Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

Compare individual to a group
by Xiaojiang Yang 07 May '20

07 May '20

External Email - Use Caution Dear FS experts, I have a group of healthy subjects. Given a new individual subject, I want to compare its cortical thickness to the healthy group so that I can find where the thickness is abnormal (thickening or thinning). I use fsaverage as the template subject to calculate mean and std of the healthy group. Since subjects in the healthy group have different ages, I do a "normalization" process to all the subjects in the group BEFORE calculating the mean and std. Thus the normalized healthy group can be regarded as all subjects having the same "standard" age. The normalization process is just multiplying some pre-obtained scale (varied by age, but not linearly ) to the file ?h.thickness.fwhm0.fsaverage.mgh of each subject that are already calculated by "recon-all --qcache" command. So the mean and std of the group are actually weighted in the sense of Freesurfer's recon-all results. My questions are: 1) If I do vertex-wise t-tests by simply comparing individual subject's thickness to the group using mris_calc but WITHOUT using mri_glmfit, can I still use mri_glmfit-sim to do multiple comparisons correction? If yes, how? 2) If the answer is no for the above question, how should I use mris_glmft to implement my above thoughts so that I can use use mri_glmfit-sim? Specifically, how can I use the weighted mean for the group? 3) Take a step back, if I consider the weight is linearly correlated with the age, how to design the fsdg and contrast file? Thank you very much! Xiao

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HCPMMP1 parcellation to aseg (.mgz)
by pooja prabhu 07 May '20

07 May '20

External Email - Use Caution Hai list, Can I get some insight on how to convert HCPMMP1 to aseg(provided we have annotation files) for fsaverage brain? For example: for aparc parcellation we use aparc2aseg and get aparc+aseg.mgz. Similarly I need for HCPMMP1. Can someone help me with this? Thank you

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New PETSurfer Questions
by Ferraro, Pilar 07 May '20

07 May '20

External Email - Use Caution Dear Freesurfer experts, As previously mentioned, we are currently trying to test the effects of different PVC corrections on metabolism estimation in a group of patients. We would like to also include MZ and MG methods in the analyses, comparing them to SGTM and no PVC. However, while both MG and MZ provide voxel-wise results, we would like to use them in ROI analyses in order to be able to compare their outputs with the ones obtained with SGTM and no PVC. Are there any procedures that you would recommend to do this? Many thanks in advance for any help, Best, Pilar > Il giorno 7 mag 2020, alle ore 6:00 PM, freesurfer-request(a)nmr.mgh.harvard.edu ha scritto: > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: HCPMMP1 parcellation to aseg (.mgz) (pooja prabhu) > 2. Re: HCPMMP1 parcellation to aseg (.mgz) (Douglas N. Greve) > 3. Re: Recon-all exited WITH errors {Disarmed} (Mason Wells) > 4. Re: freesurfer 7.0.0 in a virtual machine... (Gonzalo Rojas Costa) > 5. Re: Recon-all exited WITH errors {Disarmed} (Douglas N. Greve) > 6. Re: flirt.fsl error (NEWMAT::SingularException) when running > bbregister in Freesurfer 7.0.0 (Hoopes, Andrew) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 7 May 2020 20:55:21 +0530 > From: pooja prabhu <prabhuppooja(a)gmail.com> > Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz) > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CANeOyKnobqGKPPSdX+Pr1CmvHRYE2d+ziRvEMfz9BQJ4-RsGbA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > HCPMMP1 parcellation is multi modal parcellation > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/ > > We need the file something like we have for 'aparc' parcellation. > The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz) > How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot) > > -- > Thank You > Pooja Prabhu >

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Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
by pooja prabhu 07 May '20

07 May '20

External Email - Use Caution HCPMMP1 parcellation is multi modal parcellation https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/ We need the file something like we have for 'aparc' parcellation. The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz) How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot) -- Thank You Pooja Prabhu

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conf2highres
by Dr. Ilona Lipp 07 May '20

07 May '20

External Email - Use Caution Hi, in the version 7 release notes it says this: "conf2hires. This is an alternative method to do hi-res recon byrunning part of the stream at 1mm, then placing the 1mm surfaces on the hi-res volume. This was originally programmed for the HCP. The now-standard hi-res stream should work just as well, but we kept conf2hires for backwards compatibility.". I would be grateful if you could confirm whether this means that the conf2hires option is incorporated in the latest Freesurfer release or just that the compatibility is still ensured. If former, how can I actually run it, I tried using -conf2hires as a flag (instead of -hires), but this gave me an error message. Thanks a lot, Ilona

