Re: [Freesurfer] Fwd: Anatomical segmentation - question
Hi Doug, Can u help ? Thanks Rotem Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel 2014/1/6 Bruce Fischl > it probably doesn't matter, but Doug is the Talairach expert, so perhaps > he can comment > Bruce > > > On Mon, 6 Jan 2014, Rotem Saar wrote: > > Dear freesurfer experts, >> >> I'm performing anatomical segmentation for Philips dicoms (3T scanner). I >> got these two images from the same slice while performing step number 4 in >> the script below – from some reason, the two images don't fit. Should I >> use >> "scale brain" ? I know this is not recommended thus want to consult with u >> first – Can u please comment on why this is happening? Is there any value >> that corresponds to "how good is the segmentation" ? if yes, where can I >> find it ? >> >> My script is written below. >> >> Thanks, >> >> Rotem >> >> Anatomical segmentation: >> >> first step- 23 hours: >> >> recon-all -autorecon-all -i ~/Desktop/ FOLDER-NAME /I1.dcm -s >> FOLDER-NAME >> >> second step:(gyrus=green, sulcus=red) >> >> tksurfer -curv FOLDER-NAME lh/rh inflated >> >> third step: (talairch registretion) >> >> tkmedit FOLDER-NAME brainmask.mgz >> >> File-> transforms-> load transform AUX-> Browse-> talairch.xfm >> >> forth step: (simetry - allows changing 12df transformation. if we made any >> changes we should click "save reg" and run this command again) >> >> tkregister2 --mgz --s FOLDER-NAME --fstal --surf orig >> >> IF WE CHANGE ANYTHING, CLICK "SAVE REG" AND RUN FROM STARTING POING: >> recon-all -all -subjectid FOLDER-NAME >> >> fifth step: (scalp removal: if removed too much, rise up from the value >> 25: >> >> recon-all -skullstrip -wsthresh 25 -clean-bm -no-wsgcaatlas -s >> FOLDER-NAME >> >> to check the result press: tkmedit FOLDER-NAME brainmask.mgz lh.white -aux >> T1.mgz -aux-surface rh.white ) >> >> for hand correction: tkmedit FOLDER-NAME brainmask.mgz -aux T1.mgz >> >> tools-> configure volume brush -> MARK: mode=clone, source=Aux >> >> tools-> configure brush info (for choosing brush size) >> >> click on edit voxels: click in MIDDLE for adding voxels, RIGHT for >> removing >> voxels : slice by slice. >> >> when finish, click: File-> save main volume >> >> sisxt step: (cp for correcting segmentation) >> >> tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz -aux-surface >> rh.white >> >> seventh step: (done) >> >> recon-all -autorecon2-cp -autorecon3 -s FOLDER-NAME >> >> >> >> >> >> >> Rotem Saar-Ashkenazy >> Department of Brain and Cognitive Science >> Ben Gurion University of the Negev >> Beer-Sheva 84105 >> Israel >> >> >> > > 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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Viewing color-map in freesurfer
Hi, We followed the instructions on this link: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion#Masking to perform diffusion analysis and wanted to ask if there is an option to view the color-map in addition to the FA and ADC maps ? We want to make sure that left-right tracts are red, anterior-posterior are green ect... is this possible ? Thanks Rotem Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Mean diffusivity
Dear freesurfer experts, Can u please advise on how to extract the mean diffusivity value for each ROI from the wmparc file ? I know how to extract the FA value, but interested in the MD value also for the same regions. Thanks Rotem Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Mean diffusivity
Dear Doug, Sorry - I'm probably missing something, as trying to write what u suggested (see below email history) didn't work (not sure what am I doing wrong). I'm copying here what I did to get the average FA value to each region. Can u PLEASE write what do I need to change in order to get the MD value instead for the FA value, but keep the same format of the output ? Thanks, I really appreciate the help !! dt_recon --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I160.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 mri_vol2vol --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/lowb.nii \ --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz \ --inv --interp nearest --o /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc2diff.mgz \ --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat --no-save-reg mri_vol2vol --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/lowb.nii \ --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/aparc+aseg.mgz \ --inv --interp nearest --o /usr/local/freesurfer/subjects/FOLDER-NAME/mri/aparc+aseg2diff.mgz \ --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat --no-save-reg mri_mask /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii \ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc2diff.mgz \ /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-masked.mgz mri_segstats --seg /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc2diff.