Freesurfer

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Re: [Freesurfer] volume - surface shift in tkmedit
by Micheli, C. 25 Dec '10

25 Dec '10

Dear Bruce thank you for the quick answer. I saved the vox2ras matrix by assigning to it the voxel to millimiters transformation matrix the nifti converter read from dicom data (Siemens Magnetom Trio, 3T, sequence: standard mprage T1 't1_mprage_sag_std'). The tessellated mesh is saved in the millimiters space too (which means i applied the homogeneous transformation of voxel coordinates into millimiters) and in the millimiters space the volume and the mesh coincide. Actually the volume has been acquired as a 256X256X192 cube, and this could also cause a problem. I know realize that the volume has to be saved in RAS convention in order to be read in FreeSurfer correctly, about which i did not bother enough because the original voxel to nifti conversion matrix seems to have positioned the volume already in a convenient position. This is at least what i see when i visualized the so saved volume with tkmedit (coronal/sagittal/etc. are correctly positioned). Is everything clear about what i did? I though that since the two coordinate systems are the same they could be handled similarly in FS. How should i act on the surface in order to align it to the volume? If i would apply a topology fix on the mesh i will need the information about the white matter too, also saved in the same nifti format. In order to use this routine, do i also have to convert the volume in the proper RAS format or is it sufficient that volume and surface coincide in tkmedit visualization? (that was my intuitive criterion). About Freesurfer documentation that is what i found so far: http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?highlight=%28vox… Do you have other suggestions? There is a disclaimer on the documentation wiki. Sorry for the long email and i hope to hear from you soon. Happy Christmas! Cristiano ----- "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> schreef: > Van: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> > Aan: "C. Micheli" <c.micheli(a)fcdonders.ru.nl> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Verzonden: Woensdag 22 december 2010 15:26:37 > Onderwerp: Re: [Freesurfer] volume - surface shift in tkmedit > > Where did you get the vox2ras matrix that save_mgh takes? And what > space are the surface fiords in? There is extensive documentation on > our wiki fir the various coordinate systems we use > Cheers > Bruce > > > > On Dec 21, 2010, at 8:06 PM, "Micheli, C." <c.micheli(a)fcdonders.ru.nl> > wrote: > > > Dear all > > I would like to write an MRI anatomical volume and a surface in > freesurfer format. > > The surface is correspondent to the white matter tessellation, while > the volume represents T1 anatomical slices, both obtained from > softwares external to FreeSurfer. > > > > Using the two functions save_mgh.m and write_surf.m from the > freesurfer matlab interface files I am able to write the variables in > the proper freesurfer folders. > > > > In the original nifti format volume and surface match both in voxel > space and in millimiters space, but as soon as i visualize them in > tkmedit the surface is shifted. Any clue why this happens? Is there > any matrix that automatically translates the surface coordinates when > it is read in tkmedit? > > > > I hope to get your feedback soon > > > > Best regards > > Cristiano > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > 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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converting cortical thickness maps to NIFTI files
by Gallen, Courtney (NIH/NIDA) [F] 24 Dec '10

24 Dec '10

Hello, I'm interested in converting my cortical thickness maps to NIFTI files. Can you give me more information about how to do so? Also, is it possible to analyze freesurfer cortical thickness maps in AFNI (this is why I'm asking the question re conversion to NIFTI)? It seems as though my model is too complex to use something like qdec or fsgd (a 2x3 ANOVA with 3 covariates-1 discrete and 2 continuous). I see that I can specify my own design matrix to analyze the data with this model...but then don't see any info on what such a matrix should look like or how to proceed after that. Any help on either of these topics would be greatly appreciated! Thanks in advance Courtney Gallen Courtney Gallen Post-baccalaureate IRTA Neuroimaging Research Branch National Institute on Drug Abuse (IRP) 251 Bayview Blvd Suite 200 Baltimore, MD 21224 Tel: (443) 740-2631

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mri_mark_temporal_lobe
by FIDEL ALFARO ALMAGRO 24 Dec '10

24 Dec '10

Happy holidays for those who celebrate it today, Hi. Is there any documentation on how to use mri_mark_temporal_lobe application and what is its output? I cannot find any. Thanks in advance.

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cortical thickness of a ROI
by angela.favaro＠unipd.it 23 Dec '10

23 Dec '10

Dear all, I would appreciate any help about this point. I have a ROI created after a group comparison using functional data. I would like to explore the cortical thickness of this ROI to understand if differences in connectivity are linked to volumetric/thickness differences. I followed the instructions found in Freesurfer tutorials ('cortical thickness of a volume-defined ROI'). However, in the point 4 of the procedure I am not able to change the --reshape default. My run is: mri_surf2surf --s subj001 --trgsubject fsaverage --hemi rh --sval rh.thickness --tval rh.thickness.fsaverage.mgh --reshape-factor 7 but it continues to create (like default) a reshape with 6. For this reason, I think, the following command: mri_segstats --seg $SUBJECTS_DIR/rh.fsaverage.mask21.mgh --in rh.thickness.fsaverage.mgh --sum segstats-mask21.txt give: ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7 What can I do to solve this problem? Thank you for your help! Angela

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Can I mix different versions of freesurfer
by rong chen 23 Dec '10

23 Dec '10

Hi, I want to use FreeSurfer to analyze a longitudinal study. For each subject in my study, I already used FreeSurfer 4.2 to perform the cross-sectional analysis. However, FreeSurfer 4.2 did not have a longitudinal pipeline. Therefore, I want to use FreeSurfer 4.5 for this purpose. My question is: A) Should I rerun the cross-sectional analysis using FreeSurfer 4.5 OR B) I just run 'recon-all -base' and 'recon-all -long' using FreeSurfer 4.5, based on the cross-sectional results from version 4.2. Thanks, Rong

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WM surface and Deep Brain nuclei
by Luke Bloy 23 Dec '10

23 Dec '10

Hello, I'm new to freeSurfer and just starting to look around so I apologize if this question is a bit naive. When I look at segmentation results, that include deep brain nuclei (thalamus etc) I see that they are all contained inside of the white matter surface. is there away to edit the surface so that these boundaries are represented? I imagine that this would change the topology of the WM region thus it might be difficult, Is there away to generate surfaces form these regions on there own? Thanks Luke

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Extract Hippocampal volume after manual editing?
by McLean John (NHS Greater Glasgow & Clyde) 23 Dec '10

23 Dec '10

Hi, I have ran recon-all and got the Hippocampal volumes I desire from the aseg.stats file. However, I have manually refined some of the volumes using the tkmedit segmentation tool brushes and I now need to extract the revised volume estimates. I believe I can run 'mri_segstats' to obtain the revised volume, this seems to run the full segmentation process again, would this be the recommended way of obtaining the revised volumes or if I'm only interested in the Hippocampal volume is there a more precise command I could run to extract only this from my revised aseg.mgz segmentation file? Many Thanks John McLean ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere For more information and to find out how you can switch, visit www.connectingforhealth.nhs.uk/nhsmail ********************************************************************************************************************

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volume - surface shift in tkmedit
by Micheli, C. 22 Dec '10

22 Dec '10

Dear all I would like to write an MRI anatomical volume and a surface in freesurfer format. The surface is correspondent to the white matter tessellation, while the volume represents T1 anatomical slices, both obtained from softwares external to FreeSurfer. Using the two functions save_mgh.m and write_surf.m from the freesurfer matlab interface files I am able to write the variables in the proper freesurfer folders. In the original nifti format volume and surface match both in voxel space and in millimiters space, but as soon as i visualize them in tkmedit the surface is shifted. Any clue why this happens? Is there any matrix that automatically translates the surface coordinates when it is read in tkmedit? I hope to get your feedback soon Best regards Cristiano

2 1

Amygdala subregions
by Lin Nga 21 Dec '10

21 Dec '10

Hi all, Please excuse my naive question; I am new to FreeSurfer. I am trying to segment amygdala subregions and can't quite figure out how to do this. I didn't find anything in the tutorials or the freesurfer archives; if there is any documentation on how to do this, could someone point me in the right direction? Specifically, I'd like the regions listed below (copied from the FreeSurferColorLUT.txt): #No. Label Name: R G B A 7001 Lateral-nucleus 72 132 181 0 7002 Basolateral-nucleus 243 243 243 0 7003 Basal-nucleus 207 63 79 0 7004 Centromedial-nucleus 121 20 135 0 7005 Central-nucleus 197 60 248 0 7006 Medial-nucleus 2 149 2 0 7007 Cortical-nucleus 221 249 166 0 7008 Accessory-Basal-nucleus 232 146 35 0 7009 Corticoamygdaloid-transitio 20 60 120 0 7010 Anterior-amygdaloid-area-AAA 250 250 0 0 7011 Fusion-amygdala-HP-FAH 122 187 222 0 7012 Hippocampal-amygdala-transition-HATA 237 12 177 0 7013 Endopiriform-nucleus 10 49 255 0 7014 Lateral-nucleus-olfactory-tract 205 184 144 0 7015 Paralaminar-nucleus 45 205 165 0 7016 Intercalated-nucleus 117 160 175 0 7017 Prepiriform-cortex 221 217 21 0 7018 Periamygdaloid-cortex 20 60 120 0 7019 Envelope-Amygdala 141 21 100 0 7020 Extranuclear-Amydala 225 140 141 0 I've already ran recon-all and have aseg, aparc+aseg, and aparc.a2009+aseg available as outputs. Do I need aparc.a2005s+seg for the regions listed above? If so, how would I obtain it given the outputs of recon-all? Thanks for the help, Lin

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Freesurfer longitudinal analysis
by rong chen 21 Dec '10

21 Dec '10

Hi, I want to use FreeSurfer to analyze a longitudinal study. For each subject in my study, I already used FreeSurfer 4.2 to perform the cross-sectional analysis. However, FreeSurfer 4.2 did not have a longitudinal pipeline. Therefore, I want to use FreeSurfer 4.5 for this purpose (in the FreeSurfer wiki, it said the longitudinal pipeline in 5.0 is broken). My question is: A) Should I redo the cross-sectional analysis using FreeSurfer 4.5 OR B) I just run 'recon-all -base' and 'recon-all -long' using FreeSurfer 4.5, based on the cross-sectional results from version 4.2. Thanks, Rong

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