you figured it out. Using -f as you have is correct.

2. can you send the full terminal output?


On 04/06/2017 08:55 AM, Linda Zhang wrote:
> Dear all,
>
> I've been following the instructions for building a custom 
> registration template as written here 
> (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) and 
> here 
> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018345.html).
>  
>
>
> I'm now at the mris_preproc stage and according to the instructions, 
> the command should be:
>
> # Get thickness values in the newtemplate space for GLM analysis 
> mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s 
> subj3 ...
>
> I put my subject list into a text file and replaced --s with --f 
> [subjlist] but kept everything else the same.  I got two errors for no 
> source hemi specified and no output specified, so I added --hemi lh 
> and --out lh.surfreg.newtemplate.thick --meas thickness.  Am I 
> supposed to do this, and will the output file be used for anything 
> else down the line, i.e., should it be named something more specific?  
> I see that the next step is to rerun the make_average_subject, but I 
> don't see where the output from the mris_preproc step would figure in.
>
> On a (maybe) separate issue, when I finally ran my command line:
>
> mris_preproc --surfreg sphere.reg.newtemplate --f subjlist --hemi lh 
> --out lh.surfreg.newtemplate.thick --meas thickness
>
> I got the following error:
>
> nsubjects=100
> tmpdir is ./tmp.mris_preproc.25619
> /home/fsuser/data
> set: Variable name must contain alphanumeric characters.
>
> I'm not sure where the problem might be here.  I'm running FreeSurfer 
> v.5.3 in Virtualbox, and I haven't had any problems while running 
> recon-all on the subjects previously.
>
> Any insight would be greatly appreciated, thank you!
>
> Cheers,
> Linda
>
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Custom color maps

[Douglas N Greve]

See if annotval2surfoverlay.m does what you want. It is in v6. If you 
have v5.x, I can send you the mfile separtely


On 04/06/2017 01:00 PM, Senften, Peter wrote:
> hi,
>
> I've read through the list, and searched over the last few days, and can't 
> quite seem to find what I'm looking for. My first message wasn't clear at all 
> either (my apologies), it was one of those days where your brain ends up in a 
> bit of a fog.
>
> I am trying to get a heat map style visual output based on the destrieux 72 
> region map using cortical thickness as our measure. I'm using FS 6.0 and the 
> edits and outputs have all gone great. We are doing the analysis of the 
> cortical thickness outside of FS and would like to create a heat-map style 
> visual output of the areas that show a large effect size. My original idea 
> was to create a custom color map and somehow load that in place of the 
> default destrieux color map but I couldn't get that to work. Tried replacing 
> the FS LUT table as well and when loaded the colors remained the same as well.
>
> Hope that clarifies what I'm trying to do.
>
> Thanks,
>
> Peter
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dg wakeman 
> [dgwake...@gmail.com]
> Sent: Tuesday, April 04, 2017 12:11 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Custom color maps
>
> Hi Peter,
>
> We will need a lot more details to help. I suggest you look through
> the e-mail list a bit. I spent a lot of time helping a user or two
> with a similar issue. The key details are what are you trying to show
> (an annotation, a single label, or values)?
>
> hth
> d
>
> On Wed, Mar 29, 2017 at 11:15 AM, Senften, Peter  wrote:
>> Hello,
>>
>> I am wondering if it is possible to create a custom color map that will be
>> visible in freeview using the 3D viewer - not the coronal, axial, or sagital
>> views. I created a copy of the LUT file and then replaced the RGB values the
>> ones I wanted but haven't been able to get it to load at all.
>>
>> In the end I am trying to make pretty 3D pictures to see our regions of
>> interest better for our data. I am open to other ways of doing this.
>>
>> Thanks,
>>
>> Peter
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
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>
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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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Re: [Freesurfer] First-level GLM on externally-preprocessed functionals

[Douglas N Greve]

You should be able to do it that way. When you run mkanalysis, specify 
-funcstem fmcpr.sm0.fsaverage.lh.nii.gz, and then selxavg3-sess will 
then use that file as input. If you want to smooth, then do that 
explicitly and pass the smoothed file to mkanalysis


On 04/06/2017 12:35 PM, Christopher Markiewicz wrote:
> Hi list,
>
> We're working on making a preprocessing stream that will be generally 
> accessible to different analysis streams, including FreeSurfer. One 
> component of this is sampling functional volumes to FreeSurfer meshes, 
> and I want to test this component by running a simple first-level GLM 
> in FreeSurfer.
>
> I've always done this through the FSFAST pipeline, but that may be a 
> bit much, given that I'm starting from surface time series (the 
> equivalent of 
> `$FUNCTIONALS_DIR/$SESS_ID/bold/$RUN/fmcpr.sm0.fsaverage.lh.nii.gz`, 
> but as a GIFTI file).
>
> Supposing I have a paradigm file and the files described above, what's 
> the best way to do a basic GLM? Would it be to `mri_surf2surf` our 
> GIFTI surfaces into `fmcpr.sm0.fsaverage.lh.nii.gz` files in a FSFAST 
> directory structure, and pick up at `mkanalysis-sess`? Or is there a 
> more straightforward way to just get a simple set of contrasts to 
> compare with a volumetric analysis?
>
> Thanks in advance,
> Chris Markiewicz
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
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Re: [Freesurfer] Help on "mris_anatomical_stats"

[Douglas N Greve]

I can't replicate. Try loading the white and pial surfaces into 
freeview. If that works, please upload your subject so I can try to 
replicate the error


On 12/08/2015 11:22 AM, Lim, Lena wrote:
>
> Dear Experts,
>
> I ran a group analysis in Qdec for the left volume and found a region 
> of significant group difference. I wanted to extract this ROI. I 
> defined this label and used the “map label to subjects” option in Qdec 
> and ran the following but encountered the following error. Please 
> kindly help…
>
> [spjwker@nanlnx2 FSL]1% mris_anatomical_stats –l lh.HCA_vol.label \-b 
> -f PAC07/stats/lh.HCA_vol.stats PAC07 lh
>
> limiting computations to label lh.HCA_vol.label.
>
> reading volume /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/mri/wm.mgz...
>
> reading input surface 
> /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.white...
>
> reading input pial surface 
> /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.pial...
>
> reading input white surface 
> /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.white...
>
> Segmentation fault
>
> Many thanks,
>
> Lena
>
>
>
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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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Re: [Freesurfer] QDEC-volume, thickness and area

[Douglas N Greve]

what do you mean they do not differ in gender ratio? Just that the 
relative number of M/F is the same in each group? If there is not a 
significant interaction between gender and group, then you can usually 
merge the genders.


On 04/05/2017 05:13 PM, Lim, Lena wrote:
>
> Dear Freesurfer Experts,
>
> 1) I have 2 groups (A & B), which do not differ in terms of gender 
> ratio. If there were no significant regions for Group-Gender 
> interaction in mean cortical thickness in the QDEC analysis, can I 
> conclude that gender does not influence the effect of group on 
> thickness? The differences between A and B on mean thickness is not 
> affected by Gender? Is this valid or do I need to add Gender as a 
> covariate even though the group do not differ on gender ratio?
>
> 2) A reviewer pointed that it is not right to test for group 
> differences in volume once I have tested for thickness and area, 
> especially when there is a cluster where A and B do not differ 
> significantly in thickness and area but they differ significantly in 
> volume…Is this right?
>
> Please kindly advise.
>
> Many thanks,
>
> Lena
>
>
>
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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

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Re: [Freesurfer] MRIread (load_nifti)- Out of memory

[Douglas N Greve]

is it a compressed nifti (nii.gz)? If so, try uncompressing it first


On 04/06/2017 02:53 PM, Ilaria Sani wrote:
> Hi Bruce,
>
> Not sure this answer your question...
>
> In matlab workspace, I am able to load data in two halves:
>
> H1=MRIread(half1)
> H2=MRIread(half2)
>
> And then concatenate the volumes
> concatenate them var=cat(4,H1,H2).
>
> So, somehow matlab can handle...
>
> However, when those operations are embedded inside a function (like in the 
> case of load_nifti and MRIread) I get the error.
>
>
> Thanks,
> Ilaria
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Thursday, April 6, 2017 1:36 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
>
> Hi Ilaria
>
> do you have any reason to believe that it isn't just out of memory? If so, 
> there's not much to do other than get more RAM or use a different machine
>
> cheers
> Bruce
>
>
> On Thu,
> 6 Apr 2017, Ilaria Sani wrote:
>
>> Dear All,
>>
>>   
>>
>> I’m trying to load a pretty big diffusion MRI dataset (320x320x260x122).
>>
>> I’m running matlab 2015a 64bit on a linux machine.
>>
>>   
>>
>> I’m using MRIread, which in turn calls load_nifti.
>>
>> I’m getting the following error:
>>
>>   
>>
>> Error using  +
>>
>> Out of memory. Type HELP MEMORY for your options.
>>
>>   
>>
>> Error in load_nifti (line 158)
>>
>>hdr.vol = hdr.vol * hdr.scl_slope  + hdr.scl_inter;
>>
>>   
>>
>> Error in MRIread (line 158)
>>
>> hdr = load_nifti(fspec,headeronly);
>>
>>   
>>
>> When I load half dataset (320x320x260x61) it works ok.
>>
>> I tried to increase the Maximum array size in Matalb (default 1,000 - now 
>> 10,000), but I’m still getting the error.
>>
>> I tried to change machine (which runs matlab 2013a on linux) and it worked 
>> fine.
>>
>>   
>>
>> I think this is due to some matlab settings.
>>
>> Can anyone help?
>>
>>   
>>
>> Thanks a lot,
>>
>> Ilaria
>>
>>   
>>
>>   
>>
>> ---
>> Ilaria Sani, PhD
>> Postdoctoral Fellow, Freiwald Lab
>> The Rockefeller University
>> 1230 York Ave., New York, NY 10065.
>> Phone: (212) 327 7699
>> Fax: (212) 327 7698
>> Email: isan...@rockefeller.edu
>>
>>   
>>
>>
>>
> ___
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> 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
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Re: [Freesurfer] MRIread (load_nifti)- Out of memory

[Ilaria Sani]

Hi Bruce,

Not sure this answer your question...

In matlab workspace, I am able to load data in two halves:

H1=MRIread(half1)
H2=MRIread(half2)

And then concatenate the volumes
concatenate them var=cat(4,H1,H2).

So, somehow matlab can handle...

However, when those operations are embedded inside a function (like in the case 
of load_nifti and MRIread) I get the error.


