Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30096 discussions

DTI: problems with (high) FA values
by Rotem Saar 11 Apr '13

11 Apr '13

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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

2 1

mri_aparc2aseg issue
by Paul Beach 11 Apr '13

11 Apr '13

Hi Freesurfers, I'm currently trying to take manually made ROIs (label files) that have been incorporated into new annotation files (one for each hemisphere - rh.aug_aparc.annot & lh.aug_aparc.annot) and turn them into a new (augmented) annotation into a aseg file (an aug_aparc+aseg.mgz file). To do so I've been using the mri_aparc2aseg command and, at face value, it works well. However, some of my ROIs (specifically my insular ROIs) are being either shifted or lost in the transition from annotation to segmentation. Note that each hemisphere's new annotation files look perfect on tksurfer (which is where they were originally drawn). It's only when I try and make them fill the full cortical ribbon with the mri_aparc2aseg command that I get this issue. I piloted everything out on averaged subject and it all worked perfectly. However, when I attempted things on individual subject data I received the problem described above. I've attached a picture illustrating the discrepancy between the an averaged subject and a single subject. I have also attached my script code. The overall goal is to create a gmroi_volume which will allow me to determine an aux number of each manual ROI so as to export each one to AFNI space. I'd *really* appreciate help on how to fix this. Thanks, Paul

2 2

Re: [Freesurfer] Transform SMOOTHWM to DTI B0
by Daniel Haehn 11 Apr '13

11 Apr '13

Hi Satra et al, thanks a lot and it would be great if you could find some code! In the meantime, I tried the following based on information from Kiho Im: # we have to first remove transformation of 'vertex to RAS' embedded in smoothwm surface. mris_transform lh.smoothwm identity.xfm ./lh.smoothwm.clean # then use the flirt T1-to-b0 matrix converted from .mat to .xfm format to transform the surface mris_transform lh.smoothwm.clean T1-to-b0.xfm lh.b0.smoothwm And of course: it didn't work.. In the attached screenshot, the red surface is the original one which kind of fits the b0 image but not very well (it obviously fits the original T1 very well). The blue is the transformed surface (lh.b0.smoothwm) and is completely off. [image: Inline image 1] Do you know what I could be doing wrong? I also attached both tranforms. Maybe I just converted them wrong. Thanks!! Daniel On Thu, Apr 11, 2013 at 10:53 AM, Satrajit Ghosh <satra(a)mit.edu> wrote: > hi dan, > > if you use bbregister to match the DTI b0 to freesurfer space, then you > can transform the surface back (no guarantees on the tesselations though i > think). the only additional component here would be a tkr transform that's > based on the conformed space. i might even have some python code lying > around to do this. i'll take a look. > > cheers, > > satra > > On Thu, Apr 11, 2013 at 10:40 AM, Daniel Haehn < > daniel.haehn(a)childrens.harvard.edu> wrote: > >> Hi all, >> >> I want to transform the Freesurfer Smoothwm surfaces to DTI B0 space. >> >> I found >> http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransformsbut this describes transforming the B0 to T1 space and then match the >> surfaces. I don't want to change the DTI B0 image. >> >> What is the best way to do that? >> >> Thank you very much! >> Daniel >> >> -- >> Daniel Haehn >> FNNDSC / BCH >> +1.857.218.5140 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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. >> >> > -- Daniel Haehn FNNDSC / BCH +1.857.218.5140

2 1

Transform SMOOTHWM to DTI B0
by Daniel Haehn 11 Apr '13

11 Apr '13

Hi all, I want to transform the Freesurfer Smoothwm surfaces to DTI B0 space. I found http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms but this describes transforming the B0 to T1 space and then match the surfaces. I don't want to change the DTI B0 image. What is the best way to do that? Thank you very much! Daniel -- Daniel Haehn FNNDSC / BCH +1.857.218.5140

3 2

mgz to dicom
by Varghese Chikku 11 Apr '13

11 Apr '13

Hi All, Is there any tool,which can convert mgz files to Dicom? In Thanks chikku

3 2

Surfaces to *native* space
by Oscar Esteban 11 Apr '13

11 Apr '13

Dear all, I think my issue is quite related to this one (if not duplicated, sorry in that case): https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/027622.… As Shani, I used bbregister to coregister diffusion images to anatomical: > bbregister --s OE0_T1 --mov DTI_b0_brain.nii.gz --reg dti2anat.dat --dti --init-fsl Then, I visually checked the outcome and resampled the T1 to DTI space: > tkregister2 --mov DTI_b0.nii.gz --reg dti2anat.dat --surf > mri_vol2vol --mov DTI_b0.nii.gz --targ OE0_T1/mri/T1.mgz --reg dti2anat.dat --o T1-to-DTI.nii.gz --inv > tkregister2 --mov T1-to-DTI.nii.gz --targ DTI_b0.nii.gz --reg T1-to-DTI.nii.gz.reg Everything looks fine, but I cannot get the pial and white surfaces into dti space (please note the --reg-inv param and the ref volume DTI_b0.nii.gz, that should be important IMHO): > mri_surf2surf --s OE0_T1 --sval-xyz white --reg-inv dti2anat.dat DTI_b0.nii.gz --tval lh.white.dti --tval-xyz --hemi lh There seems to exist an orientation problem when trying to visualize the surface > tkmedit -f DTI_b0.nii.gz -surface lh.white.dti I also applied the solution that Douglas recommended Shani, without good results :(. Any light on this would be of the highest interest for me :D Thanks, Oscar -- Oscar Esteban PhD Student / Researcher Biomedical Image Technologies (BIT), UPM ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid (Spain) +34 915 495 700 ext.4234 Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5 ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland

1 0

Finding adjacent vertices/labels
by Chris McNorgan 10 Apr '13

10 Apr '13

Hello Freesurfers, I was wondering if there is information embedded in the annotation/label files that could be used to determine whether two labels represent anatomically adjacent regions? For example, I have parcellated a bunch of participants using connectomemapper into 1000 ROIs. I was just now reading Power et al. (2011), who looked at functional connectivity, but specifically excluded connections between spheroid ROIs that were less than 20mm apart. Analogously, I might wish to exclude connections between adjacent labels, but it seemed that manually creating an adjacency matrix for 1000 regions would be impractical, and a good candidate for an automated approach. I'm just not clear what information such an approach might have to work with. Can the adjacency between two vertices be determined based on their values? If so, one approach might be: for each pair of labels (A,B): get set of vertices within A get set of vertices within B for each vertex pair (Ai, Bj) if Ai and Bj are adjacent, stop, and mark A and B as adjacent Cheers, Chris

2 1

Re: [Freesurfer] Comparing HRF undershoots between conditions
by Douglas N Greve 10 Apr '13

10 Apr '13

If you run tkmedit-sess, then open the overlay configuration window, then advance the time point to the delay you want. Otherwise, you can create a contrast where you just look at the delay you want. To do this, run mkcontrast-sess with -setwdelays and specify 0 for all delays and 1 for the delay you want to see. doug On 04/10/2013 04:15 PM, SHAHIN NASR wrote: > That's the problem Doug. I have already generated the FIR model but > how can I show the sig MAP for one "particulat time point". What are > the other ways? > > > On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Shahin, there are several ways that you could do it. The one > that immediately comes to mind is to use an FIR and then test for > a difference at a particular post stimulus time point. > doug > > > > > On 04/10/2013 03:54 PM, SHAHIN NASR wrote: > > Hi, > I want to generate a map to show the significant > difference between HRF undershoot (negative peak of activity) > between two conditions independent from the positive peak. Is > there anyway, to generate this map? > > P.S.: Please note that I need a map and not a time course graph. > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel: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/ > > > > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

Rejoindre mon réseau sur LinkedIn
by Sima Chalavi 10 Apr '13

10 Apr '13

LinkedIn ------------ Sima Chalavi souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Sima Chalavi http://www.linkedin.com/e/-qq80um-hfd0ug20-5o/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir le profil de Sima Chalavi http://www.linkedin.com/e/-qq80um-hfd0ug20-5o/rso/245935493/G7CW/name/66471… ------------------------------------------ Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-hfd0ug20-5o/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

1 0

Comparing HRF undershoots between conditions
by SHAHIN NASR 10 Apr '13

10 Apr '13

Hi, I want to generate a map to show the significant difference between HRF undershoot (negative peak of activity) between two conditions independent from the positive peak. Is there anyway, to generate this map? P.S.: Please note that I need a map and not a time course graph. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer