Freesurfer December 2015

freesurfer@nmr.mgh.harvard.edu

115 participants
187 discussions

Re: [Freesurfer] 答复: about functional ROIs
by Thomas Yeo 31 Dec '15

31 Dec '15

Hi Jintao, The difference comes from the fact that the MNI template I used is 256 x 256 x 256, which was obtained by passing the FSL MNI152 template through the FreeSurfer recon-all pipeline. Therefore even though the header information are different, they are still in the same space. You can convince yourself by using freesurfer's freeview to load both the MNI template I provide and the MNI template from FSL: >> freeview FSL_MNI152_FreeSurferConformed_1mm.nii.gz $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz You should observe they are in perfect alignment (although the values have been altered by recon-all intensity normalization process). If the different headers bother you, what you can do is to use freesurfer's function mri_vol2vol to re-interpolate the volume. For example: >> mri_vol2vol --mov FSL_MNI152_FreeSurferConformed_1mm.nii.gz --targ $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --regheader --o new_volume.nii.gz --no-save-reg Regards, Thomas On Thu, Dec 31, 2015 at 2:59 PM, <shengjt2014(a)163.com> wrote: > Hello Professor Thomas， > > > > Thank you for your reply so quickly. > > > > I download the zip files on the webside you gave me, and the images look > like normal, but when I checked the header information, I found some > differences with common MNI images. > > > > Could you see the following pictures and notice the regions with blue > lines circled. > > > > > > > > Excuse me to bother you again. > > Best wishes, > > Jintao > > > > > > > *发件人: *Thomas Yeo <ythomas(a)csail.mit.edu> > *发送时间: *2015年12月31日 11:46 > *收件人: *shengjt2014(a)163.com > *抄送: *freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > *主题: *Re: about functional ROIs > > > > Hi Jintao, > > > > This might be a header error in the original files. The error is not > apparent in the FreeSurfer or FSL environment, but might be problematic > with mricron (completely my fault). > > > > Can you try the files from this zip file instead: > https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo2011MNIParcellation… > (courtesy of Chris Rorden). > > > > Please let me know if this resolves your issues. > > > > Regards, > > Thomas > > > > On Thu, Dec 31, 2015 at 10:23 AM, <shengjt2014(a)163.com> wrote: > > > > Dear Professor Yeo, > > > > My name is Sheng Jintao, and I am a master in China. > > Recently, I download the ‘Resting State Cortical Parcellation in > nonlinear MNI152 space’ in > https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011, > But when I opened images and found they are very stange. Just like this > sectional drawing. And I don’t know why, therefore, I would love to > consult you. > > Thank you, and I look forward to hearing from you. > > > > Best wishes, > > Jintao > > > > > > >

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Re: [Freesurfer] about functional ROIs
by Thomas Yeo 30 Dec '15

30 Dec '15

Hi Jintao, This might be a header error in the original files. The error is not apparent in the FreeSurfer or FSL environment, but might be problematic with mricron (completely my fault). Can you try the files from this zip file instead: https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo2011MNIParcellation… (courtesy of Chris Rorden). Please let me know if this resolves your issues. Regards, Thomas On Thu, Dec 31, 2015 at 10:23 AM, <shengjt2014(a)163.com> wrote: > > > Dear Professor Yeo, > > > > My name is Sheng Jintao, and I am a master in China. > > Recently, I download the ‘Resting State Cortical Parcellation in nonlinear > MNI152 space’ in > https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011, > But when I opened images and found they are very stange. Just like this > sectional drawing. And I don’t know why, therefore, I would love to consult > you. > > Thank you, and I look forward to hearing from you. > > > > Best wishes, > > Jintao > > > >

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Longitudinal data analysis
by John Anderson 30 Dec '15

30 Dec '15

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minimum number of vertices for cluster-correction
by Tara Miskovich 29 Dec '15

29 Dec '15

Hi all, Can someone help me find how to get the minimum number of vertices required to pass the cluster-corrected threshold with monte carlo simulations? -- Thank you, Tara

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mri_surfcluster on group
by stdp82＠virgilio.it 29 Dec '15

29 Dec '15

Hi list,I'd like to perform mri_surfcluster on a group to eliminate cluster < 5 voxels from sig.nii.gz after FDR correction.I'm running mri_surfcluster --in sig.nii.gz --hemi rh --sign abs --fdr 0.05 --minarea 5 --sum summaryfile --ocn ocnid but --subject ... must be included. How should do I do? My analysis should be run on group results, not on a subject. Thanks, Stefano

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How can I use mri_vol2surf to map the white matter volume cortical surface in order to generate a white matter map that is similar to the gray matter volume map produced by mris_preproc?
by Knut J Bjuland 28 Dec '15

28 Dec '15

DearFreeSurferexperts, HowcanIusemri_vol2surftomapthewhitemattervolumecorticalsurfaceinordertogenerateawhitemattermapthatissimilartothegraymattervolumemapproducedbymris_preproc? ShouldIusebinarymaskcreatedinMatlabtoremovelabelsthatarenotwhitematter? Best regards KnutJørgenBjuland NTNU

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visualization of a "spherical" cut
by Krieger, Donald N. 28 Dec '15

28 Dec '15

Dear List, I have a visualization problem which is not directly relevant to freesurfer but which may be easily solvable with the freesurfer tools. I have also posted this question to the ImageJ discussion list. I would like to visualize "spherical" cuts through an MR. An axial cut is the intersection of the image volume with a plane normal to a line running superior to inferior through the volume. A spherical cut is the intersection of a sphere with specified origin through the volume. Hence the visual would be a disc with radius that of the sphere and center at the origin. There would be two such discs, one for the front and one for the back. What do you think? Is there an easy way? Any thought and/or suggestions would be welcome. Thanks - Don

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missing 3volreg.afni
by Thục Trinh 27 Dec '15

27 Dec '15

Hi FS experts, I'm working on my fMRI data using FSFAST v.6 tool. But the first step of Preproc-sess was failed with an error :" *ERROR: cannot find AFNI command 3dvolreg.afni ". * I found a thread that had the same error with mine (in FS v.5.3) : http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37764.html But the link to download 3dvolreg.afni doesn't work. Is this the same 3dvolreg.afni for v.5.3 and v.6? Thanks, Trinh

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PhD position: MRI markers of neuroinflammation in treatment pharmacoresistant epilepsy
by Barbara Kreilkamp 27 Dec '15

27 Dec '15

Dear Freesurfers, A PhD studentship „Identifying non-invasive imaging markers of neuroinflammation in treatment pharmacoresistant epilepsy“ is available in the Epilepsy Research Group (ERG) at the University of Liverpool, UK and is supervised by Dr Simon Keller and Prof Tony Marson. Please find all details about this position via this link: http://www.findaphd.com/search/ProjectDetails.aspx?PJID=70289&LID=3417 *Deadline:* Friday, January 22, 2016 - apply ASAP! Best wishes and a Happy New Year! Barbara Kreilkamp PhD researcher University of Liverpool

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Integrating planes into a single volume?
by John Benfield 27 Dec '15

27 Dec '15

Is there any way to integrate the information from axial, coronal and sagittal views into a single volume? I'm looking for ways to build a more accurate/comprehensive 3d model and I'm not having any luck finding workflows or tools that allow any sort of cross-plane refinement/interpolation. Any suggestions?

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Freesurfer December 2015