Thanks,
Ilaria


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Thursday, April 6, 2017 1:36 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory

Hi Ilaria

do you have any reason to believe that it isn't just out of memory? If so, 
there's not much to do other than get more RAM or use a different machine

cheers
Bruce


On Thu,
6 Apr 2017, Ilaria Sani wrote:

> 
> Dear All,
> 
>  
> 
> I’m trying to load a pretty big diffusion MRI dataset (320x320x260x122).
> 
> I’m running matlab 2015a 64bit on a linux machine.
> 
>  
> 
> I’m using MRIread, which in turn calls load_nifti.
> 
> I’m getting the following error:
> 
>  
> 
> Error using  +
> 
> Out of memory. Type HELP MEMORY for your options.
> 
>  
> 
> Error in load_nifti (line 158)
> 
>   hdr.vol = hdr.vol * hdr.scl_slope  + hdr.scl_inter;
> 
>  
> 
> Error in MRIread (line 158)
> 
> hdr = load_nifti(fspec,headeronly);
> 
>  
> 
> When I load half dataset (320x320x260x61) it works ok.
> 
> I tried to increase the Maximum array size in Matalb (default 1,000 - now 
> 10,000), but I’m still getting the error.
> 
> I tried to change machine (which runs matlab 2013a on linux) and it worked 
> fine.
> 
>  
> 
> I think this is due to some matlab settings.
> 
> Can anyone help?
> 
>  
> 
> Thanks a lot,
> 
> Ilaria
> 
>  
> 
>  
> 
> ---
> Ilaria Sani, PhD
> Postdoctoral Fellow, Freiwald Lab
> The Rockefeller University
> 1230 York Ave., New York, NY 10065.
> Phone: (212) 327 7699
> Fax:     (212) 327 7698
> Email: isan...@rockefeller.edu
> 
>  
> 
> 
>

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Re: [Freesurfer] help

[Bruce Fischl]

Hi Dilip

yes, freesurfer will do this for you, although the labels will be 17 for 
left hippocampus and 53 for right.

cheers
Bruce
On Thu, 6 Apr 2017, Dilip Puri wrote:

> Hi everyone,
> 
> I am working on Hippocampus segmentation using Neural Networks for that I 
> need labeled images of Hippocampus corresponding to original images.
> 
> I am using OASIS Dataset for this. I want to generate labeled images using 
> FREESURFER. Is there any way to label each 3D co-ordinate
> HippoCampus -1
> Otherwise - 0
> 
> Here are sample files link
> 
> Kindly help me!
> 
> 
> Dilip Puri
> IIIT Vadodara
> 
>
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Re: [Freesurfer] long mri_ca_register error

[Bruce Fischl]

Hi Chris

it's possible we never looked at -bigventricle in the long stage. What 
was your recon-all command line?


cheers
Bruce
On Thu, 6 Apr 2017, Chris Adamson wrote:



It happens when I use -bigventricles.

 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris Adamson
Sent: Thursday, 6 April 2017 12:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] long mri_ca_register error

 

Freesurfer devs,

 

In freesurfer 6 stable I’m having a problem at the careg stage of the long. The 
relevant recon-all log is pasted below. Could you point me to where to debug 
this
problem?

 

Cheers,

 

Chris.

 

mri_ca_register -rusage 
136_S_0426_20070604.long.136_S_0426/touch/rusage.mri_ca_register.dat 
-bigventricles -smoothness 0.5 -levels 2 -A 1 -l
*base*/transforms/talairach.m3z identity.nofile -align-after -mask 
brainmask.mgz norm.mgz 
/usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
transforms/talairach.m3z

 

handling expanded ventricles...

l_smoothness = 0.50

levels = 2

smoothing gradient with 1 averages...

reading previously computed atlas xform 
/isilon/data/addo/ADNI3T/freesurfer6/136_S_0426/mri/transforms/talairach.m3z 
and applying inverse registration identity.nofile

renormalizing sequences with structure alignment, equivalent to:

    -renormalize

    -regularize_mean 0.500

    -regularize 0.500

using MR volume brainmask.mgz to mask input volume...

 

== Number of threads available to mri_ca_register for OpenMP = 2 ==

reading 1 input volumes...

logging results to talairach.log

reading input volume 'norm.mgz'...

reading GCA '/usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...

label assignment complete, 0 changed (0.00%)

TransformSample: gcam has not been inverted!

freeing gibbs priors...done.

average std[0] = 5.0

setting orig areas to linear transform determinant scaled 8.40

writing talairach.invalid.mgz

writing talairach.status.mgz

registering ventricular system...

using threshold 45.0 from atlas ventricle (20.1 +- 5.0) and caudate (70.0 +- 
5.0) distributions for initial ventricular estimate

No such file or directory

TransformSample: gcam has not been inverted!

No such file or directory

TransformSample: gcam has not been inverted!

No such file or directory

TransformSample: gcam has not been inverted!

No such file or directory

TransformSample: gcam has not been inverted!

No such file or directory

TransformSample: gcam has not been inverted!

No such file or directory

TransformSample: gcam has not been inverted!

No such file or directory

TransformSample: gcam has not been inverted!

No such file or directory

TransformSample: gcam has not been inverted!

No such file or directory

TransformSample: gcam has not been inverted!

No such file or directory

TransformSample: gcam has not been inverted!

No such file or directory

TransformSample: gcam has not been inverted!

No such file or directory

 

Dr Chris Adamson

Senior Research Officer

Developmental Imaging, Clinical Sciences

 

Murdoch Childrens Research Institute

The Royal Children’s Hospital

Flemington Road, Parkville, VIC 3052 Australia

E chris.adam...@mcri.edu.au 

www.mcri.edu.au

 

 

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Re: [Freesurfer] MRIread (load_nifti)- Out of memory

[Bruce Fischl]

Hi Ilaria

do you have any reason to believe that it isn't just out of memory? If so, 
there's not much to do other than get more RAM or use a different machine


cheers
Bruce


On Thu, 
6 Apr 2017, Ilaria Sani wrote:




Dear All,

 

I’m trying to load a pretty big diffusion MRI dataset (320x320x260x122).

I’m running matlab 2015a 64bit on a linux machine.

