Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30099 discussions

wm and pial edits - what to correct and what not?
by Markus Gschwind 07 Apr '14

07 Apr '14

Dear all, I would like to show some very frequent and typical cases of segmentation problems in my bunch of data of normal subjects (after recon-all), of which I couldn't find a description in the wiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithD… ). I am therefore not sure if these types of error are serious and will affect later results like thickness, curvature, GWR, etc. Here are the examples (c.f. attached screenshots from Freeview) 1) In the primary sensory-motor cortex it frequently happens that the "?h.white" line lies several mm within the wm border (c.f. yellow arrow), I did not observe this behavior in other places. >>Would I need to edit that? 2) Sometimes the "?h.pial" line includes also dura or parts of the skull (green arrow). >>Is it necessary to edit that as well? 3) Another question concerns the yellow parts of the wm which sometimes are much larger than the ventricles and also include both caudate nuclei (not shown). >>Is this a problem? Thanks in advance!! Markus

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by Caspar M. Schwiedrzik 06 Apr '14

06 Apr '14

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Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters
by Douglas N Greve 04 Apr '14

04 Apr '14

Can you upload the y.mgh file and fsgd file so that I can try to replicate it? What platform are you running on and what version of FS? doug On 04/02/2014 06:34 PM, Tudor Popescu wrote: > Hi Doug > Sorry, again I wasn't sure whether you'd noticed my reply amonst the > latest list messages. Hopefully there is a fix for this error. > Thanks > Tudor > > > On 2 April 2014 12:33, Tudor Popescu <tudor3(a)gmail.com > <mailto:tudor3@gmail.com>> wrote: > > > > Your mri_glmfit-sim command line is not correct and > does not match > examples in the help. Basically you need to spec > "--cache 1.3 abs" > not "--cache 1.3 --sim-sign abs" > > Thanks Doug, now it worked, however I'm getting this > error, which several other people seem to get: "Computing > spatial average of each frame > 0 1 2*** glibc detected *** mri_segstats: malloc(): > memory corruption: 0x2e8df328 ***". I am running FS 5.3.0 > through VirtualBox, 2GB ram allocated. > > What is your full command line? Sometimes this happens when > setting the cwp to 1 (or close to 1). > > > My command was > mri_glmfit-sim --glmdir > /media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh --cache 1.3 abs > therefore I did not change the --cwpvalthresh input argument, > meaning cwp presumably stayed at its default of .05. > Terminal output is attached. > What else can I try to make this command work? > > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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TRACULA longitudinal stream - length of Center variable
by Vincent Brunsch 04 Apr '14

04 Apr '14

Dear TRACULA experts, I have used the longitudinal version and find that for some subjects' tracts Len_Min is larger than Len_Center. How is this possible? (An extreme example is Len_Min: 36, Len_Max: 75, Len_Center: 4.) Best, Vincent --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com

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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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