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-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:

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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 +0000 From: Isabelle Deschamps isabelle.deschamps.1@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-A2A4-2EF526465775@ulaval.ca Content-Type: text/plain; charset="us-ascii"

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Message: 2 Date: Wed, 3 Aug 2016 20:19:09 +0900 From: Anri WATANABE z2aanri@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-eHgNA@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 ayendiki@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

---

???????????? ???????? ?? ??

---

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

---

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

---

       ????????????
       ????????
       ?? ??

---

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

Medicine

---

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

---

                   ????????????
                   ????????
                   ?? ??

---

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

University of Medicine

---

                   2016-07-13 6:16 GMT+09:00 Anastasia Yendiki
                   <ayendiki@nmr.mgh.harvard.edu>:

                         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

---

                               ????????????
                               ????????
                               ?? ??

---

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

Prefectural University of Medicine

---

                               2016-07-07 20:12 GMT+09:00 Anastasia
       Yendiki
                               <ayendiki@nmr.mgh.harvard.edu>:

                                     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

(<tract>_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 <subjd>/scripts/trac-all.log.

                                           Thanks in advance,
                                           Anri

---

                                           ????????????
                                           ????????
                                           ?? ??

---

                                           Anri WATANABE, M.D.
                                           Department of 

Psychiatry, University Hospital, Kyoto Prefectural University of Medicine

---

                                           2016-06-03 9:51 

GMT+09:00 Anri WATANABE z2aanri@koto.kpu-m.ac.jp: Hi, Anastasia. There aren't any .log files but text files like lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. I guess text files complete all pathways and measures.

---

                                           ????????????
                                           ????????
                                           ?? ??

---

                                           Anri WATANABE, M.D.
                                           Department of 

Psychiatry, University Hospital, Kyoto Prefectural University of Medicine

---

                                           2016-06-02 3:03 

GMT+09:00 Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu

...

:

                                                 Thanks, Anri. 

So the previous steps seem to have run fine. Are there any .log files created in the stats/ folder, which is created by trac-all -stat?

                                                 On Wed, 1 Jun 

2016, Anri WATANABE wrote:

                                                       Hi

Anastasia, This is a <subjid>/scripts/trac-all.log of one subject of the group.

                                                       Thanks,
                                                       Anri

---

       ????????????
                                                       ????????
                                                       ?? ??

---

                                                       Anri 

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

---

                                                       2016-05-31

22:55 GMT+09:00 Anastasia Yendiki

                               <ayendiki@nmr.mgh.harvard.edu>:

                                                             Hi 

Anri

•      Can you also
                               send your log file
  

(scripts/trac-all.log)? I'll need to see what exactly was running when the error occurred. Thanks!

                                                             a.y

                                                             On 

Sat, 28 May 2016, Anri WATANABE wrote:

Hello Anastasia,sorry for few information and let me tell you command and

error log.

                               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



                               dmrirc.example (configuration 

file) is attached to this e-mail.

Thanks in advance,

Anri

---

                               ????????????

       ????????
                                                                   ??
       ??

---

Anri WATANABE, M.D.

       Department of
                               Psychiatry,

       University
                               Hospital, Kyoto Prefectural

University of Medicine

---

       2016-05-27 22:57
                               GMT+09:00 Anastasia Yendiki

                               <ayendiki@nmr.mgh.harvard.edu>:



       Hi Anri -
                               I do not know what command line you

ran and what your

       configuration
                               file looks like, so it is very


       hard for
                               me to suggest solutions.



       Best,


       a.y



       On Fri, 27
                               May 2016, Anri WATANABE wrote:



             Hi
                               Anastasia,



                               Thank you for your answer.



                               There aren't stats/*.path.mean.txt
       files and
                                                       terminal 

says 'Could

not read

       /Applications/freesurfer/subjects/cvs_avg35.' I



                               checked

/Application/freesurfer/subjects/cvs_avg35 folder and

       couldn't find
                               COR-.info file.



                               Could you tell me any resolutions,

please?

                               Thanks,


             Anri

---

                               ????????????



                               ????????


             ??
                               ??

---

             Anri
                               WATANABE, M.D.



                               Department of Psychiatry,



                               University Hospital, Kyoto 

Prefectural University of Medicine

---

                               2016-05-21 6:48 GMT+09:00 Anastasia
       Yendiki

                               <ayendiki@nmr.mgh.harvard.edu>:




                                 Hi Anri - The FA values are

extracted in the native space of each subject, which is why

                               those are the only



                                 coordinates that you see. If you

want to display the

       results of your
                               analysis on an average



                               path, after



                                 running trac-all -stat, you 

can use the

                               stats/*.path.mean.txt files (see 

also the last part

             of
                               the TRACULA



                                 tutorial).




                                 Best,



                                 a.y




                                 On Wed, 18 May 2016, Anri WATANABE
       wrote:




                                       Dear experts,



                                       I use TRACULA to examine a

measure (FA) at each voxel

in one pathway.

                                       pathstats.byvoxel.txt files

show coordinates in

native space and after converting

                               those the new



                                       files don't show any

coordinates which are in MNI

space.

                                       Could you tell me how can I

know MNI coordinate

       values?




                                       Thank you!





                                       Regards,



                                       Anri

---

                                       ????????????



                                       ????????



                                       ?? ??

---

                                       Anri WATANABE, M.D.



                                       Department of Psychiatry,



                                       University Hospital, Kyoto
                                                       Prefectural
       University of

       Medicine

---

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