 

I’m using MRIread, which in turn calls load_nifti.

I’m getting the following error:

 

Error using  +

Out of memory. Type HELP MEMORY for your options.

 

Error in load_nifti (line 158)

  hdr.vol = hdr.vol * hdr.scl_slope  + hdr.scl_inter;

 

Error in MRIread (line 158)

hdr = load_nifti(fspec,headeronly);

 

When I load half dataset (320x320x260x61) it works ok.

I tried to increase the Maximum array size in Matalb (default 1,000 - now 
10,000), but I’m still getting the error.

I tried to change machine (which runs matlab 2013a on linux) and it worked fine.

 

I think this is due to some matlab settings.

Can anyone help?

 

Thanks a lot,

Ilaria

 

 

---
Ilaria Sani, PhD
Postdoctoral Fellow, Freiwald Lab
The Rockefeller University
1230 York Ave., New York, NY 10065.
Phone: (212) 327 7699
Fax:     (212) 327 7698
Email: isan...@rockefeller.edu

 


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Re: [Freesurfer] Custom color maps

[Senften, Peter]

hi, 

I've read through the list, and searched over the last few days, and can't 
quite seem to find what I'm looking for. My first message wasn't clear at all 
either (my apologies), it was one of those days where your brain ends up in a 
bit of a fog. 

I am trying to get a heat map style visual output based on the destrieux 72 
region map using cortical thickness as our measure. I'm using FS 6.0 and the 
edits and outputs have all gone great. We are doing the analysis of the 
cortical thickness outside of FS and would like to create a heat-map style 
visual output of the areas that show a large effect size. My original idea was 
to create a custom color map and somehow load that in place of the default 
destrieux color map but I couldn't get that to work. Tried replacing the FS LUT 
table as well and when loaded the colors remained the same as well. 

Hope that clarifies what I'm trying to do. 

Thanks,

Peter

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dg wakeman 
[dgwake...@gmail.com]
Sent: Tuesday, April 04, 2017 12:11 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Custom color maps

Hi Peter,

We will need a lot more details to help. I suggest you look through
the e-mail list a bit. I spent a lot of time helping a user or two
with a similar issue. The key details are what are you trying to show
(an annotation, a single label, or values)?

hth
d

On Wed, Mar 29, 2017 at 11:15 AM, Senften, Peter  wrote:
> Hello,
>
> I am wondering if it is possible to create a custom color map that will be
> visible in freeview using the 3D viewer - not the coronal, axial, or sagital
> views. I created a copy of the LUT file and then replaced the RGB values the
> ones I wanted but haven't been able to get it to load at all.
>
> In the end I am trying to make pretty 3D pictures to see our regions of
> interest better for our data. I am open to other ways of doing this.
>
> Thanks,
>
> Peter
>
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> properly
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[Freesurfer] First-level GLM on externally-preprocessed functionals

[Christopher Markiewicz]

Hi list,

We're working on making a preprocessing stream that will be generally
accessible to different analysis streams, including FreeSurfer. One
component of this is sampling functional volumes to FreeSurfer meshes, and
I want to test this component by running a simple first-level GLM in
FreeSurfer.

I've always done this through the FSFAST pipeline, but that may be a bit
much, given that I'm starting from surface time series (the equivalent of
`$FUNCTIONALS_DIR/$SESS_ID/bold/$RUN/fmcpr.sm0.fsaverage.lh.nii.gz`, but as
a GIFTI file).

Supposing I have a paradigm file and the files described above, what's the
best way to do a basic GLM? Would it be to `mri_surf2surf` our GIFTI
surfaces into `fmcpr.sm0.fsaverage.lh.nii.gz` files in a FSFAST directory
structure, and pick up at `mkanalysis-sess`? Or is there a more
straightforward way to just get a simple set of contrasts to compare with a
volumetric analysis?

Thanks in advance,
Chris Markiewicz
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[Freesurfer] postdoctoral Research Fellow position at Mayo Clinic

[Senjem, Matthew L., M.S.]

The Mayo Clinic Departments of Neurology and Diagnostic Radiology in Rochester, 
Minnesota are seeking applications for a fully-funded, two-year postdoctoral 
Research Fellow position to begin in July of 2017.  The Research Fellow 
position will primarily work on developing advanced multi-modal molecular and 
high-field (3T and 7T) neuroimaging to study connectomics in pre-clinical and 
clinical Alzheimer’s disease. The resulting data will be acquired and analyzed 
as part of a unique collaboration between investigators at Mayo Clinic 
Alzheimer’s Disease Research Center and the Center for Magnetic Resonance 
Research at the University of Minnesota. Basic programing skills and 
familiarity with widely used neuroimaging software platforms are required for 
successful applicants. Familiarity with the Human Connectome Project imaging 
and analyses protocols is preferred but not required. No clinical or 
Alzheimer’s specific background is required. Salary will be commensurate with 
postdoctoral experience. The position will remain open until filled by a 
successful candidate.

Please send CV, three letters of recommendation, and any inquiries to:

David T. Jones, M.D.
Mayo Clinic
Department of Neurology
Email: jones.da...@mayo.edu

A Research Fellow at Mayo Clinic is a temporary position intended to provide 
training and education in research. Individuals will train in the research 
program of a Mayo Clinic principal investigator. Qualified individuals will 
demonstrate the potential for research as evidenced by their training and 
peer-reviewed publications and should become competitive for national research 
grants. Proof of English proficiency is required for J-1 Short-Term Scholars, 
Research Scholars, Professors, Specialists, and Student Interns sponsored by 
Mayo Clinic.

