On 7/24/2020 10:27 AM, Ferraro, Pilar wrote:
External Email - Use CautionHi Douglas,
All the analyses have been run with FS version 6 indeed. If you confirm the commands below are correct, I therefore assume I should rerun all the analyses using FS 7.1.
I just have few remaining questions:
- Are there any other ROIs more than the pons that you have changed from WM to GM in FS 7.1?
Ventral Diencephalon (VentralDC) is now GM.
- Is the same problem of WM/GM classification affecting MZ corrected uptake estimation? I suppose WM/GM classification should affect only MG since it’s a 3 compartment model, but I’m not sure.
It should not
Many thanks,
Pilar
Commands:
- With Muller-Gartner (MG):
mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output
Then: mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab — sum MG_ROI.txt
- With Meltzer (MZ):
mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 —o gtm_MZ.output
Then: mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum MZ_ROI.txt
On 7/20/2020 2:56 AM, Ferraro, Pilar wrote:
????????External Email - Use Caution
Many thanks for the reply,
Yep, unfortunately MG values are always much higher than SGTM ones (in all the ROIs). I wonder whether this might be related (for MG and MZ) to the absence of a normalization using the pons as a reference.
Indeed, when I look at the file with mean values extracted for each modality, I see that the pons has always 1000 as mean uptake value for no PVC and SGTM, while for MG and MZ values in the pons range from -0.02 to -0.65 (for MG) and from 0.94 to 0.99 (for MZ).
Pons should be 1.000 in the SGM and NoPVC. Which version of FS are you using? In version 6, pons was considered white matter, but I changed it to gray matter in version 7. The bottom line on this is that you cannot compute uptake in WM in MG. So, if pons (or any other ROI) is WM, then its value is bogus.
Below are the commands I?ve used to obtain the MG and MZ values:
- With Muller-Gartner (MG):
mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output
?Then:
mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab --sum MG_ROI.txt
- With Meltzer (MZ):
mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 --o gtm_MZ.output
Then:
mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum MZ_ROI.txt
Do you recognize any errors in the commands?
Many thanks,
Pilar
Message: 13 Date: Thu, 16 Jul 2020 10:19:32 -0400 From: "Douglas N. Greve" <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> Subject: Re: [Freesurfer] PETSurfer analysis question To: <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <d56acc7d-3273-4f40-ed17-570a893b26a3@mgh.harvard.edu mailto:d56acc7d-3273-4f40-ed17-570a893b26a3@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8"
The NoPVC and SGTM values are reasonable. The MG value is pretty crazy. I don't put stock in MZ. Is the MG value much higher than SGTM in other ROIs? What is your mri_gtmpvc command?
On 7/16/2020 4:38 AM, Ferraro, Pilar wrote:
????????External Email - Use Caution
Hi Freesurfer experts,
I?ve run a PETSurfer analysis in order to compare mean?uptake values of ROIs obtained with different methods: No PVC, SGTM, MG and MZ. However, I?ve now extracted the mean values and they are extremely heterogeneous. As an example, the same ROI (lh banks of the superior temporal sulcus) has the following uptake values:
No PVC= 1.709 SGTM= 2.495 MG= 23.847 MZ= 15.564
I?m particularly worried for the huge difference between noPVC - SGTM values and MG-MZ values.
Any advice? I wonder whether this finding is normal or there is something I?ve missed.
Many thanks,
Pilar
Il giorno 15 lug 2020, alle ore 6:00 PM, freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu ha scritto:
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??1. Re: recon all Freesurfer 7.1 on Mac High Sierra fails to run ?????for some subjects (Douglas N. Greve) ??2. Re: mri_fieldsign error (Douglas N. Greve) ??3. Extracting PET Binding Values from Inflated Surface (O'Dell, Ryan)
Message: 1 Date: Wed, 15 Jul 2020 11:12:21 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] recon all Freesurfer 7.1 on Mac High Sierra fails to run for some subjects To: freesurfer@nmr.mgh.harvard.edu Message-ID: beb084b0-fe6b-c8a2-c0a5-e8bcc92769b6@mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
Can you send the recon-all.log file for some of the failures?
On 7/15/2020 10:52 AM, Annelies Vant Westeinde wrote: > ????????External Email - Use Caution > > Dear list, > > As described by others on this list, recon-all with Freesurfer 7.1 on > a Mac operating system seems to fail for around 10% of the subjects. > > The following solution was offered: > > sudo curl > https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long... > ?-o rca-long-tp-init > sudo chmod +x rca-long-tp-init > However, this did not solve the problem for me. > > I re-ran recon-all for the same subjects, but it still failed, some of > them at the following step: > > "####################################### > GCADIR /Applications/freesurfer/average > GCA RB_all_2020-01-02.gca > GCASkull RB_all_withskull_2020_01_02.gca > AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif > GCSDIR /Applications/freesurfer/average > GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs > #######################################" > > It simply stopped running there. > > Others did finish running, but instead got a segmentation fault error. > > What could I do? I have Mac High Sierra. > > > Annelies > > Annelies van't Westeinde?| PHD Candidate > Department of Women's and Children's Health | Karolinska Institutet > 171 77 Solna | Karolinskav?gen 37A > +46 760967499 > annelies.vant.westeinde@ki.se | ki.se http://ki.se/en/startpage > ______________________________________ > Karolinska Institutet ? a medical university > > > > /N?r du skickar e-post till Karolinska Institutet (KI) inneb?r detta > att KI kommer att behandla dina personuppgifter. /H?r finns > information om hur KI behandlar personuppgifter > https://ki.se/medarbetare/integritetsskyddspolicy. > > > /Sending email to Karolinska Institutet (KI) will result in KI > processing your personal data./ You can read more about KI?s > processing of personal data here > https://ki.se/en/staff/data-protection-policy. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer