Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

Neuroimaging RA position available at VA Boston
by Huiting Liu 18 Mar '13

18 Mar '13

The Memory and Neuroimaging lab (PI: Scott M. Hayes; http://www.bu.edu/brainlab/) integrated with the Memory Disorders Research Center and Neuroimaging Research Center at VA Boston Healthcare System, is currently accepting applications for a full-time neuroimaging research assistant to begin in the summer of 2013. Primary duties will include the collection, processing, and analysis of structural and functional MRI data in older adults and patients with memory impairment. The research will focus on the examination of the neural correlates of memory, as well as the relationship between physical fitness and age-related cognitive and neural decline. Applicants should have a BA or BS in neuroscience, psychology, or computer science and familiarity with Unix/Linux, Matlab, FSL or FreeSurfer. Interested applicants should send a cover letter, CV (including references), course transcripts, and a writing sample (thesis or term paper) as a single PDF to neurolab(a)bu.edu.

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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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Freesurfer March 2013