Freesurfer

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A question regarding high FA values when running DTI script
by Rotem Saar 18 Mar '13

18 Mar '13

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_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

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Re: [Freesurfer] licence file problem
by Karen Duarte 18 Mar '13

18 Mar '13

Hi freesurfer masters, so I created the '.licence' file in the freesurfer_home, with the 3 lines of the mail with licence i recieved. And when testing up freesurfer, as they say here<http://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer>, I receive the ERROR: FreeSurfer license file /home/karen/freesurfer/.license not found. This is strange! Cause when i do ~>find / -name '.licence', I receive the directory /home/karen/freesurfer/.licence. What can I do? Thanks in advance! karen

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Re: [Freesurfer] Asymmetries of cortical thickness
by Douglas N Greve 18 Mar '13

18 Mar '13

you will have to use the same stream, just specify one subject when your mris_preproc doug On 03/18/2013 08:06 AM, Sophie Maingault wrote: > > Hello, > > Iobtained a map of cortical thickness asymmetries after the > registration on the symmetric atlas. But I would to obtain the same > map with raw data I mean just by subtract lh.thickness and > rh.thickness. How can I modify the part #Create a stack of subjects in > wiki page ? I have to register to fsaverage (and not fsaverage_sym) > and then do the same thing ? > > Thanks you for your help. > > Sophie > > > > _______________________________________________ > 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/

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interchanging between FSL freesurfer
by martina.andellini＠fastwebnet.it 18 Mar '13

18 Mar '13

Hi, my name is Martina and I'm a student of biomedical engineering in Rome. I'm doin g a brain imaging research for my final exam. I'm using freesurfer for registration and segmentation of brain images instead o f FSL tools (flirt,bet and fast) and then continue to process the data with FSL. But I have a problem: after converting the image generated with freesurfer mri_ convert to ".nii" format it does not overlap with FSL's reference MNI152. I know that freesurfer uses talairach reference. Is it true? May it be the problem? How can I superimpose properly the images? Do you know any workaround? Thank you very much. Regards Martina Andellini

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Asymmetries of cortical thickness
by Sophie Maingault 18 Mar '13

18 Mar '13

Hello, I obtained a map of cortical thickness asymmetries after the registration on the symmetric atlas. But I would to obtain the same map with raw data I mean just by subtract lh.thickness and rh.thickness. How can I modify the part #Create a stack of subjects in wiki page ? I have to register to fsaverage (and not fsaverage_sym) and then do the same thing ? Thanks you for your help. Sophie

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Rejoindre mon réseau sur LinkedIn
by Huiguang He via LinkedIn 18 Mar '13

18 Mar '13

LinkedIn ------------ Huiguang He 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 Huiguang He http://www.linkedin.com/e/-qq80um-hefdm1bo-3s/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir le profil de Huiguang He http://www.linkedin.com/e/-qq80um-hefdm1bo-3s/rso/72703165/ArO9/name/664711… ------------------------------------------ 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-hefdm1bo-3s/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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ASeg Stats and Cortical Ribbon Mask in autorecon2?
by Hiroki Kurashige 17 Mar '13

