Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Displaying parcellated ROI in color but remainder of brain in grey
by Laura Taylor 04 Apr '14

04 Apr '14

Hello, I have run mri_annotation2label and then selected the labels corresponding to my ROI, creating a new annotation file using mris_label2annot. When I load my new annotation file in freeview, the ROI's are displayed nicely in different colors. However the remainder of the brain is dark black and therefore difficult to see. I have tried to change the default color of the remainder of the brain to grey by editing the aparc.annot.a2009s.ctab file for my subject so that my ROI keep the colors originally assigned to them, but all other regions are changed to: 127 127 127 0 (grey). When I do this, my ROI's all become grey and the remainder of the brain stays as dark black. Can you direct me as to which file(s) I need to edit to keep my ROI's in color but change the remainder of the brain to a different color (grey). Thank you very much, Laura

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Converting a volume from MNI152 to subject space
by Omar Singleton 04 Apr '14

04 Apr '14

Hi Freesurfers, I am trying to convert a volume from MNI152 to subject space. I tried to do what this previous question suggested: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-December/034722… I tried to create a registration matrix from subject space to MNI152: mni152reg --s AL15 However, this error appeared: ... mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.28345': Permission denied ... writing to /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.28345/refvol.fslregister.nii... ERROR: failure writing /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.28345/refvol.fslregister.nii I would then have used this command: mri_label2vol --seg lh.AItou.nii.gz --reg AL15/mri/transforms/reg.mni152.2mm.dat --invertmtx --o lh.aitou.AL15.nii.gz --temp AL15/mri/orig.mgz How can I make the mni152reg command work? Is this the correct way to do this? Thanks! Best, Omar

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Display tkmedit image of surface after mri_vol2surf with projfrac or projdist
by Righart, Ruthger 04 Apr '14

04 Apr '14

Hi All, mri_vol2surf has the flags --projfrac and --projdist. If I understand these flags correctly, the volume is sampled inbetween the white-matter surface and the pial surface (for ex. --projfrac 0.5 is midway). Is there a possibility in tkmedit/Freeview to display with a colored line for ex. --projfrac 0.5 for a given subject? (actually similar to what was done by Salat et al., NeuroImage 2009, 48, p23, fig 1A, http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf) Thank you very much in advance for your help! All the best, Ruthger

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CWP values
by Francesco Puccettone 04 Apr '14

04 Apr '14

Hello, I see that after having qdec apply MonteCarlo correction to a certain contrast, the CWP cluster-wise probability is displayed. Those values, however, are not displayed when the "Find clusters and go to max" button is used, either before or after correction. WHy is that, when it seems that the CWP statistic makes sense for all 3 "stages" (max-vertex pre-correction, mean-cluster post-correction, max-vertex post-correction)? Thank you! --Francesco

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Re: [Freesurfer] FW: registration difficulty
by Erik O'Hanlon 04 Apr '14

04 Apr '14

Apologies. forwarded it on now Thanks a million Erik Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon(a)rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: 02 April 2014 19:58 To: Erik O'Hanlon Subject: Re: [Freesurfer] FW: registration difficulty Hi Erik can you cc the list so that others (like Doug!) can respond? thanks Bruce On Wed, 2 Apr 2014, Erik O'Hanlon wrote: > > Hi Bruce, > > Thanks so much for your reply. As for the specifics of what I have tried, so > rry if it was unclear. > > I have performed the usual T1 based FS cortical and subcortical analysis and > included the -hip_subfields so I also get all the subdivision volumes. I ha > ve also run a DWI analysis in ExploreDTI and now want to use the subfield vo > lumes as masks for the purpose of tractography. I created my diff-to-orig da > t file using bbregister. I then used this in the mri_vol2vol and aligned my > aseg.mgz to my nodif image. This worked really well and I then used fslmaths > to extract out the hippocampus from the aseg2diff. This aligns nicely. I th > en tried to apply the same transformation to my subfield volumes but this di > dn't work. As you suggested, and just to clarify, > > should I now rerun the bbregsiter and create a new dat file for the subfield > volume to orig.mgz image? Do I then use this in the mri_vol2vol and align m > y subfield volume to the orig.mgz and then run a second mri_vol2vol but use > the nodif2orig.dat calculated before and use the nodif image as the --mov fi > le and the registered subfield_2orig.nii as the --targ and use the --inv -- > nearest settings as I want end up with my subfield volumes in diffusion spac > e ? > > So sorry for the confusion, really shows my lack of experience with FS. Just > getting completely mixed up at this stage. > > Again apologies for the lack of clarity and confusion but any pointers offer > ed would be fantastic. > > Thanks again > > best regards > > Erik > > __________________________________________________________________ > > Hi Erik > > so you had a separate (presumably highres) acquisition within the > hippocampus? Have you registered that with bbregister? Your best bet is > probably doing so, then composing the two registrations (and inverting one, > depending on what direction you want to go). > > cheers > Bruce > > > > On Wed, 2 Apr 2014, Erik O'Hanlon wrote: > > > > > > > Dear FS experts, > > > > I am running my first FS analysis and I'm trying to register my hippocampa > l > > subdivision volumes to my diffusion space image but cannot get good > > alignment. I ran my diffusion preprocessing in ExploreDTI so don't have th > e > > register.dat file automatically so created this using the bbregister tool > and > > registered B0 image to my orig.mgz. I then used this dat to align my aseg > to > > my diffusion space image and it worked well. The issue is when I try to us > e > > it to transform my hippocampal subfield volumes to diffusion space. They j > ust > > don't line up. Is this due to the different FOV for the subfields? Can any > one > > advise how to get these volumes to transform correctly? > > > > Any help would be greatly appreciated. > > > > Thanks > > > > Erik > > Dr. Erik O'Hanlon PhD MSc BScEng > Post Doctoral Researcher > > [IMAGE] > > RCSI Psychiatry > Royal College of Surgeons in Ireland > Beaumont Road, Beaumont, D9, Ireland > T: 8093740 > E: erikohanlon(a)rcsi.ie W: www.rcsi.ie > > RCSI DEVELOPING HEALTHCARE LEADERS > WHO MAKE A DIFFERENCE WORLDWIDE > > > > 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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tracula and libnetcdf
by Satrajit Ghosh 04 Apr '14

