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 ha scritto:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@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@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@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: 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