[Freesurfer] red and blue gradient color map for freeview

[Eun Young Choi]

Hi all,

I'd like to have a freeview color map that has both a red-yellow gradient
and a blue-light blue gradient (the typical colors for positive and
negative fcMRI correlations) and ideally no color for 0... None of the
standard color maps in freeview work well and I can't seem to find one
online. Has anyone created one? Or know where I can view the text file for
the standard color maps that come with freeview, so I can create one myself?

Thank you!
Eun Young
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Re: [Freesurfer] Freesurfer 6.0?

[VA Research]

Did you receive a reply/

Any news update for 6.0 release?

On Mon, Jul 25, 2016 at 1:01 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

>
> Hi there
>
> Do we have a potential date for the Freesurfer 6.0 release? I was told I
> would want to re-run all my subjects to create better surfaces using
> Freesurfer 6.0 and I am wondering if it really will improve surface
> extraction that much.
>
> Many thanks!
>
> Trisanna
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
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[Freesurfer] when to -qcache in longitudinal processing

[Linette Savage]

Hello Freesurfers,

My ultimate goal is a MLE analysis of 2 groups (n~25) at 2 time points.

I have followed the longitudinal processing stream (cross, base, long) although 
only ran -qcache at the cross stage. Do I need to add this flag to the base 
and/or long recon-all command? Or is the same thing achieved by running this 
code (described in the LME wiki page under Preparing your data):

mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi lh 
--meas thickness --out lh.thickness.stack.mgh
mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.stack.mgh --tval 
lh.thickness.stack.fwhm10.mgh --fwhm-trg 10 --cortex --noreshape

I'm using Freesurferv5.3.0 on OS X El Capitan although about to move to a Linux 
system.


Thanks kindly,


Linette Savage

University of Calgary

Brain Training Study

www.braintrainingstudy.ca




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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

[Elijah Mak]

Dear Anastasia,

I have also uploaded the file with the problem (22995_EM.zip), and this is
how my config file looks like after modifications:

set subjlist = (22995)
set pathlist = (fmajor_PP)
set ncpts = (7)
set reinit = (1)

Thanks again!

Best Wishes,
Elijah


-- 

Elijah Mak

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

[Anastasia Yendiki]

Hi Elijah - You add "set reinit =1" to the config file, (and remember to 
set the pathlist and subjlist to only what you want to rerun), and then 
rerun the -prior and -path steps in that order.


Best,
a.y

On Thu, 18 Aug 2016, Elijah Mak wrote:


Thanks for the tips on reinitialisation of tracts.

Apologies if I might have missed it in the online tutorial, do you have some
general guidelines for reinitialising?

Can I simply add "set reinit =1" to my configuration file, and then re-run
trac-all -path. Are there any other parameters I could tweak?

After running through more QC on other subjects, I have also noticed other
tracts that were not fully constructed. These tracts appear to be truncated
or blob-like, for a lack of better word :) I have attached the screenshot to
illustrate what I mean.

In these cases, I do the following QC routine after the general recon-all QC

1) freeview -v dmri/dtifit_FA.nii.gz -v dlabel/diff/aparc+aseg.bbr.nii.gz 
2) freeview -v $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz
subjectname/dmri/cvs/dtifit_FA.bbr.nii.gz 


Thanks a lot for your help, Anatasia!

Best Wishes,
Elijah


--

Elijah Mak

PhD Candidate | Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ



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Re: [Freesurfer] label analysis

[Douglas Greve]

Use mris_anatomical_stats


On 8/18/16 9:53 AM, Raffaele Dubbioso wrote:


Dear Freesurfer team,
I'm working on structural data analysis using Fressurfer. I have drawn 
my own labels and now I'd like to get data like thickness, curvature, 
folding index in  the same way that I usually get when I run the 
aparc.stat function.

Can you please help me how to solve this problem?

Thanks a lot and looking forward to hearing from you

Best regards,
Raffaele



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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

[Anastasia Yendiki]

Hi Elijah - It looks like the CVS case needs to be reinitialized. In 
principle you're right that if the registration is good this shouldn't be 
a problem. It's hard to tell what might've caused this in an individual 
case without looking at the data. If you want me to look into it you can 
upload all the TRACULA directories of the subject for me here:

https://gate.nmr.mgh.harvard.edu/filedrop2/

Thanks!

a.y

On Thu, 18 Aug 2016, Elijah Mak wrote:


Dear Anastasia and List,
I have been using TRACULA to process my DTI dataset using both the affine
MNI and non-linear CVS options.
In one subject, the forceps major (MNI) look very different from its CVS
counterpart (screenshot attached). I am just wondering what could lead to
this type of differences? I've checked the registrations and they look good
(overlaying FA on MNI/CVS).

Thanks!

