Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anri WATANABE]

Thanks so much!!

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-08-03 23:15 GMT+09:00 Anastasia Yendiki :

>
> That's correct!
>
> On Wed, 3 Aug 2016, Anri WATANABE wrote:
>
> Hi Anastasia,
>> Thank you for your kind explanation. I can be understanding how TRACULA
>> tracts white matter pathways.
>> At each position (in training subjects, not in new subjects of my data)
>> probability that next goes for
>> which direction to every labels in the aparc+aseg (not with setting a
>> certain ROI) is computed with use of
>> training subjects. The prior probabilities are made from training
>> subjects (your publication in 2011) and
>> they are based on manual labeling (the manual labeling tracts are
>> referred to Wakana et al. 2007). Then
>> when white matter pathways are reconstructed in my subjects, TRACULA
>> computes anatomical priors in each
>> subjects in my data in pre-processing and probability distributions from
>> anatomical priors and by fitting
>> ball-and-stick model.
>> Is this comprehension ok?
>>
>> Best Regards,
>> Anri
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>> **
>>
>> 2016-07-31 22:49 GMT+09:00 Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>:
>>
>>   Hi Anri - Instead of hard-coding some ROIs in the white matter that
>> the tract is forced to go
>>   through, TRACULA uses information like "what is the probability
>> that this tract goes
>>   lateral/anterior/etc to XXX", where XXX any of the labels in the
>> aparc+aseg. TRACULA computes
>>   these prior probabilities from a set of training subjects, where
>> the tracts have been labeled
>>   manually. So it knows how likely a tract is to go through a certain
>> aparc+aseg label, or to he
>>   left, right, anterior, etc of a certain aparc+aseg label. This is
>> computed separately at each
>>   position along the tract. It's computed from the training subjects,
>> and then used when
>>   reconstructing the tract in the new subject that you run TRACULA on.
>>
>>   Hope this helps,
>>   a.y
>>
>>   On Sun, 31 Jul 2016, Anri WATANABE wrote:
>>
>> Thanks, AnastasiaI know that TRACULA use probabilistic
>> tractography but if ROIs
>> are not
>> set how determine the origin and the end of a certain tract?
>> I think that the
>> first we
>> have to determine the origin and the end of the tract, the
>> second it constructs
>> possible
>> pathway not with the deterministic way (only 1 direction / 1
>> voxel) but with the
>> probabilistic way (considering which direction should be next
>> to). Is this
>> comprehension
>> wrong?
>> Thank you.
>>
>> Anri
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>>
>> **
>>
>> 2016-07-31 13:22 GMT+09:00 Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>:
>>
>>   Hi Anri - TRACULA does not use deterministic ROIs. It
>> uses a probabilistic
>>   model of how likely each tract is to go through or next
>> to each of the
>> labels
>>   of the freesurfer subcortical segmentation and cortical
>> parcellation, as a
>>   function of position along the trajectory of the tract.
>>
>>   Best,
>>   a.y
>>
>>   On Sun, 31 Jul 2016, Anri WATANABE wrote:
>>
>> Hi Anastasia,
>> Thank you! It seems work well!!
>> I have another question. Are ROIs for automatic
>> tractography in
>> TRACULA the same ROIs
>> presented in Wakana et al. 2007?
>>
>> Anri
>>
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 

Re: [Freesurfer] mri_label2label

[Douglas N Greve]

You should just run mri_annotation2label on fsaverage and use the label 
you want

On 08/03/2016 01:55 PM, miracle ozzoude wrote:
> Hello,
> i used mri_annotation2label to extract individual parcellations for my 
> subjects. Do I need to register my subjects to fsaverage using 
> mri_label2label before creating a mask for  ROI surface based analysis 
> using GLM dods? Thanks
> Best,
> Paul
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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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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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] brain mask and T1 are not the same size

[Douglas N Greve]

Can you try running simply
freeview -v 
/Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri/brainmask.mgz

Then save to a different file name using the "Save Volume As". Does that 
file have the right dimensions?

Then make an edit and then "Save Volume". Does that file have the right 
dims?