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-masked.mgz --sum /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa-masked Message: 26 Date: Tue, 04 Feb 2014 11:10:25 -0500 From: Douglas N Greve Subject: Re: [Freesurfer] Mean diffusivity To: freesurfer@nmr.mgh.harvard.edu Message-ID: <52f110f1.5050...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Use mri_label2vol to transfer the wmparc.mgz into the DTI space, then use mri_segstats with --seg-erode 1 to compute summaries of the MD in each region doug On 02/03/2014 10:45 PM, Rotem Saar wrote: > Dear freesurfer experts, > > Can u please advise on how to extract the mean diffusivity value for > each ROI from the wmparc file ? > I know how to extract the FA value, but interested in the MD value > also for the same regions. > > Thanks > Rotem > Rotem Saar-Ashkenazy > Department of Brain and Cognitive Science > Ben Gurion University of the Negev > Beer-Sheva 84105 > Israel > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel 2014-02-04 5:45 GMT+02:00 Rotem Saar : > Dear freesurfer experts, > > Can u please advise on how to extract the mean diffusivity value for each > ROI from the wmparc file ? > I know how to extract the FA value, but interested in the MD value also > for the same regions. > > Thanks > Rotem > Rotem Saar-Ashkenazy > Department of Brain and Cognitive Science > Ben Gurion University of the Negev > Beer-Sheva 84105 > Israel > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Extracting Mean Diffusivity values
Dear Doug, I'm now working with freesurfer 5.3, for this example, subject is "Anatomy0981". A while ago I wrote to the list trying to extract the MD values for each ROI as in the diffusion analysis that ends with the FA value for each ROI (for each subject). I wrote my FA script, and asked u to advise on how to convert it to my needs (MD instead of FA), u wrote - > Use mri_label2vol to transfer the wmparc.mgz into the DTI space, then > use mri_segstats with --seg-erode 1 to compute summaries of the MD in > each region (steps below for FA values ended fine) - this is what I did - 1) dt_recon --i /usr/local/freesurfer/ subjects/Anatomy0981/DTI/I160.dcm --s Anatomy0981 --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvals.bval /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvecs.bvec 2) mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0981/DTI/lowb.nii \ --targ /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz \ --inv --interp nearest --o /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz \ --reg /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --no-save-reg 3) mri_label2vol --mov /usr/local/freesurfer/subjects/Anatomy0981/DTI/lowb.nii \ --targ /usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg.mgz \ --inv --interp nearest --o /usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg2diff.mgz \ --reg /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --no-save-reg 4) mri_segstats --seg-erode 1 /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/Anatomy0981/DTI/fa-masked.mgz --sum /usr/local/freesurfer/subjects/Anatomy0981/stats/all_stats_MD-masked error after step 3: ERROR: Option --mov unknown Trying to use vol2vol instead of label2vol ended successfully, but then when trying to perform step 4, it failed again - ERROR: Option /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz unknown Can u advise on what am I doing wrong ? Thanks !! Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Extracting Mean Diffusivity values
Hi Doug,
Thanks you for directing me to my mistake in step 3 (see below new cmd line
in step 3). What I did is the following -
1) dt_recon --i /usr/local/freesurfer/subjects/Anatomy0981/DTI/I160.dcm --s
Anatomy0981 --o /usr/local/freesurfer/subjects/Anatomy0981/DTI --b
/usr/local/freesurfer/subjects/Anatomy0981/DTI/bvals.bval
/usr/local/freesurfer/subjects/Anatomy0981/DTI/bvecs.bvec
2) mri_vol2vol --mov
/usr/local/freesurfer/subjects/Anatomy0981/DTI/lowb.nii --targ
/usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --inv --interp
nearest --o /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz
--reg /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat
--no-save-reg
3) mri_label2vol --seg
/usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg.mgz --temp
/usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg.mgz --reg
/usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --o
/usr/local/freesurfer/subjects/Anatomy0981/mri/forMD.bshort
it created many *.bshort files
My qs:
1) Should I repeat step 3 with the wmparc.mgz or is it not necessary ?
