29 Apr
2013
29 Apr
'13
9:14 p.m.
Hi Rotem, I don't think I ever got an email notifying me. Did you use www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html ? Can you upload it again, and make sure to put my email in the contact list.
doug
On 4/29/13 9:08 PM, Rotem Saar wrote:
Dear Doug,
I have uploaded the files to the "filedrop" (file name: Rotem_try.tar.gz) and activated the link (I hope I did it OK). I will appreciate your help as I'm stuck - can't see the problem...:)
Thanks for all your help !!
Rotem
------------------------------ Message: 9 Date: Thu, 11 Apr 2013 12:51:38 -0400 From: Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] DTI: problems with (high) FA values To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <5166EA1A.8000701@nmr.mgh.harvard.edu <mailto:5166EA1A.8000701@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed That is a good value, so the regis not the problem. If you upload your dt_recon folder as well as your recon-all folder for that subject I'll take a look. doug On 04/11/2013 10:02 AM, Rotem Saar wrote: > Hi Douge, > > In your last reply to my email (that contained questions regarding > some really high FA values - see recent emails below), u asked me to > write u the first value in register.dat.mincost - > I'm copying the line I have: > > 0.280554 140.210312 156.795241 11.152485 > > Does this takes us one step further towards understanding the problem > and its solution ? > > Thanks for your time, > Rotem > > > > On 04/07/2013 06:48 AM, Rotem Saar wrote: > > Hi Doug, > > > > Thanks for your answer. > > I changed the last step as u suggested, but I think I need to clarify > > my question: > > Indeed values of the CC looks OK, but don't u think other values, like > > the ventricles are too high ? > *_yes, the ventricles look too high_* > > > > When I first run the script, I got all values and looked the the CC - > > it looked fine. Then, I wanted to validate with some other regions, > > just to show that I got the appropriate (low) FA values for regions I > > don't expect to see high values in - and things looked odd (too high). > > > > I remember Bruce also writing me that the values seems a little high, > > but we didn't further discuss. I read the following this link: > > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual > > > > "The CC has an average FA of about 0.75, gyral parcellations are about > > 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as > > expected because the CC is highly directional with no crossing fibers > > so we would expect the CC to have the highest FA. The gyral white > > matter is also directional but has fibers crossing in them, so one > > expects the FA to be lower than CC. The gray matter (putamen) is still > > lower. The ventricle has no fibers, so we expect it to have the lowest > > FA". > > > > All my values are above 0.4.... > > > > Additionally, if in the last step I'm writing --seg > > /usr/local/freesurfer/ > subjects/Rotem_try/mri/wmparc.mgz > > > > why do I get 182 regions ? in my wmparc.stats I have only 70... > The wmparc includes all the subcortical and cortical regions too, but > only the WM regions are reported in the wmparc.stats file. *_To only > report the WM regions, add to mri_segstats --ctab > $FREESURFER_HOME/_**_WMParcStatsLUT.txt_* > > > > I'm probably doing something wrong, but I can't really point to the > > problem, thus asking for your help. > _*I don't know either. If I had to guess, I'd say it is a registration > problem. What is the first value in register.dat.mincost?*_ > doug > > > > Attached is the table again, > > > > Thanks > > Rotem > > > > > > The values look about right in the table. Your pipeline looks ok, > > thought the last step uses fa_FOLDER-NAME.mask.nii instead of the > > output > > of mri_vol2vol (fa_FOLDER-NAME.nii). > > doug > > > > > > > > On 03/17/2013 02:16 AM, Rotem Saar wrote: > > > > > > Hi all, > > > I run into somthing that seems odd to me and wanted to > consult - > > > I run the following script for getting the FA values from > my DTI > > > scans: > > > > > > 1) dt_recon --i > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s > > > FOLDER-NAME --o > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec > > > 2) tkregister2 --s fsaverage --surf white --reg > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg > > > --mov > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii > > > 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz > > > -reg > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat > > > -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii > > > -fthresh 0.2 -fmax 1 > > > 4) mri_vol2vol --mov > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ > > > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s > > > FOLDER-NAME --interp nearest --o > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii > > > --reg > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat > > > 5) tkregister2 --mov > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii > > > --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz > > > --reg > > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg > > > 6) mri_segstats --seg > > > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab > > > $FREESURFER_HOME/FreeSurferColorLUT.txt --i > > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii > > > --sum > > > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME > > > > > > > > > I got a table with all the FA values (see attached), for each > > > segment, but I suspect a problem: I think that the values > > are too > > > high (I set the threshold to 0.2-1), am I right ? > > > Can u guide me regarding what I can do to solve the > problem ? in > > > addition I attached a figure of the corpus-callosum, in > > which I'm > > > interested - i't seems that the green area in not big > enough, is > > > this fixable ? > > > > > > Thanks ! > > > > > > Rotem > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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