It might be a mac thing; I've been working under linux


On 08/03/2016 01:05 PM, Isabelle Deschamps wrote:
> I am using an iMAC with mountain lion (10.8.5). I have this version of 
> Freesurfer: freesurfer-Darwin-lion-stable-pub-v5.3.0
>
> I open using a terminal Freeview:
>
> freeview -v 
> /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri/brainmask.mgz 
> \
> -f 
> /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/surf/lh.white:edgecolor=yellow
>  
> \
> /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/surf/lh.pial:edgecolor=red
>  
> \
> /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/surf/rh.white:edgecolor=yellow
>  
> \
> /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/surf/rh.pial:edgecolor=red
>  
> \
>
> Then I follow these instructions 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview).
>
> So basically, I look for areas where the skull or meninges are 
> included within the pial boundary.
>
> I use the recon edit button, making sure that the brainmask is 
> highlighted (see Screen shot attached). I use the default parameters 
> as it has worked well for me in the past. When I am done editing the 
> brainmask, I save the changes using the save volume button. Then I run 
> the following command to regenerate the pial surface.
>
> recon-all -autorecon-pial -subjid S08_FS.
>
> Let me know if I can provide other information. I am puzzled as to why 
> it worked for 3/4 of the participants but it won't work for 4 of them.
>
> Thank you again for the help,
>
> Isabelle
>
>
> Sorry, I did not see that one of the volumes was 256x256x255. I cannot
> replicate here on your data using 5.3 under linux. Can you say exactly
> what you do in freeview? Also, what version of FS are you using? And
> what platform?
>
> On 3 Aug 2016, at 12:00, <freesurfer-requ...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-requ...@nmr.mgh.harvard.edu>>
>  wrote:
>
>> Send Freesurfer mailing list submissions to
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>>
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>>
>>
>> Today's Topics:
>>
>>   1. Re: brain mask and T1 are not the same size (Isabelle Deschamps)
>>   2. Re: Coordinates in TRACULA group analysis (Anri WATANABE)
>>   3. Re: mapping error (Douglas Greve)
>>   4. Re: Multiple Comparison Question for surface-based analyses
>>  (Douglas Greve)
>>   5. Re: Coordinates in TRACULA group analysis (Anastasia Yendiki)
>>   6. Re: brain mask and T1 are not the same size (Douglas N Greve)
>>
>>
>> --
>>
>> Message: 1
>> Date: Wed, 3 Aug 2016 10:50:30 +
>> From: Isabelle Deschamps <isabelle.deschamp...@ulaval.ca>
>> Subject: Re: [Freesurfer] brain mask and T1 are not the same size
>> To: "<freesurfer@nmr.mgh.harvard.edu>"
>> <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <8f31a8f6-59c6-4d12-a2a4-2ef526465...@ulaval.ca>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> An HTML attachment was scrubbed...
>> URL: 
>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/fc0fed11/attachment-0001.html
>>
>> --
>>
>> Message: 2
>> Date: Wed, 3 Aug 2016 20:19:09 +0900
>> From: Anri WATANABE <z2aa...@koto.kpu-m.ac.jp>
>> Subject: Re: [Freesurfer] Coordinates in TRACULA group analysis
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID:
>> <caaw-jjeawc33oax6oameuect3q06ah8zyfd6nuuo32bn-eh...@mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi Anastasia,
>>
>> Thank you 

Re: [Freesurfer] mri_normalize, 110 is too dark

[tvg[fs]]

Hi Bruce,

> You can't just change which peak is the WM - lots of things downstream would 
> fail

That is unfortunate.

I've send you the subject files and the raw files via filedrop (per
these instructions
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange)


On Fri, Jul 29, 2016 at 4:38 PM, Bruce Fischl
 wrote:
> Hi Tom
>
> it's tough for us to tell without some images or the data. If you upload the
> entire subject dir of a subject that failed we will take a look. You can't
> just change which peak is the WM - lots of things downstream would fail
>
> cheers
> Bruce
>
>
>
> On Fri, 29 Jul 2016, tvg[fs] wrote:
>
>> Dear community and developers,
>>
>> I am experiencing issues during the normalization step, converting
>> NU.mgz to T1.mgz. Gray matter is falsely recognized as white matter
>> and high intensity WM is ignored. The resulting T1.mgz collapses the
>> wrong voxels into the 110 bin.
>>
>> It seems that what mri_normalize assumes a peak in the WM intensity
>> distribution that is too low.
>> In NU.mgz WM seems centered around 140 not 110. Note that this is not
>> due to RF-field inhomogeneities. It is likely of physiological origin
>>
>> - Is there a way to explicitly tell mri_normalize to use a different
>> intensity peak?
>>
>> I realize that correction can be done with control points, however I
>> understand that does not compute a new intensity distribution, but
>> merely adds voxels around CPs. This is undesirable since I have >20
>> scans to process. Also this will not correct the falsely tagged GM
>> voxels.
>>
>> I've tried to trick mri_normalize by adjusting NU.mgz intensity by -30
>> (140-30 = 110). This did not give me the wished-for effect.
>> - Is it possible to bypass preprocessing steps of mri_normalize before
>> collapsing?
>>
>> - In general it would help if there is some elaboration on the options:
>> -no1d,
>> -nosnr,
>> -gentle,
>> -f vs -fonly,
>> -prune,
>> -g,
>> -monkey
>> - is [-monkey] just shorthand for [-no1d -n 1]?
>>
>> Thanks,
>> Tom
>>
>> System:
>> Mac OS X 10.10.5
>> freesurfer-Darwin-lion-stable-pub-v5.3.0
>>>
>>> mri_normalize --version
>>
>> stable5
>> ___
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>>
>>
>>
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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Re: [Freesurfer] Anonymizing FreeSurfer files

[Douglas N Greve]

If you passed DICOMS directly to recon-all, then the only place that 
would have subject info would be the scripts/recon-all.log file; that 
file would captures the conversion, and the subject name and date of 
scan will show up there (might be some other info stored in the dicom 
file that gets printed out, not sure). I am assuming that you did not 
use the person's name as the FreeSurfer subject ID.

On 08/03/2016 02:33 PM, Keefe, Sarah wrote:
>
> Hi,
>
>
> I'm involved in a project that requires anonymizing FreeSurfer data to 
> remove all patient information. I've found that the subject folder 
> number is sometimes included in text files and logs in a FreeSurfer 
> folder. Is there any patient information stored in any of the non-text 
> files? Is there a way I could check other files for any stored patient 
> information?
>
> Thanks,
>
>
> Sarah
>
> 
>
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If 
> you are not the intended recipient, be advised that any unauthorized 
> use, disclosure, copying or the taking of any action in reliance on 
> the contents of this information is strictly prohibited. If you have 
> received this email in error, please immediately notify the sender via 
> telephone or return mail.
>
>
>
> ___
> Freesurfer mailing list
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] Anonymizing FreeSurfer files

[Keefe, Sarah]

Hi,


I'm involved in a project that requires anonymizing FreeSurfer data to remove 
all patient information. I've found that the subject folder number is sometimes 
included in text files and logs in a FreeSurfer folder. Is there any patient 
information stored in any of the non-text files? Is there a way I could check 
other files for any stored patient information?

Thanks,


Sarah


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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[Freesurfer] mri_label2label

[miracle ozzoude]

Hello,
i used mri_annotation2label to extract individual parcellations for my
subjects. Do I need to register my subjects to fsaverage using
mri_label2label before creating a mask for  ROI surface based analysis
using GLM dods? Thanks
Best,
Paul
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Freesurfer Digest, Vol 150, Issue 6

[Caroline Beelen]

My command line is:
mris_label2annot --subject fsaverage --hemi  lh  --ctab aparc.annot.ctab 
--annot myaparc  --l lh.fusiform.label 
  --l lh.inferiorparietal.label (etc.)  --nhits nhits.mgh
(I have version 5.3)

Regards, Caroline

Message: 3
Date: Wed, 3 Aug 2016 09:30:48 -0400
From: Douglas Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mapping error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <f3f77469-16ad-6fdf-f647-80aee162d...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

what is your command line?


On 8/3/16 6:00 AM, Caroline Beelen wrote:
>
> Dear FS,
>
> An aparc.annot ctab file was created but I got the following error:
>
> Colortable:aparc.annot.ctab
>
> Annotname: myaparc
>
> Nhitsfile nhits.mgh
>
> Nlabels 6
>
> Labeltresh 0 0.0
>
> Loading freesurfer/fsaverage/surf/lh.orig
>
> 1 -1 not found
>
> 2 -1 not found
>
> 3 -1 not found
>
> Etc?
>
> Mapping unhit to unknown
>
> Found 132101 unhit vertices
>
> Writing annot to freesurfer/fsaverage/lh.myaparc.annot
>
> I guess my ctab file is incorrect? I included an example of a label 
> with it.
>
> Thanks again for your help.
>
> Caroline
>
>

-Oorspronkelijk bericht-
Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens 
freesurfer-requ...@nmr.mgh.harvard.edu
Verzonden: woensdag 3 augustus 2016 18:00
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Freesurfer Digest, Vol 150, Issue 6

Send Freesurfer mailing list submissions to
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Today's Topics:

   1. Re: brain mask and T1 are not the same size (Isabelle Deschamps)
   2. Re: Coordinates in TRACULA group analysis (Anri WATANABE)
   3. Re: mapping error (Douglas Greve)
   4. Re: Multiple Comparison Question for surface-based analyses
  (Douglas Greve)
   5. Re: Coordinates in TRACULA group analysis (Anastasia Yendiki)
   6. Re: brain mask and T1 are not the same size (Douglas N Greve)