04 Apr '14

hi a.y., when running trac-preproc i'm getting this error (for dmri_motion and dmri_group), but it continues running: /software/freesurfer/bin/dmri_motion: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory what will this fail to do? also is libnetcdf now a dependency for freesurfer? the reason i ask is that i'm running this on a remote cluster for which i don't have admin privileges. cheers, satra

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Postdoctoral Fellowship in Aging Research
by Anqi Qiu 04 Apr '14

04 Apr '14

Job description: National University of Singapore (NUS) is a leading global university centre in Asia. It offers a global approach to education and research, with a focus on Asian perspectives and expertise. Computation functional anatomy laboratory at NUS (http://www.bioeng.nus.edu.sg/cfa) focuses on brain and cognition studies using neuroimaging techniques. Our group is leading a large-scale aging neuroimaging project from birth in Singapore. The project examines neurocognition, high angular resolution diffusion imaging (HARDI), resting-state fMRI, and structural MRI. We are looking for a research fellow who is interested in multi-modal MRI studies in aging, especially, who is interested in understanding aging processes of anatomical and functional connectivity and their relations with cognition as well as genetic regulation on aging brain processes. We offer high salary with medical and other benefits. Requirements: Ph. D or MD Research background on infant brain is preferable but necessary Knowledge in statistical analysis is necessary Good communication and writing skills in English language If you are interested in the jobs listed above, please send your CV to Associate Prof. Anqi QIU Department of Biomedical Engineering National University of Singapore Email: bieqa(a)nus.edu.sg Phone: +(65) 6516 7002

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question about how to calculate COV for MNE
by Joseph Dien 04 Apr '14

04 Apr '14

Hi, I have a question about how to calculate the COV for the MNE software. As I understand it from Section 4.17 of the 2.7.3 MNE manual, if one is averaging together COV matrices, one weights them by the number of observations going into each one. I also see from Section 4.17.2 that these are technically not covariance matrices so much as sum-of-squares matrices where the epochs going into each variable has been baseline corrected. Assuming my understanding so far is correct, my question is about how to proceed when making linear combinations of COV matrices, as in a difference wave, as discussed in Section 6.3. Would the following be the correct procedure? Compute the COV separately for the two conditions (say standard and rare oddballs). Subtract the two COV matrices to obtain C0. Then calculate C by dividing by Leff, which in turn is calculated as Leff= (L1*L2)/(L1+L2) where L1 is the number of observations in the first COV matrix and L2 is for the second. But if done in this way, the two COV matrices would not be weighted by their relative sample sizes. So would I also weight them by L1 and L2 during the subtraction, as done for averaging per 4.17? But then what is the purpose of the Leff calculation? Or is the idea that one would calculate a single COV based on both conditions and then one would modify COV by Leff to reflect that the signal-to-noise ratio has been reduced by combining two averages with differing sample sizes? But in the case where both samples equal, say, 10, Leff would end up equalling 100/20=5. Dividing C by 5 seems like too much. Anyway, very confused. Any guidance would be appreciated. Respectfully, Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist Maryland Neuroimaging Center University of Maryland E-mail: jdien07(a)mac.com Phone: 202-297-8117 http://joedien.com

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Re: [Freesurfer] Standard surface tessellation
by Chris McNorgan 04 Apr '14

04 Apr '14

Hi Justin, This is quite similar to a question I had asked previously: https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33421.html I believe the solution is to generate a 14000 vertex template, and then appy mri_surf2surf to all 10 subjects, which will map the vertices of all 10 subjects to your template. The 10 transformed surfaces should then correspond with one another. Chris Subject: [Freesurfer] Standard surface tessellation From: jeongwon(a)pet.wayne.edu Date: 14-04-03 03:47 PM To: freesurfer(a)nmr.mgh.harvard.edu Dear FreeSurfer, I am a beginner in FreeSurfer and wonder if it is possible in FreeSurfer to apply the same triangulation across multiple subjects, i.e. the same number of vertices and triangles at the anatomically identical locations. For instance, I have 10 subjects and want to have pial (or white matter) surfaces of individual subjects consisting of 14000 vertices which are anatomically matched. Any suggestion will be greatly appreciated. Justin.

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Subcortical segmentation for PAG
by Jeni Chen 03 Apr '14

03 Apr '14

Hi, Just wondering if the periaqueductal gray is part of the automatic segmentation process and if we can obtain the volume. I checked the aseg table but didn't see it, however, I somehow remember seeing it before... Was it ever included? Thanks. Jeni

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