Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

Hippocampal subfields
by Arsenije Subotic 22 Mar '18

22 Mar '18

Hi all I would like to use subfield specific hippocampus maps that were produced Dr Iglesias's Lab: https://sites.google.com/site/jeiglesias/hippocampal-subfields These maps are available via FreeSurfer, however our lab is trying to segment hippocampus subregions from already manually extracted hippocampuses. In other words, we have manually traced hippocampus masks in a NIFTI format that we would like to co-register with these maps. How can I directly download subfield specific hippocampal atlases in a NIFTI format so that we can use non linear co registration after? Thank you very much. Look forward hearing from you, Arsenije

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Fwd: Correnting image bias before segmentation and parcelation - due to frontal and occipital shading.
by Gamaliz 22 Mar '18

22 Mar '18

Dear Freesurfer Team, I have about 200 T1 coronal scans that were obtained with some shading in the frontal and occipital regions. Not sure if it can be seen from the attached picture, but the image fades toward the top and bottom (on the axial view). The segmentation left out a large section of the frontal and occipital, probably because the signal loss brings those voxels below the threshold for white and gray matter. I have tried to run FSL bias correction and got a small improvement, but I wonder if there is any way these faded slides can be corrected so that the segmentation is capable of seeing these as proper white and gray matter. In the attached picture, the blue is the wm surface and the red is the gray matter (wm and pial surfaces) The image shown is actually the T1.mgz from freesufer that has already gone through the nu_correct step in recon_all, the original image looks very similar... Thanks Gabriel -- gAbE

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Re: [Freesurfer] Regarding hippocampus tesellation
by Iglesias Gonzalez, Eugenio 22 Mar '18

22 Mar '18

Hi Pooja I'd suggest reading in the mgz volume with MATLAB (you can use the function MRIread in $FREESURFER_HOME/matlab) and export it to your favorite format from there Cheers Eugenio Sent from my phone, please excuse brevity and typos ________________________________ From: pooja prabhu <prabhuppooja(a)gmail.com> Sent: Thursday, March 22, 2018 9:47:52 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Regarding hippocampus tesellation Hello, This is Pooja. I am trying to segment the hippocampus using the function introduced by Freesurfer i.e -hippocampal-subfields. Segmentation was successful but the final file format is .mgz. Could you please guide me how can i tessellate the hippocampus and cortical surface? i want this surface to place the dipole so please help me. Thank -- Thank You Pooja Prabhu 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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FreeSurfer for mouse brain
by Heidi Foo 21 Mar '18

21 Mar '18

Dear FreeSurfer experts, I am currently trying to run FreeSurfer on a set of mouse brains and I have a few questions about it: 1. Is it possible to generate 2D surfaces from a set of structural scans on mouse brain in FreeSurfer? 2. Do the individual steps like Normalisation, Segmentation, Tessellation, etc rely on the Talairach space? 3. Is there any way that I can replace the Talairach atlas that the steps use in the root directories or codes? Thank you! Best Regards, Heidi Foo

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Re: [Freesurfer] Registering functional data between scan sessions
by David Beeler 20 Mar '18

20 Mar '18

Awesome, thanks Doug! For clarity, I got it working with: bbregister --s <day1subjID> --mov <day1funcvol> --reg day1func-to-day1anat.lta --init-fsl --bold bbregister --s <day2subjID> --mov <day2funcvol> --reg day2func-to-day2anat.lta --init-fsl --bold bbregister --s <day2subjID> --mov $SUBJECTS_DIR/<day1subjID>/mri/brain.mgz --reg day1anat-to-day2anat.lta --init-fsl --t1 mri_concatenate_lta day1func-to-day1anat.lta day1anat-to-day2anat.lta test/day1func-to-day2anat.lta mri_concatenate_lta -invert2 day1func-to-day2anat.lta day2func-to-day2anat.lta day1func-to-day2func.lta mri_vol2vol --mov <day1funcvol> --targ <day2funcvol> --reg day1func-to-day2func.lta --o day1func-in-day2func.nii.gz Cheers, DB

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Cortical volume parcellation
by Mark Wagshul 20 Mar '18

20 Mar '18

Hi. I'm new to using Freesurfer. We are using the parc + aseg segmentation, but would like to extract functionally-relevant cortical regions, which I don't see specified in the output. Specifically, I would like to calculate cortical thickness of the dorsal pre-frontal cortex, which overlap with parts of the cortical parcellations that I'm currently getting. Is there any way to do this within Freesurfer, or will I have to use another atlas (e.g. We could generate this on the Mni template, morph it into subject space and dilate to ensure that it captures the entire cortical surface). Thanks for any advice you can provide on this. Best, Mark _______________________ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY Sent from my iPhone