--

Message: 1
Date: Wed, 3 Aug 2016 10:50:30 +
From: Isabelle Deschamps <isabelle.deschamp...@ulaval.ca>
Subject: Re: [Freesurfer] brain mask and T1 are not the same size
To: "<freesurfer@nmr.mgh.harvard.edu>"
<freesurfer@nmr.mgh.harvard.edu>
Message-ID: <8f31a8f6-59c6-4d12-a2a4-2ef526465...@ulaval.ca>
Content-Type: text/plain; charset="us-ascii"

An HTML attachment was scrubbed...
URL: 
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--

Message: 2
Date: Wed, 3 Aug 2016 20:19:09 +0900
From: Anri WATANABE <z2aa...@koto.kpu-m.ac.jp>
Subject: Re: [Freesurfer] Coordinates in TRACULA group analysis
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<caaw-jjeawc33oax6oameuect3q06ah8zyfd6nuuo32bn-eh...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Anastasia,

Thank you for your kind explanation. I can be understanding how TRACULA
tracts white matter pathways.
At each position (in training subjects, not in new subjects of my data)
probability that next goes for which direction to every labels in the
aparc+aseg (not with setting a certain ROI) is computed with use of
training subjects. The prior probabilities are made from training subjects
(your publication in 2011) and they are based on manual labeling (the
manual labeling tracts are referred to Wakana et al. 2007). Then when white
matter pathways are reconstructed in my subjects, TRACULA computes
anatomical priors in each subjects in my data in pre-processing and
probability distributions from anatomical priors and by fitting
ball-and-stick model.
Is this comprehension ok?

Best Regards,
Anri



**


?? ??
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-31 22:49 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>:

>
> Hi Anri - Instead of hard-coding some ROIs in the white matter that the
> tract is forced to go through, TRACULA uses information like "

Re: [Freesurfer] brain mask and T1 are not the same size

[Douglas N Greve]

__
>>>> Freesurfer mailing list
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>>>>
>>>>
>>>> The information in this e-mail is intended only for the person to
>>>> whom it is
>>>> addressed. If you believe this e-mail was sent to you in error and
>>>> the e-mail
>>>> contains patient information, please contact the Partners Compliance
>>>> HelpLine at
>>>> 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.
>>>>
>>>
>>
>> -- 
>> Anthony Steven Dick, Ph.D.
>> Associate Professor
>> Director, Cognitive Neuroscience Program and Graduate Certificate in 
>> Cognitive Neuroscience
>> Department of Psychology
>> Florida International University Modesto A. Maidique Campus AHC4 454
>> 11200 S.W. 8th Street
>> Miami, FL 33199
>> Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
>> Email: ad...@fiu.edu
>> Webpage: http://myweb.fiu.edu/adick
>> Join the Society for the Study of Human Development: 
>> http://www.sshdonline.org
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> --
>>
>> Message: 9
>> Date: Wed, 3 Aug 2016 10:43:40 +0800
>> From: Thomas Yeo <ytho...@csail.mit.edu>
>> Subject: Re: [Freesurfer] Labels to MNI152, SPM compatible
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID:
>> <canzvntaw8ja0f7npk9erqsqpcbhcgxrrvnm7t3wftqtnyn4...@mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi Matyas,
>>
>> In freeview, looks fine to me. See attached.
>>
>> Can you send us your screenshot?
>>
>> Regards,
>> Thomas
>>
>> On Tue, Aug 2, 2016 at 9:39 PM, Maty?? Kuhn <matyas.k...@gmail.com> 
>> wrote:
>>> The Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz
>>> comes from
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011,
>>> and the description says it is the FSL MNI152 1mm template interpolated
>>> and intensity normalized into a 256 x 256 x 256 1mm-isotropic volume
>>> (obtained by putting the FSL MNI152 1mm template through recon-all ). So
>>> I supposed it is in MNI305 after it was processed with freesurfer. When
>>> I overlap the
>>> Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz and
>>> Template_T1_IXI555_MNI152.nii it is really shifted so I think it is not
>>> in MNI152.
>>>
>>> When I add the --invertmtx then the result is still the same, empty 
>>> image.
>>>
>>> I uploaded those images here:
>>> https://dl.dropboxusercontent.com/u/70539709/Freesurfer_question.zip ,
>>> if you want to try yourself.
>>>
>>>
>>> Thank you,
>>>
>>> Matyas
>>>
>>>
>>>
>>> Dne 2.8.2016 v 14:55 Douglas Greve napsal(a):
>>>>  From the names, it looks like both the seg vol and the template 
>>>> vol are both in mni152. Where did 
>>>> Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz 
>>>> come from? One thing you can try is to invert the registration by 
>>>> adding --invertmtx to the command line.
>>>>
>>>>
>>>> On 8/2/16 8:18 AM, Maty?? Kuhn wrote:
>>>>> Hi Freesurfer experts,
>>>>>
>>>>> I just started to use Freesurfer and I was wondering how can I convert
>>>>> images from MNI305 which uses Freesurfer to MNI152 which is used 
>>>>> by SPM.
>>>>> We would like to get MNI152 template of Yeo parcelation
>>>>> ()
>>>>> so we can overlay with our results from SPM fMRI analysis.
>>>>>
>>>>> I tried this:
>>>>> mri_label2vol --seg
>>>>> /path_to_analysis/Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz
>>>>> \
>>>>>--temp
>>>>> /path_to_analysis/Template_T1_IXI555_MNI152.nii \
>>>&g

