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 | Karolinskavägen 37A +46 760967499 annelies.vant.westeinde@ki.se | ki.sehttp://ki.se/en/startpage ______________________________________ Karolinska Institutet – a medical university
När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifterhttps://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 herehttps://ki.se/en/staff/data-protection-policy.
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 | Karolinskavägen 37A +46 760967499 annelies.vant.westeinde@ki.se | ki.se http://ki.se/en/startpage ______________________________________ Karolinska Institutet – a medical university
/När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. /Här 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
External Email - Use Caution
Hi, I am attaching some recon-all log files as requested (hope it works like that).
Thanks!
Annelies van't Westeinde | PHD Candidate Department of Women's and Children's Health | Karolinska Institutet 171 77 Solna | Karolinskavägen 37A +46 760967499 annelies.vant.westeinde@ki.se | ki.sehttp://ki.se/en/startpage ______________________________________ Karolinska Institutet – a medical university ________________________________ From: Annelies Vant Westeinde Sent: 15 July 2020 16:52 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: recon all Freesurfer 7.1 on Mac High Sierra fails to run for some subjects
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 | Karolinskavägen 37A +46 760967499 annelies.vant.westeinde@ki.se | ki.sehttp://ki.se/en/startpage ______________________________________ Karolinska Institutet – a medical university
När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifterhttps://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 herehttps://ki.se/en/staff/data-protection-policy.
This is a known problem with mri_cc on Mac. Any day now we will release 7.1.1 that will include a patch to fix this.
On 7/21/2020 7:05 AM, Annelies Vant Westeinde wrote:
External Email - Use Caution
Hi, I am attaching some recon-all log files as requested (hope it works like that).
Thanks!
Annelies van't Westeinde | PHD Candidate Department of Women's and Children's Health | Karolinska Institutet 171 77 Solna | Karolinskavägen 37A +46 760967499 annelies.vant.westeinde@ki.se | ki.se http://ki.se/en/startpage ______________________________________ Karolinska Institutet – a medical university
*From:* Annelies Vant Westeinde *Sent:* 15 July 2020 16:52 *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* recon all Freesurfer 7.1 on Mac High Sierra fails to run for some subjects 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 | Karolinskavägen 37A +46 760967499 annelies.vant.westeinde@ki.se | ki.se http://ki.se/en/startpage ______________________________________ Karolinska Institutet – a medical university
/När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. /Här 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
freesurfer@nmr.mgh.harvard.edu
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Annelies Vant Westeinde -
Douglas N. Greve