Why Mayo Clinic?  Learn and grow among the best in your field at the nation’s 
top hospital (U.S. News & World Report, 2016-2017), ranked No. 1 in more 
specialties than any other care provider. Mayo Clinic is committed to 
sustaining and growing research, believes in research-driven care and 
establishes a well-defined integration between the clinical practice and 
research. At Mayo Clinic, you’ll use the power of collaboration to achieve the 
highest standards for medical care and health improvement, working in the 
largest integrated, not-for-profit medical group practice in the world with 
over 60,000 employees. You’re invited to contribute to a unique environment 
that brings together the best in patient care, groundbreaking research and 
innovative medical education. We offer exceptional benefits, and have been 
recognized by FORTUNE magazine as one of the top 100 “Best Companies to Work 
For”.

Mayo Clinic is an equal opportunity educator and employer (including veterans 
and persons with disabilities).
-
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Re: [Freesurfer] help

[Douglas Greve]

Use

mri_binarize --i aseg.mgz --match 17 --binval -1 --o your.lefthippo.nii.gz



On 4/6/17 6:00 AM, Dilip Puri wrote:

Hi everyone,

I am working on Hippocampus segmentation using Neural Networks for 
that I need labeled images of Hippocampus corresponding to original 
images.


I am using OASIS Dataset for this. I want to generate labeled images 
using FREESURFER. Is there any way to label each 3D co-ordinate

HippoCampus -1
Otherwise - 0

Here are sample files link 



Kindly help me!


Dilip Puri 
IIIT Vadodara 


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Re: [Freesurfer] Multiple Comparisons Correction thresh error

[Douglas Greve]

I think this is a "language" problem in that it is converting the "1.3" 
into "1,3" and then getting confused. I'm not sure how to fix it, but I 
think it has to do with the LOCAL setting.



On 4/6/17 5:07 AM, teodora petrova wrote:

Hello,

I would like to correct my glm_fit results for multiple comparisons.
I am using the following commands, similar to the one in the group 
analysis tutorial:


mri_glmfit-sim  --glmdir lh.index.glmdir  --cache 1.3 abs --cwp 0.05  
--2spaces
mri_glmfit-sim  --glmdir lh.index.glmdir  --cache 2.0 pos --cwp 0.05  
--2spaces


And receive the following errors:

ERROR:thresh=1,3, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
ERROR:thresh=2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0

I am sure I am typing a point, but it is read as a comma. Any ideas why?
Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
Platform: Ubuntu MATE 16.04

Thank you very much!

Regards,
Teodora







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Re: [Freesurfer] R: R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis

[Douglas Greve]

It will be in the space that you analyzed it in. If you want the native 
space, then use -native when running preproc-sess and mkanalysis



On 4/6/17 2:34 AM, std...@virgilio.it wrote:
Furthermore, the res-001.nii which is produce in produced in the res 
folder in not the same dimension of f.nii.
I would do the whole FAST preprocessing on f.nii., maintaining the 
same dimension and open it with FSL.

Thanks
Stefano

Messaggio originale
Da: std...@virgilio.it
Data: 5-apr-2017 23.39
A: "Freesurfer support list"
Ogg: [Freesurfer] R: Re: R: Re: Whole preprocessing with FAST
without to perform a seed based analysis

Hi,

as you advise I have run selxavg3-sess with the -svres option.
I found a folder called "res" which contain "res-001.nii". Is it
the f.nii fully processed?
Thanks
Stefano

Messaggio originale
Da: "Douglas Greve" 
Data: 14-mar-2017 17.38
A: 
Ogg: Re: [Freesurfer] R: Re: Whole preprocessing with FAST
without to perform a seed based analysis

You can't  on either occasion just using preproc-sess. You can
create an analysis with those components, then run
selxavg3-sess with the -svres option. This will create a
folder called eres with volumes that have had all the nuisance
variables and low freqeuncies regressed out


On 3/14/17 12:32 PM, std...@virgilio.it wrote:

Thanks.
1- By using only preproc-sess, how can I perform "band pass
filtering"?
2- And how can I take in account the nuisance variables: the
CSF from which the top 5 principle components, the white
matter from which the top 5 principle components, motion
correction parameters (-mcextreg), 5th order polynomial. How
can I eliminate the first 4 time points?
Regards
Stefano

Messaggio originale
Da: "Douglas Greve" 
Data: 14-mar-2017 16.14
A: 
Ogg: Re: [Freesurfer] Whole preprocessing with FAST
without to perform a seed based analysis

just use preproc-sess


On 3/14/17 10:45 AM, std...@virgilio.it wrote:

Hi list,
in FS-FAST, on rs-fMRI data, is possible to run
selxavg3-sess without -a option?
I would use whole the FS-FAST to preprocess my data. I
would include the mkanalysis-sess step but I would not
perform a seed-based analysis.
Thanks
Stefano


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Re: [Freesurfer] Re. display SPM results on inflated surface? {Disarmed}

[Douglas Greve]

I got it from FSL in the $FSLDIR/data/standard, but it is distributed 
with SPM as well



On 4/5/17 9:39 PM, Kevin Aquino wrote:

Hi Douglas,

I am wondering, where did you find the mini 152 T1 map? :)

Regarding this...
Would it be better to instead run recon-all on a higher-res MNI atlas? 
and then run mri_vol2surf for that segmentation?







Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of 
Nottingham.


Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk 
, aqu...@physics.usyd.edu.au 
 | *W* *MailScanner has detected a 
possible fraud attempt from "www.physics.usyd.edu.au" claiming to be* 
https://kevinaquino.github.io 


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up and does not stop until you get into the office.

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On Thu, Mar 23, 2017 at 7:53 AM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


Just map your mni152-spm volume to the surface with mri_vol2surf and
--regheader, eg,

mri_vol2surf --mov yourspm152.nii.gz --hemi lh --projfrac 0.5 --s
mni152
--o lh.yourspm152.nii.gz

then visualize

tksurferfv mni152 lh inflated -ov lh.yourmni152.nii.gz


On 3/22/17 3:46 PM, Schoot, Lotte wrote:
> Thanks so much, I appreciate the help.
> However, I am not sure what I am supposed to do with the output
of the recon-all process.
> Can I simply use the .dat file that is outputted there in
MRI_vol2surf?
>
> Lotte
>
>
> Date: Wed, 22 Mar 2017 13:01:42 -0400
> From: Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] display SPM results on inflated surface?
> To: freesurfer@nmr.mgh.harvard.edu

> Message-ID:
<41134c50-bb0b-792c-c52b-b6850bcec...@nmr.mgh.harvard.edu
>
> Content-Type: text/plain; charset="windows-1252"
>
> If you have the T1 for the mni152 (which is somewhere in the
bowels of the spm distribution), then you just run recon-all on
it. I've done this for myself, so you can just download the result
(which I have not checked thoroughly) from here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mni152.tar.gz

>
>
>
> On 3/21/17 1:27 PM, Schoot, Lotte wrote:
>> Hi Doug and others,
>>
>> A while ago, I got this reply to my question below (thanks!). I
tried to look in to it, but I am a bit confused (probably because
I am very new to Freesurfer).
>> My results are on the MNI 152, but I don't understand what you
mean with 'run the mni152 through freesurfer'. Is this the process
to get the register.dat file that is required in mri_vol2surf?
>> What would you recommend to get the register.dat file? Is it
possible to use bbregister for that? I have tried this, but I
don't know whether it is correct:
>>
>> bbregister --s fsaverage --mov con_0001.nii --init-spm --reg
>> register.dat --bold
>>
>>
>> Thanks!
>> Lotte
>>
>>
>>> If your results are on the MNI152, you can run the mni152 through
>>> freesurfer, then use mri_vol2surf to map the data to the
surface then
>>> view it with freeview (or tksurfer). You should not confuse
this with
>>> doing the fMRI analysis on the surface. You will not have the
>>> benefits of surface-based analysis
>>
>> On 02/15/2017 03:37 PM, Schoot, Lotte wrote:
>>> /Hi all, />//>/I was wondering if you knew of a way to display SPM
>>> results onto the />/inflated surface in Freesurfer. />//>/I have
>>> tried using SurfRend but there seem to be problems which might
/>/be
>>> due to the fact the results are obtained with SPM12 and SurfRend
>>> />/was designed to work with SPM5. />//>/Thanks, />/Lotte
>>> />//>//>/___
>>> />/Freesurfer mailing list />/Freesurfer at
nmr.mgh.harvard.edu 
>> >
>> />/https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 /
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> greve

Re: [Freesurfer] R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis

[Douglas Greve]

yes, those are the residuals


On 4/5/17 5:39 PM, std...@virgilio.it wrote:

Hi,

as you advise I have run selxavg3-sess with the -svres option.
I found a folder called "res" which contain "res-001.nii". Is it the 
f.nii fully processed?

Thanks
Stefano

Messaggio originale
Da: "Douglas Greve" 
Data: 14-mar-2017 17.38
A: 
Ogg: Re: [Freesurfer] R: Re: Whole preprocessing with FAST without
to perform a seed based analysis

You can't  on either occasion just using preproc-sess. You can
create an analysis with those components, then run selxavg3-sess
with the -svres option. This will create a folder called eres with
volumes that have had all the nuisance variables and low
freqeuncies regressed out


On 3/14/17 12:32 PM, std...@virgilio.it wrote:

Thanks.
1- By using only preproc-sess, how can I perform "band pass
filtering"?
2- And how can I take in account the nuisance variables: the CSF
from which the top 5 principle components, the white matter from
which the top 5 principle components, motion correction
parameters (-mcextreg), 5th order polynomial. How can I eliminate
the first 4 time points?
Regards
Stefano

Messaggio originale
Da: "Douglas Greve" 
Data: 14-mar-2017 16.14
A: 
Ogg: Re: [Freesurfer] Whole preprocessing with FAST without
to perform a seed based analysis

just use preproc-sess


On 3/14/17 10:45 AM, std...@virgilio.it wrote:

Hi list,
in FS-FAST, on rs-fMRI data, is possible to run
selxavg3-sess without -a option?
I would use whole the FS-FAST to preprocess my data. I would
include the mkanalysis-sess step but I would not perform a
seed-based analysis.
Thanks
Stefano


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Re: [Freesurfer] How to generate binary mask image using FreeSurfer's “mri_volsynth”?

[Douglas Greve]

It should save it in the current directory. But I don't think we write 
out IMA files. Why not use nifti (nii or nii.gz)?



On 4/5/17 2:05 PM, Karan Vahi wrote:


Dear Freesurfers,


I am trying to implement the methods mentioned in this paper to deal 
with partial volume effects when quantifying metabolites: 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4849426/#__sec2title 



The first step it mentions is: A binary mask must first be created, 
which represents the 3D SVS voxel. A binary mask is an image where 
each voxel contains either 1 or 0; in this case, the SVS voxel would 
be represented by a value of 1 and all other voxels 0. There are 
multiple ways to create a binary mask; one example, which was used 
successfully in this work, is the “mask()” function within Matlab9 and 
the FreeSurfer (Fischl)10 application “mri_volsynth.”


