Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anri WATANABE]

Thanks, Anastasia
I 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 <
>> ayend...@nmr.mgh.harvard.edu>:
>>
>>   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 from 1 subject.
>> 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
>>
>> **
>>
>> 2016-07-13 6:16 GMT+09:00 Anastasia Yendiki
>> :
>>
>>   Hi Anri - This may be a bug that was fixed at some
>> point. Can
>>   you send me the scripts/trac-all.local-copy from one of
>> your
>>   subjects? Thanks!
>>
>>   a.y
>>
>>   On Mon, 11 Jul 2016, Anri WATANABE wrote:
>>
>> Hi Anastasia,There is an error in .log files of
>> left
>> corticospinal tract in cvs template and I attached
>> one
>> of file. In addition .log files of right
>> corticospinal tract in cvs template doesn't
>> exist.
>> Thanks in advance.
>>
>> 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
>>
>>
>> **
>>
>> 2016-07-07 20:12 GMT+09:00 Anastasia Yendiki
>> :
>>
>>   Hi Anri - Is there an error in the
>> stats/*.log
>> files for the different tracts?
>>
>>   a.y
>>
>>   On Tue, 5 Jul 2016, Anri WATANABE wrote:
>>
>> Dear Anastasia,
>>
>> I use TRACULA to obtain diffusion
>> measures at each voxel in a certain 

Re: [Freesurfer] Coordinates in TRACULA group analysis

[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)

  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 from 1 subject. 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

**

2016-07-13 6:16 GMT+09:00 Anastasia Yendiki
:

      Hi Anri - This may be a bug that was fixed at some point. Can
      you send me the scripts/trac-all.local-copy from one of your
      subjects? Thanks!

      a.y

      On Mon, 11 Jul 2016, Anri WATANABE wrote:

            Hi Anastasia,There is an error in .log files of left
            corticospinal tract in cvs template and I attached
            one
            of file. In addition .log files of right
            corticospinal tract in cvs template doesn't exist. 
            Thanks in advance.

            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
           

**

            2016-07-07 20:12 GMT+09:00 Anastasia Yendiki
            :

                  Hi Anri - Is there an error in the stats/*.log
            files for the different tracts?

                  a.y

                  On Tue, 5 Jul 2016, Anri WATANABE wrote:

                        Dear Anastasia, 

                        I use TRACULA to obtain diffusion
            measures at each voxel in a certain pathway for
                        group analysis, but
                        there aren't stats/*.path.mean.txt
            files. I found .log files
                        (_PP.avg33_mni_bbr.log) which
            exist
                        1 file per 1 tract, except corticospinal
            tract which has 2 .log files.

                        Command: trac-all –stat –c
            $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

                        Error log: Loading output reference
            volume from
                       
            /Applications/freesurfer/subjects/cvs_avg35

                        corRead(): can't open file
            /Applications/freesurfer/subjects/cvs_avg35/COR-.info

                        ERROR: Could not read
            /Applications/freesurfer/subjects/cvs_avg35


                        I 

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anri WATANABE]