2) How do I plot all MD values like I did before for FA values ? trying to
use -
mri_segstats --seg-erode 1
/usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --i
/usr/local/freesurfer/subjects/Anatomy0981/DTI/fa-masked.mgz --sum
/usr/local/freesurfer/subjects/Anatomy0981/stats/all_stats_MD-masked
always end with the same message - it wants a segmentation volume but
nothing works ("unknown")... I used aseg.mgz for example and other options
- nada. However, If I omit the "-erode 1" it reports the table, but for FA
values. What do I need to change in step 3 and how can I fix the last step ?
Thank you for your help
Rotem
2014-03-17 8:42 GMT+02:00 Rotem Saar :
> Dear Doug,
>
> I'm now working with freesurfer 5.3, for this example, subject is
> "Anatomy0981". A while ago I wrote to the list trying to extract the MD
> values for each ROI as in the diffusion analysis that ends with the FA
> value for each ROI (for each subject).
> I wrote my FA script, and asked u to advise on how to convert it to my
> needs (MD instead of FA), u wrote -
>
> > Use mri_label2vol to transfer the wmparc.mgz into the DTI space, then
> > use mri_segstats with --seg-erode 1 to compute summaries of the MD in
> > each region
>
> (steps below for FA values ended fine) - this is what I did -
>
> 1) dt_recon --i /usr/local/freesurfer/
> subjects/Anatomy0981/DTI/I160.dcm
> --s Anatomy0981 --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b
> /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvals.bval
> /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvecs.bvec
>
> 2) mri_vol2vol --mov
> /usr/local/freesurfer/subjects/Anatomy0981/DTI/lowb.nii \
> --targ
> /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz \
> --inv --interp nearest --o
> /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz \
> --reg
> /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --no-save-reg
>
> 3) mri_label2vol --mov
> /usr/local/freesurfer/subjects/Anatomy0981/DTI/lowb.nii \
> --targ
> /usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg.mgz \
> --inv --interp nearest --o
> /usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg2diff.mgz \
> --reg
> /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --no-save-reg
>
> 4) mri_segstats --seg-erode 1
> /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz --ctab
> $FREESURFER_HOME/FreeSurferColorLUT.txt --i
> /usr/local/freesurfer/subjects/Anatomy0981/DTI/fa-masked.mgz --sum
> /usr/local/freesurfer/subjects/Anatomy0981/stats/all_stats_MD-masked
>
> error after step 3: ERROR: Option --mov unknown
> Trying to use vol2vol instead of label2vol ended successfully, but then
> when trying to perform step 4, it failed again -
> ERROR: Option
> /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz unknown
>
> Can u advise on what am I doing wrong ?
>
> Thanks !!
>
>
>
>
> Rotem Saar-Ashkenazy
> Department of Brain and Cognitive Science
> Ben Gurion University of the Negev
> Beer-Sheva 84105
> Israel
>
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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Re: [Freesurfer] Freesurfer Digest, Vol 109, Issue 21
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 ? 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... I'm probably doing something wrong, but I can't really point to the problem, thus asking for your help. 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/I1.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 > all_stats_fa_Rotem_try Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Fwd: Freesurfer Digest, Vol 109, Issue 21
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 ? 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... I'm probably doing something wrong, but I can't really point to the problem, thus asking for your help. 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/I1.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 > all_stats_fa_Rotem_try Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] DTI: problems with (high) FA values
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/I1.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/subje
[Freesurfer] Fwd: Freesurfer Digest, Vol 110, Issue 20
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 > Subject: Re: [Freesurfer] DTI: problems with (high) FA values > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <5166ea1a.8000...@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/freesur
Re: [Freesurfer] Fwd: DTI questions
