Freesurfer

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30070 discussions

ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data
by Greg Harris 18 Mar '06

18 Mar '06

Dear Karl, Has anybody had any success with the midline rois given by the atlas curvature.buckner40.filled.desikan_killiany that is automatically applied by autorecon3 under the newest stable release, version 3.0? Our trouble lies in the regions labeled corpuscallosum and <anything>cingulate: this atlas is giving us a corpus callosum that is exactly the ventral cingulate sulcus, and the 4 cingulate gyrus segments, which is what we are interested in in this case, incorrectly exclude their ventral portion. I presume this has been made to work at mgh, because Rahul Desikan's paper contains an illustration that is anatomically correctly labeled for these regions. We are providing an orig/001.mgz image to the autorecon1 step that is talairach aligned, skull stripped, and resampled to 1.0 mm voxels, but otherwise is a signed 16-bit T1-weighted MRI scan. We have thousands of them, collected over the past 15 years. We are writing a nifti .nii file, and converting it with mri_convert -it nii -ic 128 128 96 -oc 128 128 96 -iid -1.0 0.0 0.0 /raid1/structural/MR/9517294/0036195/10_ACPC/0036195_10_T1_brain.nii /raid1/data/methods/atlas/parcel/lobes/cloud_study/clipped_atlas_hand_masks/iowa_cortex_atlas/FreeSurfer_Subjects/IowaFifty_2005_0036195/mri/orig/001.mgz We actually mean to numerically measure the extent -- the area and thickness, say -- of anatomical regions of interest including <anything>cingulate and apply statistical tests to these data. A line of guff about Type I and Type II errors and what is only presumable when identifying anatomical rois would be of no interest, and considered needlessly defensive. After all, the other 29 regions of Desikan's really great atlas are in working order! Do we need to convince Rahul Desikan to release the "correct" *h.curvature.buckner40.filled.desikan_killiany.gcs files with FreeSurfer 3.0 that correspond to his paper? Greg Harris The University of Iowa College of Medicine Psychiatry NeuroImaging Lab

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paint binary
by Nahab, Fatta (NIH/NINDS) [E] 17 Mar '06

17 Mar '06

I just installed the new stable release on OSX. Installation ran smoothly and I made the changes in .cshrc. On starting freesurfer ('csurf'), I receive the following error: These binaries used by csurf not found in /Applications/freesurfer/bin: paint This binary is not in the directory (it was on my prior install which is in a different directory) and freesurfer doesn't seem to be running anything after I click 'ok' on the dialog box. Thanks for your help, Fatta

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RE: [Freesurfer] New average subject and stable release, v3.0
by Goldman, Aaron (NIH/NIMH) [C] 16 Mar '06