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Brainstem registration
by Chungmin Han 20 Mar '18

20 Mar '18

Dear whomever it may concern, I'm Chungmin, a graduate research assistant in University of Texas at Austin, I'm fairly new to using freesurfer, I'd appreciate to get some advice on what I'm facing, *I've had this posted but for some reason lost track of it so I'm uploading it again.* I have fMRI limited FOV collected on brainstem + little cerebellum/visual area, I've tried SPM manual registration to MNI space, falls in 1-2mm (1-2 voxels) away from accurate registering brainstem correctly, I have T1 mprage in 1mm resolution, but seems T1 registration to MNI space has a bit of error around "Brainstem" area. is there a way to create transformation matrix *optimized to fit brainstem in MNI space*? Registering cortical region slightly bit wrong is okay to me at this moment, https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures I've noticed this has been posted pretty recently, but would like to figure out how to align in standard space for comparison. I've also thought of inverse registering from MNI to each native space, however, if the transformation focuses on maximizing registration on the cortical level (T1) I don't think inverse registration solves the issue, The area that I'm interested in is lateral nuclei, reticular formation etc. so it would rather be focused on the midbrain, not even at the level of diencephalon, and Additional question, would using fsaverage be more beneficial over MNI152 registration? in terms of brainstem warped into the standard space more accurately. Thank you in advance :) Best PS How do you reply to your own question after someone replies? Chungmin Chungmin Han Graduate Research Assistant The University of Texas at Austin 204 E. Dean Keeton St Austin TX 78712 Mobile: 512-717-1671

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Re: [Freesurfer] mir_vol2surface registration file error
by Charlotte Grosse Wiesmann 20 Mar '18

20 Mar '18

Hi Srishti, your volume maps are in some template space right? (the template you can open them on) This might be some MNI template space, but not necessarily the same the other people have used. You can register these to one another, e.g. with ANTS: Start ANTS in terminal > ants.sh 3 TheirTemplate.nii YourTemplate.nii This will give you a transformation matrix (xxx_Warp.nii and xxx_Affine.txt) that you can use to warp your ROIs to their template space: > WarpImageMultiTransform 3 YourROI.nii output_image -R TheirTemplate.nii xxx_Warp.nii.gz xxx_Affine.txt Then you can open the output image (Your ROI warped to their template space) and their ROI on their template with fslview, or compute any analysis to compare them. I don't understand why you would use mri_vol2surf if you only want the volume. What this function does is to map the volume to the surface, so if you don't need the surface you don't need the fct. Best Charlotte ----- Original Message ----- From: "23srishtigoel" <23srishtigoel(a)gmail.com> To: "wiesmann" <wiesmann(a)cbs.mpg.de> Sent: Tuesday, March 20, 2018 2:16:21 PM Subject: Re: [Freesurfer] mir_vol2surface registration file error Hi Charlotte, Thank you so much for your detailed response, I really appreciate it. With respect to your third point, comparing volume maps, what exactly do you mean by registering our template to their MNI152 template? What exactly will be our template file? I was using the same mri_Vol2surf for comparing the volume maps as well, for example: mri_vol2surf --src negative_allsocial.nii --mni152reg --hemi lh --o ./neg_allsocial.nii --projfrac 0.5 Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig(a)email.unc.edu skype: srishti.goel12 On Mon, Mar 19, 2018 at 6:14 AM, Charlotte Grosse Wiesmann < wiesmann(a)cbs.mpg.de> wrote: > Hi Shrishti, > > 1) by recon-all I meant recon-all in the freesurfer pipeline ( > https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all ) to reconstruct the > subject's cortical surfaces because if I got you right you have the maps on > the surface (SN_like_cortical_lh.gz) and in the volume. If you only want to > compare the maps in the volume you can skip this part I only compare the > volume maps. > > 2) As far as I know with mri_vol2surf and tksurfer you can use a number of > different formats including .nii (if not you can convert with mri_convert) > > 3) I'm not sure I understand your question. Make sure both of your volume > maps are registered to the same MNI152 template. (Best is if you ask the > people who gave you their maps to also give you the template. Then you can > register your template to that template (e.g., using ANTS) and the > transformation matrix you obtain to map your maps onto the other > template.) If both volume maps are in the same space you can both open > them with fslview on the template they have been registered to (fslview > template.nii map1.nii map2.nii) and compare them visually. > > Best > > Charlotte > > > > ----- Original Message ----- > From: "23srishtigoel" <23srishtigoel(a)gmail.com> > To: "wiesmann" <wiesmann(a)cbs.mpg.de> > Sent: Sunday, March 18, 2018 5:37:40 PM > Subject: Re: [Freesurfer] mir_vol2surface registration file error > > Hi Charlotte, > > Thank you so much for your help, I really appreciate it and this is super > helpful for me. I just want to clarify a couple small thing > > 1) By running recon-all on that subject do you mean reconstructing that > subject's DICOM basically? > 2) I notice that the extension you are using is .mgh so would I have to > convert the volume maps (which is SN_like_cortical.nii) into mgh/mgz/gz as > well? > 3) Also, would you be able to elaborate a little on how to view the volumes > on the MNI. I have used fslview and I think I know how to map our volume > maps on the MNI152 volume space but I am not sure what would be the best > way to use fslview to view it. > > Thanks once again! > > Best, > Srishti > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srishtig(a)email.unc.edu > skype: srishti.goel12 > > > On Sun, Mar 18, 2018 at 10:55 AM, Charlotte Grosse Wiesmann < > wiesmann(a)cbs.mpg.de> wrote: > > > Hi Srishti, > > > > I had a similar problem recently, so I will try to help. To compare your > > maps with the surface maps SN_like_cortical_lh.gz of the others you need > to > > map your volume to the surface of the same subject they are using. > > > > That is, you first have to run recon-all on that subject (unless they > gave > > you the link to the subject folder for which recon-all has already been > > run. Say, the name of the subject folder is SUBJECT-ID). > > > > Then, you need to map your volume to the surface of that subject: > > mri_vol2surf --src negative_allsocial_proportion.nii --regheader > > SUBJECT-ID --hemi lh --o ./neg_allsocial_lh.mgh [more options] > > > > Then, you should be able to look at both surface maps on your subject > > surface, e.g., with tksurfer > > > > tksurfer SUBJECT-ID lh inflated -overlay ./neg_allsocial_lh.mgh -overlay > > SN_like_cortical_lh.mgh -fthresh 0.5 > > > > For the volume, you need to map your volume maps to the same MNI152 > volume > > space the other volume maps are in, and then you should be able to view > > them both on the according MNI template with any brain volume viewer > > program (e.g., fslview,...). > > > > Hope this helps. > > > > Best, > > > > Charlotte > > > > > > > > > > ----- Original Message ----- > > From: "srishti goel" <23srishtigoel(a)gmail.com> > > To: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> > > Sent: Saturday, March 17, 2018 2:48:23 PM > > Subject: Re: [Freesurfer] mir_vol2surface registration file error > > > > Hi, > > > > I tried using bbregister to register my files with the following command: > > > > > > bbregister --mov negative_allsocial.nii --bold --s SN_like_cortical_lh.gz > > --init-rr --lta register.lta > > > > and this is the error I received: > > > > > > reading source './tmp.bbregister.173331/template.nii'... > > > > mri_robust_register.bin: only pass single frame MRI source > > ./tmp.bbregister.173331/template.nii. > > > > > > > > > > No such file or directory > > > > > > > > > > I would like to re-iterate my issue as that might be helpful. We have > > carried out a meta analysis and want to compare our meta analytic maps to > > someone's else's map. Our meta analytic map is negative_allsocial.vmp > which > > we converted to a nifti using neuroelf and now have the > > negative_allsocial.nii. We want to see how someone else's map which is > the > > SN_like_cortical_lh.gz (they said to view this on a subject file to which > > they gave us the link) compares to our map. We would also further want to > > see how our map compares to their volume map which is > > SN_like_subcortical.nii (these are in MNI152 volume space). We are using > > mri_vol2surf to view compare the two files. > > > > > > > > > > mri_vol2surf --src negative_allsocial_proportion.nii --src_type analyze > > --srcreg [REGISTRATION MATRIX] --hemi lh --o ./neg_allsocial.nii > --projfrac > > 0.5 > > > > > > > > > > > > And for the registration matrix I tried using bbregister as told my the > > freeSurfer help group. > > > > I can send the files as well if required and would highly appreciate some > > prompt help on this. > > > > > > > > > > Thanks so much! > > > > > > > > > > Best, > > > > Srishti > > > > > > > > Best, > > Srishti > > Social/Clinical Research Specialist > > Child Imaging Research and Life Experiences Lab > > University of North Carolina at Chapel Hill > > email (W): srishtig(a)email.unc.edu > > skype: srishti.goel12 > > > > > > On Fri, Mar 9, 2018 at 11:15 AM, Douglas Greve < dgreve(a)mgh.harvard.edu > > > > wrote: > > > > > > > > > > > > You create it with bbregister. See the multimodal integration tutorial > > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview > > > > On 3/6/18 6:36 PM, srishti goel wrote: > > > > > > > > I am sorry but that is what I am unsure about it. I don't know how to > > obtain a registration matrix or which registration matrix to use for > this. > > > > Best, > > Srishti > > Social/Clinical Research Specialist > > Child Imaging Research and Life Experiences Lab > > University of North Carolina at Chapel Hill > > email (W): srishtig(a)email.unc.edu > > skype: srishti.goel12 > > > > > > On Mon, Mar 5, 2018 at 3:24 PM, Douglas N Greve < > > greve(a)nmr.mgh.harvard.edu > wrote: > > > > > > Why did you remove the registration file? --srcreg below > > > > > > On 02/28/2018 04:13 PM, srishti goel wrote: > > > Hello, > > > > > > Thank you so much! I used the following command as you said and got an > > > error : must specify a source registration file or --regheader > > > > > > mri_vol2surf --src negative_allsocial_avgnull.nii --src_type analyze > > > --trgsubject fsaverage --hemi lh --o ./neg_allsocial.nii --projfrac 0.5 > > > > > > > > > Best, > > > Srishti > > > Social/Clinical Research Specialist > > > Child Imaging Research and Life Experiences Lab > > > University of North Carolina at Chapel Hill > > > email (W): srishtig(a)email.unc.edu <mailto: srishtig(a)email.unc.edu > > > > skype: srishti.goel12 > > > > > > > > > On Wed, Feb 28, 2018 at 10:13 AM, Douglas Greve > > > < greve(a)nmr.mgh.harvard.edu <mailto: greve(a)nmr.mgh.harvard.edu >> > wrote: > > > > > > you need to add --trgsubject fsaverage to your mri_vol2surf > > > command line > > > > > > > > > On 2/27/18 12:23 PM, srishti goel wrote: > > >> Hello, > > >> > > >> We are trying to project a volume map onto a surface. Our network > > >> based volume map is a .vmp file and our surface is a nifti file. > > >> We were able to convert the volume maps from .vmp to nifti. > > >> Our volume map is: negative_allsocial_proportion.nii > > >> Our surface is: SN_like_cortical_lh.nii > > >> The output file is named: neg_allsocial.nii > > >> > > >> We are trying to use the following command to now project the > > >> volume map on surface and the issues we are facing are: > > >> 1) We are unsure of what the purpose of the registration file is > > >> and where in the mir_vol2surf command should we specify the surface > > >> 2) If it is a matrix for something related to the surface on > > >> which we want to project our volume then how should we go about > > >> obtaining the registration file appropriate for our comparison. > > >> > > >> _Command:_ > > >> mri_vol2surf --src negative_allsocial_proportion.nii --src_type > > >> analyze --srcreg [REGISTRATION MATRIX] --hemi lh --o > > >> ./neg_allsocial.nii --projfrac 0.5 > > >> > > >> _Then to project it:_ > > >> tksurfer fsaverage lh inflated -ov neg_allsocail.nii > > >> > > >> > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer(a)nmr.mgh.harvard.edu > > >> <mailto: Freesurfer(a)nmr.mgh.harvard.edu > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> < https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu <mailto: Freesurfer(a)nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > < 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 > > > < 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. > > > > > > > > > > > > > > > _______________________________________________ > > > 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 > > > > 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/ > > > > _______________________________________________ > > 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 > > > > > > _______________________________________________ > > 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. > > > > > > > > _______________________________________________ > > 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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Hippocampal Subfield Atlas
by Roberto Medeiros de Souza 20 Mar '18

20 Mar '18

Hello, Does anyone know in which freesurfer folder I find the atlas corresponding to the following publication: "A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation of in vivo MR"? Thanks, Roberto

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Extract mean functional activation value on surface parcellation
by zuxfoucault Wong 19 Mar '18

19 Mar '18

Dear FreeSurfer experts: When I registered the map of functional activation on each hemisphere, how can I extract mean activation value based on each parcellation region on the surface? According to FreeSurfer tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0/Individual… , the measures extracted by mri_segstats is the functional activation map resampled to the individual's anatomical space by mri_vol2vol. Can mri_segstats extract mean activation value based on each parcellation region in a surface-based way? Thank you for your time! Best, Foucault

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