Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

averaging surface labels?
by Yagmur Ozdemir 19 19 Mar '18

19 Mar '18

Hello FreeSurfer experts, I am trying to create a group average of labels defined on inflated surface, and so far I tried mri_label2vol which succesfully got the labels to volume space and binarized for averaging, however when I sample this back to the inflated surface of fsaverage, using mri_label2label, the location is completely wrong and the label looks very distorted. I tried to use mri_vol2surf and mri_vol2roi instead for the latter portion and both did not work. Do you have any suggestions? I think mri_vol2surf can work if I have a register.dat file for fsaverage vol->surf but so far I didn't come across one and couldn't see how to create one. Also I think if I can create overlays out of the labels, then I can do mri_concat to average them out and with mri_cor2label get them out as labels again. However I did not come across a script that creates overlays out of labels. Thank you for all the thoughts and suggestions Best Idil

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no file ‘volumesAmygdla.txt’ from FS6.0 - Jan. 2017 release
by Alexopoulos, Dimitrios 19 Mar '18

19 Mar '18

I ran the following command to generate surfaces and hippo subfields on 6.0 (Jan. 2017 version) using both a T1 mprage and T2 space (both 1mm isotropic). recon-all –s subject –i dicom.dcm –hippocampal-subfields-T1T2 T2.nii.gz T1T2 –all. The command appears to have run successfully but I get a note at the end of the processing stream that there is no file ‘volumesAmygdla.txt’ (see screen message below). Is this expected even though I’m not using the later developmental release? Jim ----------------------------------------------------------------------- Not resampling, only changing vox2ras matrix To check registration, run: tkregister2 --mov T2inT1space.mgz --targ /data/nil-bluearc/shimony/neonatal/wunder_9_10yo/freesurfer6_0/processed_data/neo321e_fs/mri/norm.mgz --regheader --reg /tmp/reg mri_vol2vol done mv: cannot stat 'volumesAmygdala.txt': No such file or directory Everything done! It took 1921.1425 seconds Started at Wed Mar 14 17:04:06 CDT 2018 Ended at Thu Mar 15 05:35:24 CDT 2018 #@#%# recon-all-run-time-hours 12.522 recon-all -s neo321e_fs finished without error at Thu Mar 15 05:35:24 CDT 2018 done jimalex@linux1% ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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isxconcat-sess error: trgsubject
by Yagmur Ozdemir 19 19 Mar '18

19 Mar '18

Hello Freesurfer developers, I am trying to concatenate session files of different subjects using isxconcat-sess. I am not really sure why " INFO:trgsubject is self, this will fail unless all sessions are the same subject" pops up as I understand this is what isxconcat-sess is meant to do, and I used --subject fsaverage in some tries. I am not sure if there is something I am doing wrong, or the problem is coming from the "//" in the output lines. When I took out either Sess01 and Sess02 from the list to be sure it wasn't a problem specific to it, I got the same error. Below is the error output. Best Idil INFO: trgsubject is self, this will fail unless all sessions are the same subject group/rtopyTR2.lh/log/isxconcat.log cd /home/vm01/local/freesurfer/Project_bold isxconcat0-sess -f sessid -m mask -o group/rtopyTR2.lh/masks.nii.gz -a rtopyTR2.lh ------------------------------------ /home/vm01/local/freesurfer/Project_bold mri_concat /home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess03/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess04/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess07/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess08/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess09/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess10/bold/rtopyTR2.lh//mask.nii.gz --o group/rtopyTR2.lh/masks.nii.gz ninputs = 8 Checking inputs ERROR: dimension mismatch between /home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz and /home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz

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T1 / T2 WMH Segmentation
by Rockers, Elijah D. 19 Mar '18

19 Mar '18

Hello, I noticed that recon-all automatically segments hypointesities in the white matter regions. Is there any possibility of using Freesurfer to segment T2 FLAIR WMH? I did not see anything in the Wiki documentation about it. Thanks, - Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Different DWI protocols
by Cano Catala, Marta 19 Mar '18

19 Mar '18

Dear TRACULA experts, I'm running a longitudinal trac-all analysis and I'm wondering whether or not I could include different DWI acquisition protocols both between subjects and within subjects in the same analysis. Thank you, M. Cano

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mri_segment error
by Z Hessam 19 Mar '18

19 Mar '18

Hello FreeSurfer develpers I'm attempting to run " recon-all " command on a file of dicom data, and encounter with an error command: recon-all -s dyegmoh exited with ERRORS at Thu Feb 8 17:08:16 +0330 2018 how can i understand why this error happens and what should i do to solve it?

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mir_vol2surface registration file error
by Charlotte Grosse Wiesmann 19 Mar '18

19 Mar '18

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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mir_vol2surface registration file error
by srishti goel 18 Mar '18

18 Mar '18

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

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Freesurfer Input Imaging
by Daniel Alejandro Reyna Torres 16 Mar '18

16 Mar '18

Hello, is there any recommendation from Freesurfer for MRI images used during recon-all? i.e., should we use a sagittal MRI, coronal or transversal? For instance, I have one subject with these 3 different orientations. I ran recon-all on the 3 of them and got the results for the reconstruction. I was wondering how can we know which would be more accurate. I have a guess but not sure. Thanks team. Regards, Daniel

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complete list of structures for SubCortGray
by prasser 16 Mar '18

16 Mar '18

Hi, >From https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats "SubCortGray - includes thalamus, caudate, hippocampus, amygdala, accumbens, ventral DC, substancia nigra (if there). This is a simple voxel count of structures identified as subcortical GM." Could you please let me know if "thalamus, caudate, hippocampus, amygdala, accumbens, ventral DC, substancia nigra (if there)" is the complete list of structures identified as subcortical GM or are there others? A simple voxel count of thalamus, caudate, hippocampus, amygdala, accumbens, ventral DC, substancia nigra (if there) does not seem to match the subcortgray value from aseg.stats. Versions 5.3, 6.0. Thanks.

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