Can you try running simply freeview -v /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri/brainmask.mgz
Yes, so the original brainmask has the following dimensions (as before) mri_info /Users/Isabelle/Desktop/Tryout/brainmask.mgz Volume information for /Users/Isabelle/Desktop/Tryout/brainmask.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0
Then save to a different file name using the "Save Volume As". Does that file have the right dimensions?
The new brainmask saved under brainmask_resaved has the wrong dimensions:
Volume information for /Users/Isabelle/Desktop/Tryout/brainmask_resaved.mgz type: MGH dimensions: 256 x 256 x 255 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -127.5, zend: 127.5
Then make an edit and then "Save Volume". Does that file have the right dims?
The brainmask_resaved once edited keeps the wrong dimensions:
Volume information for /Users/Isabelle/Desktop/Tryout/brainmask_resaved.mgz type: MGH dimensions: 256 x 256 x 255 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -127.5, zend: 127.5
It might be a mac thing; I've been working under linux
I think it might be--however it is weird that only some participants were affected by this. I do not have access to computers running linux. Is there a way to solve this problem? I cannot exclude 4 participants.
Thank you again for your help,
Isabelle
On 4 Aug 2016, at 12:00, freesurfer-request@nmr.mgh.harvard.edu wrote:
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Today's Topics:
- Re: mri_normalize, 110 is too dark (tvg[fs])
- Re: brain mask and T1 are not the same size (Douglas N Greve)
- Re: mri_label2label (Douglas N Greve)
- Re: Coordinates in TRACULA group analysis (Anri WATANABE)
- mri_label2label holes (Fred Dick)
- Re: Labels to MNI152, SPM compatible (Maty?? Kuhn)
- Re: mri_label2label holes (Douglas Greve)
- Re: mri_label2label holes (zkaufman@nmr.mgh.harvard.edu)
- Re: mri_label2label holes (Douglas Greve)
- Re: mri_label2label holes (Bruce Fischl)
- Re: mri_label2label holes (Bruce Fischl)
- Re: Labels to MNI152, SPM compatible (Thomas Yeo)
- Re: Poor automatic segmentation of the cerebellum (Bruce Fischl)
- Re: Flattening the surface (Younghoon Kim)
Message: 1 Date: Wed, 3 Aug 2016 17:39:56 -0400 From: "tvg[fs]" tvg214+fs@nyu.edu Subject: Re: [Freesurfer] mri_normalize, 110 is too dark To: Bruce Fischl fischl@nmr.mgh.harvard.edu Cc: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: CAMBOMk8jO5qBUHJ=MDnyRFUuG3G_18Ng_1aK+rOYTSoOceTs0w@mail.gmail.com Content-Type: text/plain; charset=UTF-8
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 fischl@nmr.mgh.harvard.edu 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
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Message: 2 Date: Wed, 3 Aug 2016 17:40:57 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] brain mask and T1 are not the same size To: freesurfer@nmr.mgh.harvard.edu Message-ID: 57A264E9.7090207@nmr.mgh.harvard.edu Content-Type: text/plain; charset=windows-1252; format=flowed
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:
- Re: brain mask and T1 are not the same size (Isabelle Deschamps)
- Re: Coordinates in TRACULA group analysis (Anri WATANABE)
- Re: mapping error (Douglas Greve)
- Re: Multiple Comparison Question for surface-based analyses (Douglas Greve)
- Re: Coordinates in TRACULA group analysis (Anastasia Yendiki)
- 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 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 ofMedicine
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 PrefecturalUniversity 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 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 errorin .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, KyotoPrefectural 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: Loadingoutput reference volume from
/Applications/freesurfer/subjects/cvs_avg35 corRead(): can'topen file
/Applications/freesurfer/subjects/cvs_avg35/COR-.info ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35 I attacheddmrirc.example (configuration file) and <subjd>/scripts/trac-all.log.
Thanks in advance, Anri
???????????? ???????? ?? ??
Anri WATANABE, M.D. Department ofPsychiatry, University Hospital, Kyoto Prefectural University of Medicine
2016-06-03 9:51GMT+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 ofPsychiatry, University Hospital, Kyoto Prefectural University of Medicine
2016-06-02 3:03GMT+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 Jun2016, Anri WATANABE wrote:
HiAnastasia, This is a <subjid>/scripts/trac-all.log of one subject of the group.
Thanks, Anri
???????????? ???????? ?? ??
AnriWATANABE, 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>: HiAnri
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 OnSat, 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 (configurationfile) 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 terminalsays '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, KyotoPrefectural 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, youcan use the
stats/*.path.mean.txt files (seealso 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 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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