Dear Anastasia, The T1 images were acquired in a sagittal orientation, and the DTI images in an axial orientation. Does this help ? Thanks Rotem 2013/6/25 Anastasia Yendiki > > Hi Rotem - No problem. Were these scans by any chance acquired with a > coronal slice prescription? In the axial views that you sent, the artifact > that you're pointing to looks like misalignment between consecutive coronal > slices, which could be due to head motion. > > a.y > > > On Tue, 25 Jun 2013, Rotem Saar wrote: > > Dear Anastasia, >> >> I tried several times to upload these images in a non-compressed way, but >> they were too big and my posts were rejected, with no opportunity for any >> other upload way. >> Is there any other way for me to upload it so that everyone can see it ? >> >> Attached are the images in a non-compressed fashion. I will be very happy >> if >> u will have a look, and post your answer to me and the list to save some >> time, until I will be able to consider another way to upload them. >> >> I know that we should write to all the list, but at the moment if the >> images >> are not visible this won't help - so I will really appreciate if u will >> have >> a look but also tell me what is the best way to upload them so that all >> list >> members will be able to see them. >> >> Thank u very much for your help. >> >> Rotem >> >> 2013/6/25 Anastasia Yendiki >> >> Sorry, can't open the image. >> >> On Sun, 23 Jun 2013, Rotem Saar wrote: >> >> Hi there, >> >> Long time:). Well I wrote to the list several times >> regarding high FA values >> I got when performing DTI analysis. >> Today we know that the problem was an additional >> direction (we had 17 >> directions instead of 16 - we used a Philips >> scanner,1.5T). So we deleted >> the additional slices and the high values indeed >> disappeared, but then >> another problem came up (tried several subjects so >> the problem is not >> specific to a subject) - >> >> I noticed an artifact that I can't explain - please >> see the attached >> pictures. >> >> This artifact existed even before I deleted the >> additional slices, also - I >> see the artifact also when loading the masked >> volume...It is cyclic - run >> over all slices... >> >> any ideas ? >> >> I'm using version 5.2 and I know the command lines >> are correct (send it to u >> in the past). >> >> Thanks for your help >> >> Rotem >> >> >> >> >> 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<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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] A question regarding a "nii-read" error I get when running a script for FA values output
Hi, My name is Rotem, I'm a PhD. student and recently started to work with freesurfer software (freesurfer-Linux-centos4-stable-pub-v5.1.0). QUESTION For several weeks, I have been trying to operate a script for FA values, with no success, and would really appreciate your help with shading some light regarding the problem and it's solution. I have a data set, after an anatomical segmentation (file is attached, named "Anatomical segmentation for fs", this is the script I'm using for brain anatomical segmentation). What I'm trying to run now is the DTI script, in which I run commands that at least for my understanding spouse to give me at the end a table with all the FA values for each brain region (ROI). The script I'm using to do this is attached and called "DTI_RUN_NEW_FOR_FS". *After running phase 5*, in which a mask file should be created (indeed I have checked and the file is created in the same folder it should be): fmri4-P67A-D3-B3:/usr/local/freesurfer/subjects> mri_mask /usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.nii /usr/local/freesurfer/subjects/FOLDER_NAME/mri/brainmask.mgz /usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii DoAbs = 0 Found 16777216 voxels in mask Writing masked volume to /usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii...done. *I run phase 6, and then get the following error message:* fmri4-P67A-D3-B3:/usr/local/freesurfer/subjects> 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 $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg /usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --i usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.nii --sum /usr/local/freesurfer/subjects/FOLDER_NAME/stats/all_stats_fa_FOLDER_NAME sysname Linux hostname fmri4-P67A-D3-B3 machine i686 user fmri4 Loading /usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz Loading usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii niiRead(): error opening file usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii ERROR: loading usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii I think the problem is between phase 5 and 6, and is related to file format (.nii) but don't have a hint regarding what can I do to solve this:( Can someone please write me the correct code line ? I would really appreciate your kind help since I run out of ideas for solutions. Thanks in advance, Rotem Anatomical Description: Binary data DTI_RUN_NEW_FOR_FS Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] A question regarding high FA values when running DTI script