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 from 1 subject. 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
>> **
>>
>> 2016-07-13 6:16 GMT+09:00 Anastasia Yendiki > >:
>>
>>   Hi Anri - This may be a bug that was fixed at some point. Can
>>   you send me the scripts/trac-all.local-copy from one of your
>>   subjects? Thanks!
>>
>>   a.y
>>
>>   On Mon, 11 Jul 2016, Anri WATANABE wrote:
>>
>> Hi Anastasia,There is an error in .log files of left
>> corticospinal tract in cvs template and I attached
>> one
>> of file. In addition .log files of right
>> corticospinal tract in cvs template doesn't exist.
>> Thanks in advance.
>>
>> 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
>>
>> **
>>
>> 2016-07-07 20:12 GMT+09:00 Anastasia Yendiki
>> :
>>
>>   Hi Anri - Is there an error in the stats/*.log
>> files for the different tracts?
>>
>>   a.y
>>
>>   On Tue, 5 Jul 2016, Anri WATANABE wrote:
>>
>> Dear Anastasia,
>>
>> I use TRACULA to obtain diffusion
>> measures at each voxel in a certain pathway for
>> group analysis, but
>> there aren't stats/*.path.mean.txt
>> files. I found .log files
>> (_PP.avg33_mni_bbr.log) which
>> exist
>> 1 file per 1 tract, except corticospinal
>> tract which has 2 .log files.
>>
>> Command: trac-all –stat –c
>> $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example
>>
>> Error log: Loading output reference
>> volume from
>>
>> /Applications/freesurfer/subjects/cvs_avg35
>>
>> corRead(): can't open file
>> /Applications/freesurfer/subjects/cvs_avg35/COR-.info
>>
>> ERROR: Could not read
>> /Applications/freesurfer/subjects/cvs_avg35
>>
>>
>> I attached dmrirc.example (configuration
>> file) and /scripts/trac-all.log.
>>
>>
>> Thanks in advance,
>> 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
>>
>>
>> **
>>
>> 2016-06-03 9:51 GMT+09:00 Anri WATANABE
>> :
>>   Hi, Anastasia.
>> There aren't any .log files but text
>> 

[Freesurfer] Siemens SPECTRA 3T - Help with sequences

[Felipe Picon]

Dear colleagues,
I’m a researcher psychiatrist who is currently testing image acquisitions
with different sequences on a Siemens 3T SPECTRA scanner. I would like to
learn from you if any of you had experience with this scanner in the
collection of high-resolution structural images (MPRAGE), DTI, and Resting
State Functional Connectivity images. We only have access to a 12-channel
Head Coil, though. Luckily the scanner has the possibility of acquiring 128
direction of DTI.
If any of you can share with me any good quality sequences that could fit
this set of characteristics it would be highly appreciated
Thank you very much
Best regards,
Felipe Picon

-- 
*Felipe Picon, MD, MSc*
Child and Adolescent Psychiatrist
=
ADHD Neuroimaging Researcher at the
Adult ADHD outpatient research program PRODAH-A
 - HCPA
 - UFRGS 
Porto Alegre - RS - Brazil
Vice-Coordinator of the Technology Addiction Study Group - GEAT

Secretary of the Early Career Psychiatrists Section - World Psychiatric
Association 
Corresponding Member of the American Academy of Child and Adolescent
Psychiatry - AACAP
=
Web based CV   Google Scholar
Profile 
felipepi...@gmail.com
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[Freesurfer] group analysis/ region of interest (ROI) approach

[miracle ozzoude]

Hey FreeSurfer experts,
Does anyone know the steps i have to perform if I want to conduct surface
based thickness analysis using GLM but with ROI approach. Thank you very
much.
Best,
Paul
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[Freesurfer] Longitudinal single time point cross sectional comparison

[Emmanuel Nwosu]

Dear Freesurfer users,

I have longitudinal data with three time points but want to run a cross
sectional comparison on the first instance between group on just one time
point (using QDEC). Any Idea on how I could do that on longitudinal data.
Thanks for your help.


Emmanuel Nwosu
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Re: [Freesurfer] error during longitudinal -long stream

[Jinsong Tang]

Hi Martin，

I tried 2 times again (run 4 analysis at the same time).  This time, it
works well, The link to fsaverage  is automatically created. I did not
replicate the error message.

Thank you so much!