16 Mar '06

Hi, Is the fsaverage folder used when I run recon-all -all? Thanks, -Aaron- -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, March 06, 2006 6:13 PM To: martinos-tech(a)yahoogroups.com; Freesurfer Mailing List Subject: [Freesurfer] New average subject and stable release, v3.0 Sorry in advance for the long email ... We have a new average subject that we are recommending that people use instead of "average7". This subject can also replace the "talairach" subject as well. The name of the "fsaverage", and it can be found in the distribution itself: $FREESURFER_HOME/subjects/fsaverage To set up a link in your SUBJECTS_DIR, do the following: cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage fsaverage There is a README file in $FREESURFER_HOME/subjects/fsaverage that describes how this subject was created. IMPORTANT: Differences between average7 and fsaverage, and FIX_VERTEX_AREA with impacts on mri_surfcluster and mri_glmfit. As some people have noted, the total surface area of average7 was much less than that of a typical subject (by about 40%). This caused the areas of clusters as reported by mri_surfcluster to be too small. HOWEVER, a bug in the routine that computed the vertex area caused the clusters to be 50% too large. So, the net effect was that the clusters were about the right size :). Stay with me. The surface area of the new average subject (fsaverage) is that of a typical subject, SO, it is IMPORTANT that it be used in conjunction with the fixed vertex area. This affects only two programs: mri_surfcluster and mri_glmfit. After today (March 6, 2006), if you use average7 with mri_surfcluster or mri_glmfit, they will give the following error: ERROR: you have selected subject average7. It is recommended that you use the fsaverage subject in $FREESURFER_HOME/subjects. If you really want to use average7, re-run this program with --really-use-average7 as the first argument. If you chose to do so, then it will print out: INFO: you have selected subject average7 (and REALLY want to use it) instead of fsaverage. So I'm going to turn off fixing of vertex area to maintain compatibility with the pre-stable3 release. The results should be the same as when you ran it prior to the stable3 release. If you have used average7 along with Monte Carlo or Permutation simulation, inferences based on those simulations should still be correct. The only problem will be that the cluster area might be a little different. If you have used a non-average subject as your common surface space or an average subject that you created prior to March 1, 2006, then the cluster sizes will appear to drop by a third the next time your run mri_glmfit or mri_surfcluster. Again, any mri_glmfit simulation results will still be valid. For backwards compatibility, you can add --no-fix-vertex area to either mri_surfcluster or mri_glmfit. The new versions of mri_surfcluster or mri_glmfit will include the following line in their summary/logfile output: # FixVertexAreaFlag 1 The value will either be 1 or 0 depending upon whether it was fixed or not fixed. Again, sorry for the long-winded email. I know this is pretty confusing, so don't hesitate to write with questions as we get this sorted out. PLEASE send questions to the group to help in this process. thanks doug Nick Schmansky wrote: >Freesurfer community, > >A new stable release, v3.0, is now available. >The Release Notes page describing what's new, >and a link to the download page, is here: > >http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes > >All users, including those using prior 'dev' >releases, are encouraged to upgrade to this >release. > >Updates to the stable release will be issued >if major bugs are found (and fixed), and as >new features which do not affect existing >functionality become available. > >The Freesurfer development team > > >_______________________________________________ >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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Translate label file from average subject to all subjects
by Jonathan Wisco 16 Mar '06

16 Mar '06

Hi, I would like to translate a label created from an average subject inflated surface to all the subjects. How would I do that? Should I first use mri_surf2surf to resample the average subject inflated surface to all the other subjects? Would a label that was created on the average subject then automatically be translatable to the subjects? Thanks, Jon -- Jonathan J. Wisco, Ph.D. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Building 149, 13th St. Charlestown, MA 02129 E-mail: jjwisco(a)nmr.mgh.harvard.edu Tel: 617-851-8492 Fax: 617-726-7422

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Freesurfer & SuSE Linux
by Venkat subramanian 16 Mar '06

16 Mar '06

Dear Freesurfer Experts, Could youplease clarify whether the new freesurfer stable release version 3 is compatible with SuSE Linux 10.0 (kernel 2.6.13)? Many thanks, Venkat. Dr. Venkatasubramanian, Asst. Professor of Psychiatry, National Institute of Mental Health & Neurosciences, Bangalore, India. --------------------------------- Yahoo! Travel Find great deals to the top 10 hottest destinations!

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RE: [Freesurfer] cortical labels
by Kevin Teich 16 Mar '06

16 Mar '06

> but I would still like to know if there is anyway to build an mgz > image of the grey volume segmented accordingly to ?h.aparc.annot. I > hope you can help me. In tksurfer, you can import an annotation as a segmentation file. This will fill the voxels between surfaces with the label in the annotation file. Then you can save this segmentation as a new volume. -- Kevin Teich

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Testing FreeSurfer installation error
by Chunchun Ni 15 Mar '06

15 Mar '06

I installed the freesurfer following exactly as the instructions on the website. When I test it, "recon-all -s bert -all" doesn't work, it runs for a few min. and shows "flirt: Command not found. ERROR: running flirt". When I try to use my own data, convert dicom to mgt, "mri_convert" command shows "can't find dicom". What's the problem with the installation? Any help? Thanks Chunchun

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Autorecon1
by Martin Ystad 15 Mar '06

15 Mar '06

Hi, I have processed some of my subjects on a previously released dev-version (20060210). I have changed to the new stable release. Do I need to run the -autorecon1 step again, or will -autorecon2 and -3 suffice to bring the previously run subjects up to date? (the brainmask-volumes have been edited, so I'd like to keep these changes) Another question; if I run the -autorecon2-wm flag, will I save a lot of computing time if I manually remove the Optic Nerve before doing so? Thanks, Martin Ystad University of Bergen, Norway.