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/I1.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_marsal.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, 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 ? I'm attaching the table I got, and to be specific, I'm very much interested in the Corpus-Colosseum values, which are high (not surprising) but when I wanted to validate with some other structures, like the "left putamen" I saw 0.53 which is to my opinion too high ? I would really appreciate if you can have a look at the table I attached here. Can u guide me regarding what I can do to solve the problem ? Is that any way to confirm that after the mask, I am left only with white matter ? Thanks ! Rotem all_stats_FA_FOR_FS Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] A question regarding high FA values when running DTI script
Hi Bruce, Thanks for your answer and sorry about the delay in mine. Registration seems fine, but I came up with some questions regarding it - 1) When testing the registration, using the "compare" button, I can see both the diffusion and what is suppose to be the anatomical slices - but why do the anatomical data it smoothed and doesn't look like a clear anatomical image ? can this be related ? maybe i did something wrong ? 2) Another thing I thought about was that the corpuse-callosum values are very high, but values for the ventricles are really low - so that even really small shifts in the registration can bring to a situation that values in the ventricles are higher than expected. Do u suggest manual intervention in registration that will mainly follow the mid-sagittal slice ? I don't mean ignoring the others, but mainly test the fit according the mid-sagittal slice. If u have any other ideas for why this is happening - I would appreciate it if u share them with me in order to think of a solution. Thanks ! Rotem 2013/2/18 Bruce Fischl > Hi Rotem > > that does sound high. Have you checked the registation between your > diffusion data and the anatomicals? > > cheers > Bruce > > > > On Mon, 18 Feb 2013, 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/** >> I1.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_**marsal.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, 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 ? >> I'm attaching the table I got, and to be specific, I'm very much >> interested >> in the Corpus-Colosseum values, which are high (not surprising) but when I >> wanted to validate with some other structures, like the "left putamen" I >> saw >> 0.53 which is to my opinion too high ? >> I would really appreciate if you can have a look at the table I attached >> here. >> Can u guide me regarding what I can do to solve the problem ? Is that any >> way to confirm that after the mask, I am left only with white matter ? >> >> Thanks ! >> >> Rotem >> >> >> > > 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<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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] A question regarding high FA values when running DTI script
2013/3/5 Rotem Saar > Hi > > Attached is some pictures that might help ? Is this what you meant ? > Looking at this again - something is weird but I can't say what... > I can ZIP the data of one subject and send it to you but I don't feel > comfortable asking you to personally examine it... > Hopefully the upcoming course will shed some light on these problems... > > thanks > > Rotem > > 2013/2/26 Bruce Fischl > >> Hi Rotem >> >> that's always a problem with FA estimation (the partial volume stuff I >> mean). It's hard to diagnose this without seeing some images. Can you send >> some of the registration? >> >> cheers >> Bruce >> >> >> >> On Tue, 26 Feb 2013, Rotem Saar wrote: >> >> Hi Bruce, >>> >>> Thanks for your answer and sorry about the delay in mine. >>> Registration seems fine, but I came up with some questions regarding it - >>> >>> 1) When testing the registration, using the "compare" button, I can see >>> both the diffusion and what is suppose to be the anatomical slices - but why >>> do the anatomical data it smoothed and doesn't look like a clear >>> anatomical image ? can this be related ? maybe i did something wrong ? >>> >>> 2) Another thing I thought about was that the corpuse-callosum values >>> are very high, but values for the ventricles are really low - so that even >>> really small shifts in the registration can bring to a situation that >>> values in the ventricles are higher than expected. Do u suggest manual >>> intervention in registration that will mainly follow the mid-sagittal >>> slice ? I don't mean ignoring the others, but mainly test the fit according >>> the >>> mid-sagittal slice. >>> >>> If u have any other ideas for why this is happening - I would appreciate >>> it if u share them with me in order to think of a solution. >>> >>> Thanks ! >>> >>> Rotem >>> >>> 2013/2/18 Bruce Fischl >>> Hi Rotem >>> >>> that does sound high. Have you checked the registation between >>> your diffusion data and the anatomicals? >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 18 Feb 2013, 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/**I1.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_**marsal.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 >>> --cta
[Freesurfer] Pineal gland volume?