When I am trying the following command in FreeSurfer:

mri_volsynth --dim 3 4 5 2 --vol try.IMA

I am getting this output:

Inline image 1


But, I don’t know where it is saving the output file. And, I am also 
not sure whether I am using mri_volsynth correctly. What is --dim nc 
nr ns nf in https://surfer.nmr.mgh.harvard.edu/fswiki/mri_volsynth 
?


Also which pixels suppose to be 1's and which 0's?


Any help is appreciated.



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[Freesurfer] recon-all -parallel osx sierra

[jasi3k]

Dear all,

I am using Freesurfer 6.0 to run recon-all on 0.8 isotropic data. Whenever I 
use the parallel flag I get this error.

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

Same subject without the parallel flag runs smoothly but of course takes much 
longer. I have seen a similar problem on the list and the suggestion was to 
make a clean install of Freesurfer 6.0, which I did but unfortunately it didn’t 
help.

Any suggestions will be appreciated.

Best,
Jan







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[Freesurfer] Error during recon-all

[Das S.]

Dear FreeSurfer  Developers,

I was trying to use the command recon-all -autorecon1 -subjid bert and got an 
error.
When I checked I found the error was coming while executing the below command:
nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc 
./tmp.mri_nu_correct.mni.7555/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.7555/0/ 
-iterations 1000 -distance 50

When I executed the command separately I got below error message:

Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at 
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165.
nu_correct: crashed while running nu_estimate_np_and_em (termination 
status=65280)
ERROR: nu_correct

Can you please suggest why the error is coming and how to remove it.


Many thanks
Sarbani


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[Freesurfer] Custom registration template

[Linda Zhang]

Dear all,

I've been following the instructions for building a custom registration
template as written here (
http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) and here (
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018345.html
).

I'm now at the mris_preproc stage and according to the instructions, the
command should be:

# Get thickness values in the newtemplate space for GLM analysis
mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3
...

I put my subject list into a text file and replaced --s with --f [subjlist]
but kept everything else the same.  I got two errors for no source hemi
specified and no output specified, so I added --hemi lh and --out
lh.surfreg.newtemplate.thick --meas thickness.  Am I supposed to do this,
and will the output file be used for anything else down the line, i.e.,
should it be named something more specific?  I see that the next step is to
rerun the make_average_subject, but I don't see where the output from the
mris_preproc step would figure in.

On a (maybe) separate issue, when I finally ran my command line:

mris_preproc --surfreg sphere.reg.newtemplate --f subjlist --hemi lh --out
lh.surfreg.newtemplate.thick --meas thickness

I got the following error:

nsubjects=100
tmpdir is ./tmp.mris_preproc.25619
/home/fsuser/data
set: Variable name must contain alphanumeric characters.

I'm not sure where the problem might be here.  I'm running FreeSurfer v.5.3
in Virtualbox, and I haven't had any problems while running recon-all on
the subjects previously.

Any insight would be greatly appreciated, thank you!

Cheers,
Linda
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Re: [Freesurfer] Multiple Comparisons Correction thresh error

[teodora petrova]

Hello, 
I forgot to mention in my previous email that the system locale is in Swedish. 
Can this be the reason?
Regards,Teodora

On Thursday, April 6, 2017, 1:07:56 PM GMT+2, teodora petrova 
 wrote:Hello, 
I would like to correct my glm_fit results for multiple comparisons. I am using 
the following commands, similar to the one in the group analysis tutorial: 
mri_glmfit-sim  --glmdir lh.index.glmdir  --cache 1.3 abs  --cwp 0.05  
--2spacesmri_glmfit-sim  --glmdir lh.index.glmdir  --cache 2.0 pos  --cwp 0.05  
--2spaces 
And receive the following errors: 
ERROR:thresh=1,3, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 ERROR:thresh=2,0, must 
be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 
I am sure I am typing a point, but it is read as a comma. Any ideas why?
Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Platform: Ubuntu MATE 16.04 Thank you very much!
Regards,Teodora 

 



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[Freesurfer] help

[Dilip Puri]

Hi everyone,

I am working on Hippocampus segmentation using Neural Networks for that I
need labeled images of Hippocampus corresponding to original images.

I am using OASIS Dataset for this. I want to generate labeled images using
FREESURFER. Is there any way to label each 3D co-ordinate
HippoCampus -1
Otherwise - 0

Here are sample files link


Kindly help me!


Dilip Puri 
IIIT Vadodara 
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[Freesurfer] QA Tools v1.2 and future release

[Yong Li]

Dear Freesurfer Experts,

As one of the new freesurfers, I really appreciate the excellent work of
authors as well as great support of users' forum.

A good guess of mine is that authors, e.g., Vasanth or Louis etc., are busy
updating QA tools after the FSv6 release since the QA Tools v1.2 was
written for FSv5.3. If so, is it possible to provide an estimated release
date please so as to adjust my plan? Thanks for understanding!

In case, it might take a while to release the next QA Tool, may I dare to
provide my attempts of code updating of some functions in QA Tools? The
following are the brief list of code adapting steps:
1. modified codes for generating file order list in recon_checker;
2. modified codes for matching segment names for instance from
DefaultAsegMeans.txt in gparcmean_from_table;
3. adapted default_FOF and default_status_log for FSv6.