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cortical labels
by Pellegrini, Stefano (NIH/NINDS) [F] 15 Mar '06

15 Mar '06

Hi everybody, I have seen that the aseg.mgz file allows to see the segmentation of the whole brain volume in different areas. Is there any way to obtain an mgz file with the cortical gray matter volume labeled in such a way that every cortical region has a different intensity value? thanks, -stefano

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Re: surfcluster gives very different results run two ways on the same file
by Doug Greve 14 Mar '06

14 Mar '06

Frida has helped find another bug (thanks Frida!). When running mri_surfcluster with average7 inside your csd file, make sure to specify --subject average7 --really-use-average7 or else it will underestimate the clustersize and cause the significances to be too low. I'll mod the code when I get back from CA. doug On Tue, 14 Mar 2006, Frida Polli wrote: > yes, that indeed fixes it - you might want to put some of this stuff in the > documentation or send out an email or something b/c i spent two weeks running > another analysis b/c i thought my clusters weren't meeting significance, and > only discovered this discrepancy when i did a regular mri_surfcluster :). so > i can imagine since many people are still using average7, this would be > really importnat for them to know. i am cc'ing nurit from moshe;s lab, as i > know she's been using it - there are probably others. that having been said, > thanks for the tool - its great. > thanks, frida > On Monday, March 13, 2006, at 04:44 PM, Doug Greve wrote: > >> >> >> Oh, I know what happened. It only fixes the vertex area when you pass >> average7 in explicitly. When you use a csd, it get's the subject name >> from the csd. The ratio of the areas is 1.5. I think it will work if >> you specify --subject average7 with the csd (and >> --really-use-average7). Can you try that and let me know? >> >> doug >> >> >> On Mon, 13 Mar 2006, Frida Polli wrote: >> >>> hi doug >>> i am very confused. i used mri_surfcluster on one file in two different >>> ways, and for one cluster, got two different sizes for all the clusters >>> (see example of one cluster below). the first way is just the standard >>> way, the second way is using csd files and having it output CWPs. >>> >>> for one cluster, the first way gave me the following result: >>> 4 3.230 71230 1065.25 8.0 12.9 25.4 1788 >>> >>> the second way gave me the following result: >>> 4 3.230 71230 710.17 8.0 12.9 25.4 0.36277 >>> 0.35092 0.37500 1788 >>> >>> as you can see, this is the same cluster, but with two wildly discrepant >>> values for surface area. what is going on, and which is correct? >>> >>> the first way, i ran: >>> mri_surfcluster --really-use-average7 --src >>> BG3b_glmfit/rh.ASevASc_6s_BwGroup3b.fsfast.glmdir/ >>> BwGroupError3b_NvSZ_contrast/sig.mgh --hemi rh --srcsubj average7 --thmin >>> 1.3 --minarea 100 --sum rh.BG3_6s.sum >>> >>> the second way i ran: >>> mri_surfcluster --src >>> BG3b_glmfit/rh.ASevASc_6s_BwGroup3b.fsfast.glmdir/ >>> BwGroupError3b_NvSZ_contrast/sig.mgh --csd >>> csdfiles/BG3b_ASevASc_6s_rh_MCSIMz-BwGroupError3b_NvSZ_contrast.csd --sum >>> BG3b_glmfit/rh.ASevASc_6s_BwGroup3b.fsfast.glmdir/ >>> BwGroupError3b_NvSZ_contrast/sig.cluster.sum --ocp >>> BG3b_glmfit/rh.ASevASc_6s_BwGroup3b.fsfast.glmdir/ >>> BwGroupError3b_NvSZ_contrast/sig.cluster.mgh --thmax infinity >>> >>> in /space/ventzl/1/users/SUBJECTS_DIR >>> >>> thanks, frida >>> >>> >>> >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> In order to help us help you, please follow the steps in: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> > Frida Polli > PhD Candidate, Suffolk University > Research Fellow in Psychiatric Neuroimaging > Massachusetts General Hospital > CNY 149-2608, 13th Street > Charlestown, MA 02129 > phone: (617) 724 4604 > fax: (617) 726 4078 > email: fpolli(a)nmr.mgh.harvard.edu > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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