Dear Freesurfer experts, I wondered if its possible to extract the volume of the *pineal gland* using the basic cortical + sub-cortical segmentation (recon-all)? I could not find the volume of this ROI in the output. If the volume output for this ROI is available - please guide me where to look (maybe I missed it?) If not - does manual ROI drawing and following,volume calculation is possible using freesurfer? Thanks ! Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] pineal gland
Dear Bruce and Doug, Thank u for your replay saying that it is possible to manually draw the pineal gland using freeview and extract stats for it. Can u please refer me to a link on wiki that explain how to do it? I'm not familiar with this procedure and although Doug explain it in brief I feel I need to follow some manual...is there something on the net? If not - can u please specify the steps I need to go through? Also, I have a full recon-all for the subjects I want to extract the volume of the pineal gland (using freesurfer version 3 something...). If I want to extract the volume of a specific ROI today using and advance freesurfer version (5+) - Do I need to run recon-all again with the newer version? Many thanks ! Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Diffusion analysis qs - gradient matrix
Dear freesurfer experts, For diffusion analysis in freesurfer - I want to know which gradient matrix freesurfer expects. The thing is - when I look at the gradient matrix created using a MATLAB script that reads the directions from the dicom header - I get one table, but the bvecs file created in MRIconvert (for converting dicoms to nifti) looks different. This is the situation when an angle is applied during the acquisition of the dMRI scans, which means that each subject has its own gradient matrix. So my question is which table should I use for diffusion analysis in freesurfer? The one that was created from the dicom header or the one created for NIFTI format using MRIconvert ? Thanks Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Diffusion analysis qs
tal Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO ?63110 Email: mha...@wustl.edu > > From: Rotem Saar > Reply-To: Freesurfer support list > Date: Monday, July 21, 2014 1:54 PM > To: "freesurfer@nmr.mgh.harvard.edu" > Subject: [Freesurfer] Diffusion analysis qs - gradient matrix > > Dear freesurfer experts, > > For diffusion analysis in freesurfer - I want to know which gradient matrix > freesurfer expects. > > The thing is - when I look at the gradient matrix created using a MATLAB > script that reads the directions from the dicom header - I get one table, > but the bvecs file created in MRIconvert (for converting dicoms to nifti) > looks different. > > This is the situation when an angle is applied during the acquisition of the > dMRI scans, which means that each subject has its own gradient matrix. > > So my question is which table should I use for diffusion analysis in > freesurfer? The one that was created from the dicom header or the one > created for NIFTI format using MRIconvert ?? > > Thanks Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Diffusion analysis qs
Dear Anastasia, I followed your suggestion: I calculated the FA maps in freesurfer using the script below (see last message): I did it with both the rotated and the not rotated gradient table. The FA maps were identical as u said. BUT ! - when I used the rotated gradient table in FSL and tried to create the FA & MD maps (as in the first step of tracula), I got the attached results: http://tinypic.com/r/skzwqa/8 Does this map seems ok to u ? I think that something is wrong but can't specify what. I will appreciate your help here again:) Hi Rotem - The FA values are actually invariant to a rotation of the gradient vectors. You can test that yourself. If, however, you get different FA maps with the different gradient tables, then something else is going on and not a simple rotation. a.y On Wed, 23 Jul 2014, Rotem Saar wrote: > Dear Anastasia & Michael, > > Thank u for your answers (I attached my last email and your answers at the > end of this email. > > I still want to specify my question. If I only want to extract FA values > using the following script (see script below), and I know that an angle was > applied during the dMRI scans, should I use the rotated gradient matrix ? > > When I first analyzed 20 subjects with the gradient matrix that is published > for a T3 Philips magnet (I also read the gradients from the dicom header - > they were the same) I got reasonable results - but now I don't know what to > think of them... > > source ~/Desktop/fs_script > > dt_recon --i /usr/local/freesurfer/subjects/Anatomy0207/DTI/I160.dcm --s > Anatomy0207 --o /usr/local/freesurfer/subjects/Anatomy0207/DTI --b > /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvals.bval > /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvecs.bvec > > To check results, run: > > tkregister2 --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii > --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --surf > > tkregister2 --s fsaverage --surf white --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii.reg --mov > /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii > > tkregister2 --s fsaverage --surf white --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii.reg --mov > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii > /usr/local/freesurfer/subjects/Anatomy0207/DTI/adc.nii > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/mri/ brain.mgz/usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii:reg= register.dat:colo > rmap=heat:heatscale=.2,.2,1 > > tkmedit Anatomy0207?orig.mgz -aux brain.mgz -seg wmparc.mgz -reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat -overlay > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii -fthresh 0.2 -fmax 1 > > mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ > ??? --targ /usr/local/freesurfer/subjects/Anatomy0207/mri/ wmparc.mgz > \ > ??? --inv --interp nearest --o > /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ > ??? --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg > > mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ > ??? --targ > /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg.mgz \ > ??? --inv --interp nearest --o > /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz \ > ??? --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ > ???/usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+ aseg2diff.mgz:colormap > =lut > > > mri_mask /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ > /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz > > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa- masked.mgz/usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+ aseg2diff.mgz:colormap > =lut > > mri_segstats --seg > /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --i > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz --sum > /usr/local/freesurfer/subjects/Anatomy0207/stats/all_stats_fa-masked > > It'd be nice if things were that simple, but! > > Although the pre-processing is done with FSL tools, tractography is done > with locally written code. Some gradient sets may appear to work with FSL, > but they won't work for us. For example, so
[Freesurfer] Fwd: Diffusion analysis qs
Dear Anastasia, I followed your suggestion: I calculated the FA maps in freesurfer using the script below (see last message): I did it with both the rotated and the not rotated gradient table. The FA maps were identical as u said. BUT ! - when I used the rotated gradient table in FSL and tried to create the FA & MD maps (as in the first step of tracula), I got the attached results: http://tinypic.com/r/skzwqa/8 Does this map seems ok to u ? I think that something is wrong but can't specify what. I will appreciate your help here again:) Hi Rotem - The FA values are actually invariant to a rotation of the gradient vectors. You can test that yourself. If, however, you get different FA maps with the different gradient tables, then something else is going on and not a simple rotation. a.y On Wed, 23 Jul 2014, Rotem Saar wrote: > Dear Anastasia & Michael, > > Thank u for your answers (I attached my last email and your answers at the > end of this email. > > I still want to specify my question. If I only want to extract FA values > using the following script (see script below), and I know that an angle was > applied during the dMRI scans, should I use the rotated gradient matrix ? > > When I first analyzed 20 subjects with the gradient matrix that is published > for a T3 Philips magnet (I also read the gradients from the dicom header - > they were the same) I got reasonable results - but now I don't know what to > think of them... > > source ~/Desktop/fs_script > > dt_recon --i /usr/local/freesurfer/subjects/Anatomy0207/DTI/I160.dcm --s > Anatomy0207 --o /usr/local/freesurfer/subjects/Anatomy0207/DTI --b > /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvals.bval > /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvecs.bvec > > To check results, run: > > tkregister2 --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii > --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --surf > > tkregister2 --s fsaverage --surf white --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii.reg --mov > /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii > > tkregister2 --s fsaverage --surf white --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii.reg --mov > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii > /usr/local/freesurfer/subjects/Anatomy0207/DTI/adc.nii > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/mri/ brain.mgz/usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii:reg= register.dat:colo > rmap=heat:heatscale=.2,.2,1 > > tkmedit Anatomy0207?orig.mgz -aux brain.mgz -seg wmparc.mgz -reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat -overlay > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii -fthresh 0.2 -fmax 1 > > mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ > ??? --targ /usr/local/freesurfer/subjects/Anatomy0207/mri/ wmparc.mgz > \ > ??? --inv --interp nearest --o > /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ > ??? --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg > > mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ > ??? --targ > /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg.mgz \ > ??? --inv --interp nearest --o > /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz \ > ??? --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ > ???/usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+ aseg2diff.mgz:colormap > =lut > > > mri_mask /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ > /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz > > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa- masked.mgz/usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+ aseg2diff.mgz:colormap > =lut > > mri_segstats --seg > /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --i > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz --sum > /usr/local/freesurfer/subjects/Anatomy0207/stats/all_stats_fa-masked > > It'd be nice if things were that simple, but! > > Although the pre-processing is done with FSL tools, tractography is done > with locally written code. Some gradient sets may appear to work with FSL, > but they won't work for us. For example, so