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

That's correct!

On Wed, 3 Aug 2016, Anri WATANABE wrote:


Hi Anastasia,
Thank you for your kind explanation. I can be understanding how TRACULA tracts 
white matter pathways. 
At each position (in training subjects, not in new subjects of my data) 
probability that next goes for
which direction to every labels in the aparc+aseg (not with setting a certain 
ROI) is computed with use of
training subjects. The prior probabilities are made from training subjects 
(your publication in 2011) and
they are based on manual labeling (the manual labeling tracts are referred to 
Wakana et al. 2007). Then
when white matter pathways are reconstructed in my subjects, TRACULA computes 
anatomical priors in each
subjects in my data in pre-processing and probability distributions from 
anatomical priors and by fitting
ball-and-stick model. 
Is this comprehension ok?

Best Regards, 
Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-31 22:49 GMT+09:00 Anastasia Yendiki :

  Hi Anri - Instead of hard-coding some ROIs in the white matter that the 
tract is forced to go
  through, TRACULA uses information like "what is the probability that this 
tract goes
  lateral/anterior/etc to XXX", where XXX any of the labels in the 
aparc+aseg. TRACULA computes
  these prior probabilities from a set of training subjects, where the 
tracts have been labeled
  manually. So it knows how likely a tract is to go through a certain 
aparc+aseg label, or to he
  left, right, anterior, etc of a certain aparc+aseg label. This is 
computed separately at each
  position along the tract. It's computed from the training subjects, and 
then used when
  reconstructing the tract in the new subject that you run TRACULA on.

  Hope this helps,
  a.y

  On Sun, 31 Jul 2016, Anri WATANABE wrote:

Thanks, AnastasiaI know that TRACULA use probabilistic tractography 
but if ROIs
are not
set how determine the origin and the end of a certain tract? I 
think that the
first we
have to determine the origin and the end of the tract, the second 
it constructs
possible
pathway not with the deterministic way (only 1 direction / 1 voxel) 
but with the
probabilistic way (considering which direction should be next to). 
Is this
comprehension
wrong?
Thank you.

Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-07-31 13:22 GMT+09:00 Anastasia Yendiki 
:

      Hi Anri - TRACULA does not use deterministic ROIs. It uses a 
probabilistic
      model of how likely each tract is to go through or next to 
each of the
labels
      of the freesurfer subcortical segmentation and cortical 
parcellation, as a
      function of position along the trajectory of the tract.

      Best,
      a.y

      On Sun, 31 Jul 2016, Anri WATANABE wrote:

            Hi Anastasia,
            Thank you! It seems work well!!
            I have another question. Are ROIs for automatic 
tractography in
            TRACULA the same ROIs
            presented in Wakana et al. 2007?

            Anri



            
**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
            
**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural University of 
Medicine
            
**

            2016-07-27 13:17 GMT+09:00 Anastasia Yendiki
            :

                  Hi Anri - The problem is in this line:

                               set cmd = ($cmd --ref 
$cvstempdir/$cvstemp)

    

Re: [Freesurfer] Multiple Comparison Question for surface-based analyses

[Douglas Greve]

On 8/3/16 3:45 AM, Ajay Kurani wrote:

Hi Doug,
   Thank you very much for your update regarding this issue.

1)Just curious, will LGI be included in this report as this is another 
analysis of interest?
I was not planning to. The 809 subjects that I used for thickness do not 
have lGI run on them, but I think it is possible to run it on a subset 
without too much trouble. Not sure when I'll get to it.