Best Wishes,
Elijah


--

Elijah Mak

PhD Candidate | Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ



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Re: [Freesurfer] FSFAST ROI atlas

[Harms, Michael]

Yes, the Gordon parcellation paper:

http://www.ncbi.nlm.nih.gov/pubmed/25316338





-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From:  on behalf of Sabin Khadka 
Reply-To: Freesurfer support list 
Date: Thursday, August 18, 2016 at 8:55 AM
To: "Harms, Michael" 
Cc: Freesurfer support list 
Subject: Re: [Freesurfer] FSFAST ROI atlas





Hi Michael- Thanks very much for the file. Is there published paper or other documents that I could use as reference for these annotation?




Cheers,

Sabin Khadka




On Wed, Aug 17, 2016 at 12:53 PM, Harms, Michael 
 wrote:





They are attached (assuming that the FS list allows small attachments).
There is a script that details exactly how it was done.





-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 
314-747-6173
St. Louis, MO  63110 Email: 
mha...@wustl.edu






From: Sabin Khadka 
Date: Wednesday, August 17, 2016 at 11:25 AM
To: Freesurfer support list , "Harms, Michael" 


Subject: Re: [Freesurfer] FSFAST ROI atlas









Hi Michael- Is there anyway I can get those Gordon parcellation annot files?




Cheers,

Sabin Khadka




On Wed, Aug 17, 2016 at 10:59 AM, Harms, Michael 
 wrote:






FYI: I supplied a version of the “Gordon” parcellation in .annot format to Bruce a while back.  He had expressed an interest in possibly including it as part of FS 6.0.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 
314-747-6173
St. Louis, MO  63110 Email: 
mha...@wustl.edu







From:  on behalf of Doug Greve 
Reply-To: "freesur...@nmr.mgh.harvard.edu" 
Date: Wednesday, August 17, 2016 at 9:55 AM
To: "freesur...@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] FSFAST ROI atlas





I don't know anything about the Power atlas. For the HCP, if they have it in annotation format, then you can run mri_aparc2aseg to map it into the anatomical volume, then specify that volume when you run fcseed-config. To get the mri_aparc2aseg command line,
 look in the recon-all to find out how aparc+aseg.mgz is created


On 8/17/16 9:28 AM, Sabin Khadka wrote:



Hi Doug- Do you think it is possible to use these atlas? If so could you point me to steps that needed to be done.


Thanks for your help!





Cheers,

Sabin Khadka




On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve 
 wrote:



I have not used them myself.



On 8/15/16 10:23 AM, Sabin Khadka wrote:








HI all- 


I am using FSFAST to extract ROI time series values for further connectivity analysis. I've used Desikan, Destriuex and DKT atlas. 


However, I was wondering if anyone has used Power 
et.al 2011 rois and/or HCP's newly defined 180/per hemi rois to extract time series data. If so could you please advise me on how do it (if they are at all possible). 




Cheers,

Sabin Khadka





 



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Re: [Freesurfer] FSFAST ROI atlas

[Sabin Khadka]

Hi Michael- Thanks very much for the file. Is there published paper or
other documents that I could use as reference for these annotation?

Cheers,
Sabin Khadka

On Wed, Aug 17, 2016 at 12:53 PM, Harms, Michael  wrote:

>
> They are attached (assuming that the FS list allows small attachments).
> There is a script that details exactly how it was done.
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
> From: Sabin Khadka 
> Date: Wednesday, August 17, 2016 at 11:25 AM
> To: Freesurfer support list , "Harms,
> Michael" 
>
> Subject: Re: [Freesurfer] FSFAST ROI atlas
>
> Hi Michael- Is there anyway I can get those Gordon parcellation annot
> files?
>
> Cheers,
> Sabin Khadka
>
> On Wed, Aug 17, 2016 at 10:59 AM, Harms, Michael  wrote:
>
>>
>> FYI: I supplied a version of the “Gordon” parcellation in .annot format
>> to Bruce a while back.  He had expressed an interest in possibly including
>> it as part of FS 6.0.
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave. Tel: 314-747-6173
>> St. Louis, MO  63110 Email: mha...@wustl.edu
>>
>> From:  on behalf of Doug Greve <
>> gr...@nmr.mgh.harvard.edu>
>> Reply-To: "freesurfer@nmr.mgh.harvard.edu" > u>
>> Date: Wednesday, August 17, 2016 at 9:55 AM
>> To: "freesurfer@nmr.mgh.harvard.edu" 
>> Subject: Re: [Freesurfer] FSFAST ROI atlas
>>
>> I don't know anything about the Power atlas. For the HCP, if they have it
>> in annotation format, then you can run mri_aparc2aseg to map it into the
>> anatomical volume, then specify that volume when you run fcseed-config. To
>> get the mri_aparc2aseg command line, look in the recon-all to find out how
>> aparc+aseg.mgz is created
>>
>> On 8/17/16 9:28 AM, Sabin Khadka wrote:
>>
>> Hi Doug- Do you think it is possible to use these atlas? If so could you
>> point me to steps that needed to be done.
>>
>> Thanks for your help!
>>
>> Cheers,
>> Sabin Khadka
>>
>> On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve <
>> gr...@nmr.mgh.harvard.edu> wrote:
>>
>>> I have not used them myself.
>>>
>>> On 8/15/16 10:23 AM, Sabin Khadka wrote:
>>>
>>> HI all-
>>>
>>> I am using FSFAST to extract ROI time series values for further
>>> connectivity analysis. I've used Desikan, Destriuex and DKT atlas.
>>>
>>> However, I was wondering if anyone has used Power et.al 2011 rois
>>> and/or HCP's newly defined 180/per hemi rois to extract time series data.
>>> If so could you please advise me on how do it (if they are at all
>>> possible).
>>>
>>> Cheers,
>>> Sabin Khadka
>>>
>>>
>>> ___
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>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>>> du/mailman/listinfo/freesurfer The information in this e-mail is
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>>> information, please contact the Partners Compliance HelpLine at
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>>> in error but does not contain patient information, please contact the
>>> sender and properly dispose of the e-mail.
>>
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>> but does not c

[Freesurfer] label analysis

[Raffaele Dubbioso]

Dear Freesurfer team,
I'm working on structural data analysis using Fressurfer. I have drawn my
own labels and now I'd like to get data like thickness, curvature, folding
index in  the same way that I usually get when I run the aparc.stat
function.
Can you please help me how to solve this problem?

Thanks a lot and looking forward to hearing from you

Best regards,
Raffaele
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Re: [Freesurfer] Error with long_mris_slopes: Surface files do not exist

[Martin Reuter]

Hi Nick,

I don’t understand what you are trying to do. I don’t think ?h.surface is a 
valid file (it is not created or used by freesurfer). Surfaces are for example 
?h.white or ?h.pial. Also you say that thickness files exist and that the 
long_mris_slopes analysis worked for thickness. You cannot run that command for 
a “surface”. Thickness is a measure defined on the surface, so when running it 
for thickness, this is a surface based analysis. Again, there is no ?h.surface 
file and it should not be there.

Best, Martin

> On Aug 16, 2016, at 7:23 PM, Corriveau-Lecavalier Nick 
>  wrote:
> 
> Hi Martin,
> 
> 
> I ran the -long for one subject again, but the ''rh.surface'' and 
> ''lh.surface'' are still missing, even though to process finished without 
> error  (the thickness files do exist and are in their right place). Also, it 
> would be a surprisingly weird coincidence if something went wrong with all of 
> my subjects during the -long process.
> 
> 
> Do you have any idea why these files are still missing? I joined the 
> recon-all.log for the -long processes as well.
> 
> 
> Regards,
> 
> __
> 
> De : freesurfer-boun...@nmr.mgh.harvard.edu 
>  
>  > de la part de Martin Reuter 
> mailto:mreu...@nmr.mgh.harvard.edu>>
> Envoyé : 16 août 2016 05:45
> À : Freesurfer support list
> Objet : Re: [Freesurfer] Error with long_mris_slopes: Surface files do not 
> exist
> 
> Hi Nick,
> 
> it looks like the base finished without error. But if your *.long.basid/surf/ 
> are missing the lh.thickness , then something went wrong when processing the 
> -long runs. I would recommend to run a single subject step by step to see 
> what goes wrong (could be IO problems or disk space etc).
> 
> Best, Martin
> 
> De : Corriveau-Lecavalier Nick
> Envoyé : 15 août 2016 17:06
> À : freesurfer@nmr.mgh.harvard.edu 
> Objet : Error with long_mris_slopes: Surface files do not exist
> 
> 
> Hello FreeSurfer developers,
> 
> 
> I am trying to run the long_mris_slopes command for surfaces. It worked well 
> the thickness, but when I run it for surfaces, my terminal tells me that the 
> surface file (lh.surface or rh.surface) is missing. It appears that all my 
> subjects are missing those files. I've search the list and no similar error 
> seems to have been reported.
> 
> 
> This is the exact command I used:  long_mris_slopes --qdec 
> /Applications/freesurfer/subjects/longitudinal_training/long_training.dat 
> --meas surface --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack 
> --do-label --time weeks --qcache fsaverage --sd 
> /Applications/freesurfer/subjects/
> 
> 
> I am running a on a OS X El Captain software, and the FreeSurfer version I am 
> using is the most recent one. I also joined the recon-all.long of one of my 
> subject (of the base, since I'm running longitudinal data), in case it could 
> help.
> 
> 
> Regards,
> 
> 
> Nick
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