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recon-all-rms error < 2.00
by jiahui 07 May '20

07 May '20

External Email - Use Caution Hello FreeSurfer Developers, I run the recon-all -all command:this true error?how to resolve this problem? ERROR: 245/300: dt: 0.9000, rms radial error=134. 782, avgs=0 250/300: dt: 0.9000, rms radial error=134. 022, avgs=0 255/300: dt: 0.9000, rms radial error=133.265, avgs=0 260/300: dt: 0.9000, rMS radial error=132.513, avgs=0 265/300: dt: 0.9000, rms radial error=131. 766, avgs=0 270/300: dt: 0.9000, rmS radial error=131. 022 , avgs=0 275/300: dt: 0.9000, rMS radial error=130 .283, avgs=o 280/300: dt: 0.9000, rMS radial error=129.548, avgs0 285/300: dt: 0.9000, rmS radial error=128.817 , avgs=0 290/300: dt: 0.9000, rms radial error=128 .090, avgs=0 295/300: dt: 0.9000, rMS radial error=127 .367 , avgs=0 300/300: dt: 0.9000, rMs radial error=126.648, avgs=0 final distance error %24.71 pass 1: epoch 1 of 3 starting distance error %19.14 pass 1: epoch 2 of 3 starting distance error %19.08 starting distance error X19.04 final distance error %19.04 pass 1: epoch 1 of 3 starting distance error %19.50 pass 1: epoch 2 of 3 starting distance error %19.45 starting distance error %19. 41 final distance error %19.43 recon-all -s 100034 finished without error at 2020# 05A 05E 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

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freesurfer 7.0.0 in a virtual machine...
by Gonzalo Rojas Costa 07 May '20

07 May '20

External Email - Use Caution Hi: How can install freesurfer 7.0.0 in a virtual machine ? Sincerely, Gonzalo Rojas Costa

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recon-all-rms error < 2.00
by jiahui 06 May '20

06 May '20

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Hippocampus Subfields Segmentation
by Muhammad Naveed Iqbal Qureshi 06 May '20

06 May '20

External Email - Use Caution Hi FreeSurfer experts, I preprocess my data with FreeSurfer v 6. After it I ran developmental version of freesurfer to get the hippocampus subfields ROI and volume. I get the following output: # Hippocampal subfield volumes as created by segmentHA_T1.sh 1 1 0 618.413010 Hippocampal_tail 2 2 0 308.580548 subiculum-body 3 3 0 112.098146 CA1-body 4 4 0 146.657166 subiculum-head 5 5 0 202.046082 hippocampal-fissure 6 6 0 144.323840 presubiculum-head 7 7 0 513.572092 CA1-head 8 8 0 207.825661 presubiculum-body 9 9 0 75.481830 parasubiculum 10 10 0 332.502880 molecular_layer_HP-head 11 11 0 230.190313 molecular_layer_HP-body 12 12 0 174.264695 GC-ML-DG-head 13 13 0 76.776264 CA3-body 14 14 0 163.024711 GC-ML-DG-body 15 15 0 150.412851 CA4-head 16 16 0 150.002992 CA4-body 17 17 0 85.262570 fimbria 18 18 0 149.769932 CA3-head 19 19 0 61.819269 HATA 20 20 0 1333.761205 Whole_hippocampal_body 21 21 0 1748.804555 Whole_hippocampal_head 22 22 0 3700.978770 Whole_hippocampus I can see in the hipposubfields.lh.T1.v21.stats and lh.hippoSfVolumes-T1.v21.txt files with separate information for the head and tail volumes of each subfield. May I know what is the file name containing the corresponding separate head and tail ROIs that were use to calculate the above mentioned volumes? I can only find full subfield in all the ROI files. Thank you. Regards, Naveed

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mean for a bash script from mris_calc.
by Knut J Bjuland 06 May '20

06 May '20

External Email - Use Caution Dear Freesurfer experts, I have tried to use mris_calc to calculate mean and std and export the variable to bash with this command, mean=$(mris_calc mghfile std), but the array is not stored in mean. Is there any other way to calculate, mean and use it in a bash script apart from using matlab? Best regards Knut Jørgen Bjuland

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