2)As for the cortical thickness I originally used 15mm in the analysis 
so based on your email I think using 5-10mm may be more prudent in 
order to minimize FPR.  From your email, I understand that 
mris_surf2surf (command I use to convert individual subject to 
fsaverage or template and smooth to 10-15mm) assumes an ACF estimation 
of smoothness which DOES NOT take into account the long tail 
distribution.  Does this mean that when using mri_mcsim on my own 
template, the cluster extents for a given smoothness will be 
undersampled due to the fact that the "true" smoothness is more than 
what is estimated in the simulation, correct?  For instance, when I 
select 15mm in qdec, it would point to the 21mm folder 
(fwhm.dat=20.8mm estimate), and I would select a given cluster extent 
for p=0.05.  However, in this case, 15mm may translate to a larger 
FWHM than the estimated 21mm, correct?
Sort of. It is the Gaussian assumption that is incorrect, so there is no 
one FWHM that is correct (it is not a question of it simply being too 
small).


3)You mentioned that I can use mri_glmfit-sim which is permutation 
testing based.  I am struggling a bit in understanding how this 
differs from the simulation ran with mri_mcsim/qdec?  Does qdec monte 
carlo simulation option run mri_glmfit-sim in the background to 
estimate the smoothness which looks up the cluster extent within the 
mri_mcsim based on the estimated FWHM?  If so, is this estimate 
incorrect due to the fact that the long tails are not taken into account?
Permutation uses your data and permutes (ie, randomly swaps) the class 
label associated with a subject, the data with this new labeling are 
analyzed and clusters computed. Under the null, the label is irrelevant, 
so clusters are interpreted as false positives. After several thousand 
of these swaps, one builds a list of the probability of seeing a cluster 
of a certain size under the null, and this is used to generate the 
p-value.  Permutation will then naturally take into account all the 
non-Gaussian aspects of the data. The monte carlo (MC) simulation is 
similar, but it uses smoothed synthesized gaussian noise instead of the 
real data and so the gaussian assumption is  built into it.



Thanks,
Ajay

On Mon, Aug 1, 2016 at 11:43 PM, Ajay Kurani > wrote:


Hello Freesurfer Experts,
   Recently there were two article published regarding clusterwise
simulations for volumetric fmri analyses and potential errors for
underestimating clusterwise extent thresholds.

1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes
2) biorxiv.org/content/early/2016/07/26/065862


One issue pointed out from these articles seems software specific,
however the second issue is determining the proper clustersize. 
The heavy-tail nature of spatial smoothness seems to be ignored

and a gaussian shape is generally assumed, leading to an
underestimation of the spatial smoothness which can affect cluster
size calculations.  The issues are highlighted in the second
article above.

I created my own monte carlo simulation in Freesurfer for a
specific brain template and I wanted to find out if these concerns
also apply to my surface based simulations?  I am not sure if it
does since the monte carlo tool is a GRF simulation as opposed to
an analytic equation, however given that these articles were
highlighted very recently, I wanted to ensure I am running things
appropriately for surface based cortical thickness/dti analyses.

Thanks,
Ajay




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Re: [Freesurfer] mapping error

[Douglas Greve]

what is your command line?


On 8/3/16 6:00 AM, Caroline Beelen wrote:


Dear FS,

An aparc.annot ctab file was created but I got the following error:

Colortable:aparc.annot.ctab

Annotname: myaparc

Nhitsfile nhits.mgh

Nlabels 6

Labeltresh 0 0.0

Loading freesurfer/fsaverage/surf/lh.orig

1 -1 not found

2 -1 not found

3 -1 not found

Etc…

Mapping unhit to unknown

Found 132101 unhit vertices

Writing annot to freesurfer/fsaverage/lh.myaparc.annot

I guess my ctab file is incorrect? I included an example of a label 
with it.


Thanks again for your help.

Caroline



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The information in this e-mail is intended only for the person to whom it is
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dispose of the e-mail.

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anri WATANABE]

Hi Anastasia,

Thank you for your kind explanation. I can be understanding how TRACULA
tracts white matter pathways.
At each position (in training subjects, not in new subjects of my data)
probability that next goes for which direction to every labels in the
aparc+aseg (not with setting a certain ROI) is computed with use of
training subjects. The prior probabilities are made from training subjects
(your publication in 2011) and they are based on manual labeling (the
manual labeling tracts are referred to Wakana et al. 2007). Then when white
matter pathways are reconstructed in my subjects, TRACULA computes
anatomical priors in each subjects in my data in pre-processing and
probability distributions from anatomical priors and by fitting
ball-and-stick model.
Is this comprehension ok?