After these adaptation, QA Tools ran through and I only encountered some
'syntax error' in terminal for 2 segments, 5th-Ventricle and
WM-hypointensities, that I have to ask the experts to guide me through this
point if it's of your interests. To ensure the QA Tools functioning well, I
tested 116 elderly patients and detected reasonable outliers per patient.
Therefore, I would like to double that my code updating based on my general
understanding of QA Tool still fit to the basic purpose of authors by
asking the following theoretical questions:

1. SNR and segments outliers detection are measures of quality assessment
in QA Tools. Have other factors such as subject's motion, image bias,
resolution etc. been considered in QA Tools or future release? The default
SNR threshold is 16 based on any reference? The max SNR of my patients so
far is 32. Any idea of scores of healthy elderly controls?

2. The QA Tools v1.2 analyzes aseg.stats output. Is it possible to include
output of brainstem substructures and HippocampalSubfields of FSv6? If yes,
I would like to adapt the codes and provide you some feedback if you think
that I can help bit.

3. Future directions mentioned in QA Tools wiki site are interesting and
thoughtful. Are other features like 'Detect outliers in aparc and aparc2009
volumes' on the way?

4. Is there a function to summarize all QA measures to csv files, like the
quantifyBrainstemStructures.sh in brainstem substructures?

Thank you in advance!

Kind regards,

Yong Li, PhD
_
Department of Neurology,
Klinikum rechts der Isar,
Technische Universität München,
Munich, Germany
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[Freesurfer] Multiple Comparisons Correction thresh error

[teodora petrova]

Hello, 
I would like to correct my glm_fit results for multiple comparisons. I am using 
the following commands, similar to the one in the group analysis tutorial: 
mri_glmfit-sim  --glmdir lh.index.glmdir  --cache 1.3 abs  --cwp 0.05  
--2spacesmri_glmfit-sim  --glmdir lh.index.glmdir  --cache 2.0 pos  --cwp 0.05  
--2spaces 
And receive the following errors: 
ERROR:thresh=1,3, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 ERROR:thresh=2,0, must 
be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 
I am sure I am typing a point, but it is read as a comma. Any ideas why?
Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Platform: Ubuntu MATE 16.04 Thank you very much!
Regards,Teodora 

 



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Re: [Freesurfer] Fwd: recon-all error

[Antonin Skoch]

Dear Patricia,

this is I suppose the last issue concerning symbolic links, related with part 
of code starting with following comment:

 # if fsaverage is not in subjects dir, put it there

I think that the most straightforward  solution of this issue is to manually 
copy the fsaverage subject to $SUBJECTS_DIR before invocation of recon-all. 

Antonin



forgot to attach the printscreen 
 
2017-04-06 9:49 GMT+02:00 Patr?cia Klobu?iakov? < 
patricia.klobusiak...@gmail.com>: 
 
> Hi Antonin, 
> 
> I edited recon-all file, but another error was reported. This error 
> concerns symbolic links, too. Is there any way I could make it work on this 
> virtual machine? I coud try to substitute all ln commands with cp or 
> something like that. 
> 
> Thanks. 
> 
> Patricia 
> 
> 2017-04-04 13:43 GMT+02:00 Antonin Skoch : 
> 
>> Dear Patricia, 
>> 
>> see this thread: 
>> 
>> freesurfer@nmr.mgh.harvard.edu/msg51797.html" 
>> title="http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51797.html";
>>  
>> target="_blank">http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51797.html
>>  
>> 
>> Your working directory probably resides on the filesystem which does not 
>> support symbolic links. You probably could workaround this by editing your 
>> recon-all and replace line 
>> 
>> set cmd2 = (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix) 
>> by 
>> 
>> set cmd2 = (cp $hemi.white.preaparc.$suffix $hemi.white.$suffix) 
>> 
>> Antonin Skoch 
>> 
>> 
>> 
>> Hello FreeSurfer Developers,  I have installed Freesurfer on Windows 
>> using VMware - CentOS 64-bit (the one from FSLuser Linux installation). 
>>  Everytime I run recon-all, there is an error. 
>>  The same error occurs  when I try to rum mri2mesh command in SIMNIBS 
>> toolbox which uses Fresurfer (recon-all), too. I'm sending screenshots and 
>> logfile attached. 
>>   Version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
>> uname -a: Linux fslvm6.localdomain 2.6.32-431.5.1.el6.x86_64          #1 
>> SMP Wed Feb 12 00:41:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux 
>>  Thanks for your help. 
>> 
>>  Best,  Patricia ___
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Re: [Freesurfer] Fwd: recon-all error

[Patrícia Klobušiaková]

Hi Antonin,

I edited recon-all file, but another error was reported. This error
concerns symbolic links, too. Is there any way I could make it work on this
virtual machine? I coud try to substitute all ln commands with cp or
something like that.

Thanks.

Patricia

2017-04-04 13:43 GMT+02:00 Antonin Skoch :

> Dear Patricia,
>
> see this thread:
>
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51797.html
>
> Your working directory probably resides on the filesystem which does not
> support symbolic links. You probably could workaround this by editing your
> recon-all and replace line
>
> set cmd2 = (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix)
> by
>
> set cmd2 = (cp $hemi.white.preaparc.$suffix $hemi.white.$suffix)
>
> Antonin Skoch
>
>
>
> Hello FreeSurfer Developers,  I have installed Freesurfer on Windows using
> VMware - CentOS 64-bit (the one from FSLuser Linux installation).
>  Everytime I run recon-all, there is an error.
>  The same error occurs  when I try to rum mri2mesh command in SIMNIBS
> toolbox which uses Fresurfer (recon-all), too. I'm sending screenshots and
> logfile attached.
>   Version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> uname -a: Linux fslvm6.localdomain 2.6.32-431.5.1.el6.x86_64  #1
> SMP Wed Feb 12 00:41:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
>  Thanks for your help.
>
>  Best,  Patricia
>
>
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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
> 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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