Best,

Jinsong

On Fri, Jul 29, 2016 at 11:44 AM, Martin Reuter  wrote:

> Hi Jinsong,
>
> can you give an example of what exactly does not work.
>
> Thanks, Martin
>
>
> On 07/29/2016 12:26 PM, Jinsong Tang wrote:
>
> Hi Martin,
>
> I checked all data are completed except the link to  fsaverage,
> lh.EC_average and rh.EC_average.   I run one analysis from the terminal.
> it works. if I run multiple analysis at the same time, it failed.
> When I manually linked the 3 files, then run multiple analysis at the same
> time, it works good.
>
> Best,
>
> Jinsong
>
> On Wed, Jul 27, 2016 at 8:11 AM, Martin Reuter <
> mreu...@nmr.mgh.harvard.edu> wrote:
>
>>
>> Hi Jinsong,
>>
>> maybe not everything was copied? The link to fsaverage should be
>> automatically created if it is missing. I often process cross in a
>> different directory from base and long (and create symlinks to the cross
>> subject dirs). It automatically creates fsaverage then.
>> Try to replicate your problem with a single subject that failed. First
>> try to do everything on the same computer, then try to do what you did
>> before (copying parts of it).
>>
>> Best, Martin
>>
>>
>>
>> On 07/20/2016 12:56 PM, Jinsong Tang wrote:
>>
>> Hi Martin,
>>
>> We run all cross, base and long with 5.3. I guess the problem maybe we
>> run cross on  a computer and then copy the results to another computer to
>> run the cross and long. the "*fsaverage" is not copied. Does this
>> matter？*
>>
>> Best，
>>
>> Jinsong
>>
>> On Wed, Jul 20, 2016 at 12:21 AM, Martin Reuter <
>> mreu...@nmr.mgh.harvard.edu> wrote:
>>
>>> Hi Jinsong,
>>>
>>> I have never seen this. Stable 5.3 is very stable and I doubt it is a
>>> bug. How did you process base and cross sectionals? Also with 5.3 ?
>>>
>>> I would recommend to process cross and base with 5.3, then re-run the
>>> long and see if you can replicate this problem. Let me know what happens.
>>>
>>> Best, Martin
>>>
>>>
>>> > On Jul 20, 2016, at 12:48 AM, Jinsong Tang < 
>>> tangjinson...@gmail.com> wrote:
>>> >
>>> > Hi all,
>>> >
>>> > I found an error during the longitudinal -long stream:
>>> >
>>> > recon-all -long P1001-2 P1001 -all
>>> > ..
>>> >
>>> > FREESURFER_HOME /space/raid/fmri/freesurfer
>>> > Actual FREESURFER_HOME /space/raid/fmri/freesurfer
>>> > build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>>> > Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21
>>> UTC 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux
>>> > ..
>>> >
>>> > mris_spherical_average -erode 1 -orig white -t 0.4 -o
>>> P1001-2.long.P1001 label lh.entorhinal lh sphere.reg lh.EC_average
>>> lh.entorhinal_exvivo.label
>>> >
>>> > painting output onto subject P1001-2.long.P1001.
>>> > processing subject lh.EC_average...
>>> >
>>> MRISread(/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg):
>>> could not open file
>>> > eroding label 1 times before writing
>>> > thresholding label stat at 0.400 before writing
>>> > Not a directory
>>> > mris_spherical_average: could not read surface file
>>> /space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg
>>> > Not a directory
>>> > Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21
>>> UTC 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux
>>> >
>>> > recon-all -s P1001-2.long.P1001 exited with ERRORS at Fri Jul  8
>>> 21:33:02 PDT 2016
>>> >
>>> >
>>> > Please help me fix this error!
>>> >
>>> > Thanks and best regards,
>>> >
>>> > Jinsong
>>> >
>>> >
>>> > ___
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> ___
>>> 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.
>>>
>>>
>>
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> --
>> Martin Reuter, PhD
>> Assistant Professor of Radiology, Harvard Medical School
>> Assistant 

[Freesurfer] Running recon-all with T1 and FLAIR

[Silas]

Dear FreeSurfer team,


I'm doing a structural analysis with 50 MS patients and 50 healthy controls 
(T1, T2 and FLAIR). The MS patients have multiple lesions mainly in white 
matter. My co-worker did manual editing (bullet points) in the FLAIR images, 
and i would like to use these edits when running recon-all in order to avoid 
further manual editing.


The data i'm working with is already resliced to 1 mm and co-registered in 
MNI-space.

1) Can i use this data or would it be preferable to use the original T1's?