Best Regards,
Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-31 22:49 GMT+09:00 Anastasia Yendiki :

>
> Hi Anri - Instead of hard-coding some ROIs in the white matter that the
> tract is forced to go through, TRACULA uses information like "what is the
> probability that this tract goes lateral/anterior/etc to XXX", where XXX
> any of the labels in the aparc+aseg. TRACULA computes these prior
> probabilities from a set of training subjects, where the tracts have been
> labeled manually. So it knows how likely a tract is to go through a certain
> aparc+aseg label, or to he left, right, anterior, etc of a certain
> aparc+aseg label. This is computed separately at each position along the
> tract. It's computed from the training subjects, and then used when
> reconstructing the tract in the new subject that you run TRACULA on.
>
> Hope this helps,
> a.y
>
> On Sun, 31 Jul 2016, Anri WATANABE wrote:
>
> Thanks, AnastasiaI know that TRACULA use probabilistic tractography but if
>> ROIs are not
>>
>> set how determine the origin and the end of a certain tract? I think that
>> the first we
>> have to determine the origin and the end of the tract, the second it
>> constructs possible
>> pathway not with the deterministic way (only 1 direction / 1 voxel) but
>> with the
>> probabilistic way (considering which direction should be next to). Is
>> this comprehension
>> wrong?
>> Thank you.
>>
>> Anri
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>> **
>>
>> 2016-07-31 13:22 GMT+09:00 Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>:
>>
>>   Hi Anri - TRACULA does not use deterministic ROIs. It uses a
>> probabilistic
>>   model of how likely each tract is to go through or next to each of
>> the labels
>>   of the freesurfer subcortical segmentation and cortical
>> parcellation, as a
>>   function of position along the trajectory of the tract.
>>
>>   Best,
>>   a.y
>>
>>   On Sun, 31 Jul 2016, Anri WATANABE wrote:
>>
>> Hi Anastasia,
>> Thank you! It seems work well!!
>> I have another question. Are ROIs for automatic tractography
>> in
>> TRACULA the same ROIs
>> presented in Wakana et al. 2007?
>>
>> Anri
>>
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>>
>> **
>>
>> 2016-07-27 13:17 GMT+09:00 Anastasia Yendiki
>> :
>>
>>   Hi Anri - The problem is in this line:
>>
>>set cmd = ($cmd --ref $cvstempdir/$cvstemp)
>>
>>   It should be changed to this:
>>
>>set cmd = ($cmd --ref
>> $cvstempdir/$cvstemp/mri/norm.mgz)
>>
>>   For this to take effect, you need to run "which
>> trac-all"
>> and make the change in
>>   the trac-all file that the which commands shows you.
>>
>>   Hope this helps,
>>
>>   a.y
>>
>>   On Fri, 15 Jul 2016, Anri WATANABE wrote:
>>
>> Hi, AnastasiaThis is trac-all.local-copy 

Re: [Freesurfer] brain mask and T1 are not the same size

[Isabelle Deschamps]

s,

In freeview, looks fine to me. See attached.

Can you send us your screenshot?

Regards,
Thomas

On Tue, Aug 2, 2016 at 9:39 PM, Maty?? Kuhn <matyas.k...@gmail.com> wrote:
The Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz
comes from
http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011,
and the description says it is the FSL MNI152 1mm template interpolated
and intensity normalized into a 256 x 256 x 256 1mm-isotropic volume
(obtained by putting the FSL MNI152 1mm template through recon-all ). So
I supposed it is in MNI305 after it was processed with freesurfer. When
I overlap the
Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz and
Template_T1_IXI555_MNI152.nii it is really shifted so I think it is not
in MNI152.

When I add the --invertmtx then the result is still the same, empty image.

I uploaded those images here:
https://dl.dropboxusercontent.com/u/70539709/Freesurfer_question.zip ,
if you want to try yourself.


Thank you,

Matyas



Dne 2.8.2016 v 14:55 Douglas Greve napsal(a):
 From the names, it looks like both the seg vol and the template vol are both in mni152. Where did Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz come from? One thing you can try is to invert the registration by
 adding --invertmtx to the command line.


On 8/2/16 8:18 AM, Maty?? Kuhn wrote:
Hi Freesurfer experts,

I just started to use Freesurfer and I was wondering how can I convert
images from MNI305 which uses Freesurfer to MNI152 which is used by SPM.
We would like to get MNI152 template of Yeo parcelation
(    )
so we can overlay with our results from SPM fMRI analysis.

I tried this:
mri_label2vol --seg
/path_to_analysis/Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz
\
   --temp
/path_to_analysis/Template_T1_IXI555_MNI152.nii \
   --reg
$FREESURFER_HOME/average/mni152.register.dat \
   --o /path_to_analysis/output_mni152.nii

which resulted in image full of zeros (so maybe problem with
registration?). The "Template_T1_IXI555_MNI152.nii" is the MNI152
template which is used by Computational anatomical toolbox 12 for SPM
from Christian Gaser and his group.

Thanks in advance for any suggestions,

Matyas
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Message: 10
Date: Wed, 3 Aug 2016 02:45:47 -0500
From: Ajay Kurani <dr.ajay.kur...@gmail.com>
Subject: Re: [Freesurfer] Multiple Comparison Question for
surface-based
analyses
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CA+uskrDgnhv2SaRJHGHUQQVJseuEKQC6ov-=f7n0dyrtsge...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Doug,
  Thank you very much for your update regarding this issue.

1)Just curious, will LGI be included in this report as this is another
analysis of interest?

2)As for the cortical thickness I originally used 15mm in the analysis so
based on your email I think using 5-10mm may be more prudent in order to
minimize FPR.  From your email, I understand that mris_surf2surf (command I
use to convert individual subject to fsaverage or template and smooth to
10-15mm) assumes an ACF estimation of smoothness which DOES NOT take into
account the long tail distribution.  Does this mean that when using
mri_mcsim on my own template, the cluster extents for a given smoothness
will be undersampled due to the fact that the "true" smoothness is more
than what is estimated in the simulation, correct?  For instance, when I
select 15mm in qdec, it would point to the 21mm folder (fwhm.dat=20.8mm
estimate), and I would select a given cluster extent for p=0.05.  However,
in this case, 15mm may translate to a larger FWHM than the estimated 21mm

Re: [Freesurfer] Multiple Comparison Question for surface-based analyses

[Ajay Kurani]

Hi Doug,
   Thank you very much for your update regarding this issue.

1)Just curious, will LGI be included in this report as this is another
analysis of interest?

2)As for the cortical thickness I originally used 15mm in the analysis so
based on your email I think using 5-10mm may be more prudent in order to
minimize FPR.  From your email, I understand that mris_surf2surf (command I
use to convert individual subject to fsaverage or template and smooth to
10-15mm) assumes an ACF estimation of smoothness which DOES NOT take into
account the long tail distribution.  Does this mean that when using
mri_mcsim on my own template, the cluster extents for a given smoothness
will be undersampled due to the fact that the "true" smoothness is more
than what is estimated in the simulation, correct?  For instance, when I
select 15mm in qdec, it would point to the 21mm folder (fwhm.dat=20.8mm
estimate), and I would select a given cluster extent for p=0.05.  However,
in this case, 15mm may translate to a larger FWHM than the estimated 21mm,
correct?

3)You mentioned that I can use mri_glmfit-sim which is permutation testing
based.  I am struggling a bit in understanding how this differs from the
simulation ran with mri_mcsim/qdec?  Does qdec monte carlo simulation
option run mri_glmfit-sim in the background to estimate the smoothness
which looks up the cluster extent within the mri_mcsim based on the
estimated FWHM?  If so, is this estimate incorrect due to the fact that the
long tails are not taken into account?


Thanks,
Ajay

On Mon, Aug 1, 2016 at 11:43 PM, Ajay Kurani 
wrote:

> Hello Freesurfer Experts,
>Recently there were two article published regarding clusterwise
> simulations for volumetric fmri analyses and potential errors for
> underestimating clusterwise extent thresholds.
>
> 1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes
> 2) biorxiv.org/content/early/2016/07/26/065862
>
> One issue pointed out from these articles seems software specific, however
> the second issue is determining the proper clustersize.  The heavy-tail
> nature of spatial smoothness seems to be ignored and a gaussian shape is
> generally assumed, leading to an underestimation of the spatial smoothness
> which can affect cluster size calculations.  The issues are highlighted in
> the second article above.
>
> I created my own monte carlo simulation in Freesurfer for a specific brain
> template and I wanted to find out if these concerns also apply to my
> surface based simulations?  I am not sure if it does since the monte carlo
> tool is a GRF simulation as opposed to an analytic equation, however given
> that these articles were highlighted very recently, I wanted to ensure I am
> running things appropriately for surface based cortical thickness/dti
> analyses.
>
> Thanks,
> Ajay
>
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