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 greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mapping error To: freesurfer@nmr.mgh.harvard.edu Message-ID: f3f77469-16ad-6fdf-f647-80aee162dbfc@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 0.00000
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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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)
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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 aprobabilistic 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 tractographyin 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 "whichtrac-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 Universityof 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 fixedat 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 templateand 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 inthe stats/*.log files for the different tracts?
a.y On Tue, 5 Jul 2016, AnriWATANABE 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+09:00Anri 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. Arethere any .log files created in the stats/ folder, which is created by trac-all -stat?
On Wed, 1 Jun 2016,Anri WATANABE wrote:
HiAnastasia, 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
2016-05-3122:55 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.exampleError log: Loading output reference volume from
/Applications/freesurfer/subjects/cvs_avg35 corRead(): can't open file /Applications/freesurfer/subjects/cvs_avg35/COR-.infoERROR: 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 PrefecturalUniversity 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 youran 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 'Couldnot 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 areextracted in the native space of each subject, which is why
those are the only coordinates that you see. If youwant to display the
results of your analysis on an average path, after running trac-all -stat, you can usethe
stats/*.path.mean.txt files (see alsothe last part
of the TRACULA tutorial). Best, a.y On Wed, 18 May 2016, Anri WATANABE wrote: Dear experts, I use TRACULA to examine ameasure (FA) at each voxel
in one pathway.
pathstats.byvoxel.txt filesshow coordinates in
native space and after converting
those the new files don't show anycoordinates which are in MNI
space.
Could you tell me how can Iknow 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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