My thought was to run the following command:

recon-all -subject subjectname -i /path/to/input_volume -FLAIR 
/path/to/FLAIR_volume_with_edits -FLAIRpial -all

2) Does this look correct? Is there anything i should be aware of?

3) Does it make a difference running recon-all -all with the FLAIR image - 
compared to running recon-all -autorecon3 with the FLAIR after running 
recon-all -all with only the T1?

4) I've also thought about using the lesion segmentation toolbox for SPM and 
completely avoid manual editing - is this preferable to using the FLAIR with 
manual editing?

5) How is the general strength of analysing corpus callosum structurally in MS 
patients using FreeSurfer?


Best, Silas
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Re: [Freesurfer] significance overlay in freeview

[Caroline Beelen]

Dear Ruopeng,



Yes, I'm running FS 5.3. :)

But then how can I see the correct significance overlay? Cause even when 
leaving out some commands (which may or may not work in 5.3), freeview does 
load, but seems to only display the DK-atlas on fs average (... and gets stuck 
sometimes too), as I described below.

I cant find the right command ...



So I guess my actual question is: Which command should i use to view a 
(correct) significance overlay in FS 5.3?



Thank you very much for your help!



Regards, Caroline


 Hi Caroline,

Are you running FS 5.3? The command on the webpage is based on the upcoming 
6.0, I believe. So some of the command line options are not available in 5.3.

Best,
Ruopeng

> On Jul 29, 2016, at 9:11 AM, Caroline Beelen  
> wrote:
>
> Dear FS team,
>
> Apologies in advance for perhaps again a rather basic question. I attempted 
> to load the aparc overlay in freeview by using the written command from the 
> group analysis page, however it failed to load correctly.
>
> I used the following command:
> freeview -f 
> fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=roi.lh.area.dyslect_basic.glmdir/dyslect/sig.mgh:overlay_threshold=4,5
>  -viewport 3d
> ? roi.lh.area.dyslect_basic.glmdir is the file obtained from the GLM-analysis 
> and dyslect is the contrast folder within this file (main effect of 
> dyslexia), containing a sig.mgh file (all seems fine)
>
> Unfortunately, I got an error that it does not recognize 
> ?overlay_treshold=4,5?. I used freeview ?h and tried certain commands alike, 
> but they didn?t work. When leaving out this part, I got another error that it 
> failed to recognize ?annot_outline=1?. Again, leaving this out too, freeview 
> loads itself and the DK-regions become visible. However, nothing else seems 
> to get activated, and even not when putting ?configure overlay? (which is set 
> to sig.mgh) to 1.3 as minimum and 3 as maximum. So basically nothing happens.
> When looking at the command line it says that it implemented the colortable 
> of DK-atlas (even twice), but it tells me nothing else. Also, after closing 
> and reloading Freeview by using the similar command and then clicking on 
> ?configure overlay? the screen sometimes gets stuck, giving me the impression 
> that something must be wrong with the command.
>
> Could you please help me out and provide me the right command-line for 
> loading the overlay of the significance map of 
> ?roi.lh.area.dyslect_basic.glmdir/dyslect??
>
> Thanks in advance!
>
> Kind regards, Caroline
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[Freesurfer] Where are time series from adjusted (post selxavg3) ROIs

[ERIK JAHNER]

Dear Freesurfer experts

I have been going through the documentation trying to figure out how to 
extract the time series for an ROI (Posteriorcingulate) after removing the 
regressors that I put in my mkanalysis-sess.  I have run the selxavg3. 
1. Is this time course what is in the meanfunc.nii.gz?
2.  If it is, how do I pull this out in matrix format (.mat) out of the where I 
basically get one mean adjusted value for the ROI at each timepoint? (e.g. For 
the Posteriorcingulate, I want 210 values representing the mean activation 
after removing the effect of my covariates wm and css for each of the 210 
timepoints). 
3. Is this information in the X.mat file? If so, what is its location?

Thanks
Erik Jahner
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