17 Mar '13

Dear freesurferers, I have two questions about the recon-all with -autorecon2 option. First one is about ASeg Stats (mri_segstats). In the following status log, I found that ASeg Stats step was executed as a final step of -autorecon2: status file for recon-all Sat Mar 16 21:50:42 JST 2013 #@# EM Registration Sat Mar 16 21:50:42 JST 2013 #@# CA Normalize Sat Mar 16 22:13:19 JST 2013 #@# CA Reg Sat Mar 16 22:15:14 JST 2013 #@# CA Reg Inv Sun Mar 17 01:57:37 JST 2013 #@# Remove Neck Sun Mar 17 01:58:47 JST 2013 #@# SkullLTA Sun Mar 17 02:00:06 JST 2013 #@# SubCort Seg Sun Mar 17 02:23:38 JST 2013 #@# Merge ASeg Sun Mar 17 02:50:50 JST 2013 #@# Intensity Normalization2 Sun Mar 17 02:50:50 JST 2013 #@# Mask BFS Sun Mar 17 02:54:56 JST 2013 #@# WM Segmentation Sun Mar 17 02:54:58 JST 2013 #@# Fill Sun Mar 17 02:57:59 JST 2013 #@# Tessellate lh Sun Mar 17 02:58:54 JST 2013 #@# Smooth1 lh Sun Mar 17 02:59:01 JST 2013 #@# Inflation1 lh Sun Mar 17 02:59:04 JST 2013 #@# QSphere lh Sun Mar 17 02:59:28 JST 2013 #@# Fix Topology lh Sun Mar 17 03:02:37 JST 2013 #@# Make White Surf lh Sun Mar 17 03:23:10 JST 2013 #@# Smooth2 lh Sun Mar 17 03:33:13 JST 2013 #@# Inflation2 lh Sun Mar 17 03:33:17 JST 2013 #@# Curvature Stats lh Sun Mar 17 03:35:12 JST 2013 #@# Tessellate rh Sun Mar 17 03:35:17 JST 2013 #@# Smooth1 rh Sun Mar 17 03:35:23 JST 2013 #@# Inflation1 rh Sun Mar 17 03:35:26 JST 2013 #@# QSphere rh Sun Mar 17 03:35:50 JST 2013 #@# Fix Topology rh Sun Mar 17 03:39:04 JST 2013 #@# Make White Surf rh Sun Mar 17 03:56:40 JST 2013 #@# Smooth2 rh Sun Mar 17 04:06:43 JST 2013 #@# Inflation2 rh Sun Mar 17 04:06:46 JST 2013 #@# Curvature Stats rh Sun Mar 17 04:08:41 JST 2013 #@# ASeg Stats Sun Mar 17 04:08:46 JST 2013 recon-all -s bert finished without error at Sun Mar 17 04:11:54 JST 2013 According to the help document for recon-all, ASeg Stats should run in the -autorecon3 step, not in -autorecon2. Is this some kind of bug? http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1?action=pri… Second questions is about Cortical Ribbon Mask. At the Manual-Intervention Workflow Directives in recon-all help, Cortical Ribbon Mask is classified into the part of -autorecon3. However, the Step Description Summaries says that the -autorecon2 stage ends at the Cortical Ribbon Mask. Which one is right? http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all Thanks, Hiroki

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Coordinates of center of gravity of a cluster in Freesurfer
by Maleki, Nasim 16 Mar '13

16 Mar '13

Hi all, I would like to calculate the coordinates of center of gravity of a cluster in Freesurfer. Is there a way to do this in Freesurfer? Thanks, Nasim

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Use a dfs file for measurements
by Valtina Pouegue 16 Mar '13

16 Mar '13

Hi Freesurfers, I,ve done a segmentation with Brainsuite and as result I have dfs file for Pial surfaxe L/R hemisphere. I would like to do some measurement with mris_anatomical_stats of Freesurfers. But this fonction of FreeSurfer only accept surface of extension like ( .pial). How can I do this conversion ? Thanks . VP

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Re: [Freesurfer] Caret to Freesurfer
by Nick Schmansky 15 Mar '13

15 Mar '13

Kara, the gifti format is used to convert between caret and freesurfer surfaces. use mris_convert (see --help). Nick > Matt, > > Yes, I think the plan is to discuss this and other potential options. I > had a feeling you may know the most, but I thought I would send out the > question in case anyone else has tried. As it stands, it sounds like no > method currently exists for a Caret surface-to-Freesurfer transition? > > I am still trying to understand Freesurfer basics, but it sounds like the > longitudinal pipeline generally requires the same input data as > across-subject. My hope is that, since the surfaces are already > constructed, I can avoid the need for an (infant) atlas, but I am still > figuring out what that means in terms of files I need/conversion/etc. > > Thanks for your help, and I look forward to further discussion this > afternoon. > > Kara > > > ________________________________________ > From: Matt Glasser [matt(a)ma-tea.com] > Sent: Thursday, March 14, 2013 7:14 PM > To: Bruce Fischl; Ellspermann, Kara > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Caret to Freesurfer > > She wants to go from Caret to FreeSurfer, rather than from FreeSurfer to > Caret, which is what I do. > > Kara, I believe we are meeting tomorrow to discuss the options for this? > > I don't know anything about the FreeSurfer longitudinal pipeline, but it > would take going through the pipeline and finding all of the inputs needed > and converting them or generating them. I think the main goal here is to > use the longitudinal surface registration. > > Matt. > > On 3/14/13 8:04 PM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >>Hi Kara >> >>I think the answer is yes as there are people at Wash U that do this >>routinely. Maybe Matt Glasser or someone else can chime in? >> >>cheers >>Bruce >> >> >>On Thu, 14 Mar 2013, Ellspermann, Kara wrote: >> >>> I am new to Freesurfer, and I am trying to input/process preterm infant >>> brain data (ultimately attempting longitudinal registration). I already >>>have >>> surfaces generated from Caret, as well as the original T1/T2 images. >>> My >>> question is: Does anything exist to take processed data from Caret into >>> Freesurfer? If not, is there a good way to process the T1/T2 images in >>> Freesurfer despite the differences in contrast and intensity (and >>>anatomy)? >>> >>> Thank you in advance for your advice, >>> Kara >>> >>>_______________________________________________ >>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. > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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