Freesurfer April 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
229 discussions

Easy automated workflow for separating non-contiguous labels
by Michael Waskom 10 Apr '14

10 Apr '14

Hi Freesurfers, Some of the Freesurfer annotations (specifically the Yeo atlases) have multiple disconnected regions with the same label. What's the best way to separate these annotations (or the labels produced by mri_annotation2label) so that I can get multiple label files where each label has all contiguous vertices? In other words, I want to do something like a clustering procedure, and I'd like to stay on the surface. Can this be done (easily)? Thanks Michael

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caudate and putamen to surface
by gong jinnan 10 Apr '14

10 Apr '14

Dear all, I want to use caudate and putamen as seed in surface to do PROBTRACK in FSL. For doing that, I acquired target surface which in the cortex seed using kris_convert and label2surf script. But I met some problems in extracting caudate and putamen in the surface. At first I used "mdi_extract_label sub1/mri/aseg.auto.noCCseg.mgz 11 /test/L_Caudate.mgz” and it generated L_Caudate.mgz correctly. And then in order to do mri_vol2surf I did bbregister used “bbregister —s sub1 —mov sub1/mri/brain —init-fsl —reg sub1/mri/register.dat”. Then “mdi_vol2surf —src /test/L_Caudate.mgz —srcreg sub1/mri/register.dat —promfrac 0.5 —hemi lh —out /test/L_Caudate2surf.mgz”. Everything looked like went well by the time. But it’s weird when “mri_binarize —i /test/L_Caudate2surf.mgz —min 0.5 —o /test/L_Caudate2surf_bin.mgz” , it showed “Dound 0 values in range” and “Found 0 voxels in final mask”. I checked /test/L_Caudate.mgz and found it was correct. I am wondering is that because of register.dat which I am not very clear how to acquire it correctly? Or is that because lh.white was default used in mri_vol2surf? Could you give me any advises to work around this program? And may be about how to acquire register.dat in this context and how to transform this kind of ROI to surface. Thanks a lot! Sincerely, Jinnan

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mris_divide_parcellation same divisions between subjects
by Corinna Bauer 10 Apr '14

10 Apr '14

Hello all, I am planning to use mris_divide_parcellation to split the Desikan atlas into smaller ROIs, but will need the new ROIs to be consistent between subjects. Can I achieve this if I register each subject to fsaverage space and then apply the inverse transform to the divided parcellations (which are currently done on the fsaverage brain)? If so, for extracting each label, what would be used for the label number? (i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*${subj_dir}/hardi_labels/ctx-rh-insula.nii) Thanks Corinna

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basic high res data question
by Torrisi, Sam (NIH/NIMH) [F] 10 Apr '14

10 Apr '14

Good afternoon gurus- I’m new to FS and working with 0.7mm iso 7T MPRAGEs. After bias-correction with AFNI’s 3dUnifize, recon-all ran without hitch but downsampled everything to 1mm. Now I have basically the same sentiment and question as this thread from ~2 years ago (i’m linking to the middle for simplicity): http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg22852.html What’s the very latest on this? Thanks! -Salvatore (Sam) Torrisi Section on the Neurobiology of Fear and Anxiety National Institute of Mental Health

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how to convert fsaverage space mask into other subject original space
by Rujing Zha 10 Apr '14

10 Apr '14

Hi FS experts and others, I try to check my group analysis result by seeing the subjects' original space corresponding area. So I need to know how to convert my mask from fsaverage space into specific subject's space. Thanks All the best. RujingZha

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Re: [Freesurfer] Intermediate stages of cortical inflation
by Xuelong Zhao 10 Apr '14

10 Apr '14

Is it also possible to track the inflation all the way to the sphere? I was hoping that I could take snapshots of equi-area intermediate forms as the cortex is unfolded onto the sphere instead of stopping at the inflated cortex. Thanks. > Date: Wed, 9 Apr 2014 08:31:46 -0400 > From: fischl(a)nmr.mgh.harvard.edu > To: freesurfer(a)nmr.mgh.harvard.edu > CC: greve(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Intermediate stages of cortical inflation > > you can use -w 1 to write out every step in the inflation process and > choose what you want. If you want it to preserve surface area during > inflation (as opposed to just at the end), also include -scale 1 > > cheers > Bruce > > > On Wed, 9 Apr 2014, Xuelong Zhao wrote: > > > Hi, > > > > I would like to ask whether it is possible to display different levels of > > cortical inflation? > > > > I have been using the command: mris_inflate > > > > but the -dist and -n flags do not seem to make that much difference. Also, > > if I use fsaverage lh.orig as the input file and using the default options > > for mris_Inflate I don't seem to be able to recover the lh.inflated surface. > > > > Are there any alternative commands to control the level of inflation? > > Thanks. > > > > > > > > > _______________________________________________ > 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. >

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Mac OSX installations incomplete? What to do?
by Markus Gschwind 10 Apr '14

10 Apr '14

Dear Freesurfers, As discovered here, http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35160.html it seams that some Mac OSX installations suffered from incomplete files. I just veryfied that I had downloaded the complete image and wget says yes: Logging in as anonymous ... Logged in! > ==> SYST ... done. ==> PWD ... done. > ==> TYPE I ... done. ==> CWD (1) /pub/dist/freesurfer/5.3.0 ... done. > ==> SIZE freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg ... > 3394499614 > File has already been retrieved. > 2014-04-04 18:24:26 (0.00 B/s) - > 'freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg' saved > [3394499614] So this is what I installed recently and it seems that there are some files missing (at least some of the fsl-functions in bin). Doug, you said that you suspected that it could be a problem of the installer script? What should we do (also Eiran) in order to complete the installation? Thanks for you work! Markus

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Advanced Clinical Neuroimaging Course, Brussels, May 30-31, 2014
by Laurent Hermoye 10 Apr '14

10 Apr '14

Advanced Clinical Neuroimaging Course, Brussels, May 30-31, 2014 <http://www.imagilys.com/advanced-clinical-neuroimaging-course-2014/>

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Re: [Freesurfer] fsaverage mesh has duplicate pt
by Xuelong Zhao 10 Apr '14

10 Apr '14

Hi, I loaded the lh.orig cortex for fsaverage into Matlab. My colleague and I found that it actually has a duplicate point. The index of the duplicate points are: 1 40970 I checked that both have the same vertices coordinates: -36.7233 -18.4039 64.3611 I'm not sure if this is intentional or not but wanted to draw the freesurfer community's attention to this in case it is a bug. Also, I believe a similar issue is present for fsaverage's lh.pial and rh.orig (I haven't checked other cortices). Regards, AZ

2 1

Freeview, fsaverage_sym & aparc.annot
by Peggy Skelly 09 Apr '14

09 Apr '14

Hi Freesurfer experts, I'm trying to view aparc.annot on a fsaverage_sym surface. I can load aparc.a2009a.annot with freeview -f $SUBJECTS_DIR/fsaverage_sym/surf/lh.pial:annot=aparc.a2009s.annot but attempting freeview -f $SUBJECTS_DIR/fsaverage_sym/surf/lh.pial:annot=aparc.annot results in freeview crashing. The command window output is in the attached text file. (Freeview 1.0 May 14, 2013; Mac OS 10.9.2) Thanks, Peggy

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Freesurfer April 2014