External Email - Use Caution
Hi,
I’m testing mri_sclimbic_seg in the new FS version (7.3.2). My structurals are 0.8mm isotropic, so I’m adding the —conform flag, but still get this error:
[cid:6758653C-0371-4C06-8D50-100648474ED0]
Any ideas? And, BTW, I had to set the environmental variable HDF_USE_FILE_LOCKING to FALSE to get the tool running. Perhaps a tip to add to the wiki, if not people can now see it here.
Thanks for your great work! Cheers, Markus
Markus Handal Sneve, Ph.D. Center for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo
This is actually a bug :(. You can get around it by feeding it a "conformed" volume, but you are going to run into another problem with another bug. We are working to fix them. I think we should have a fix in a day or so.
On 9/21/2022 4:17 PM, Markus Handal Sneve wrote:
External Email - Use Caution
Hi,
I’m testing mri_sclimbic_seg in the new FS version (7.3.2). My structurals are 0.8mm isotropic, so I’m adding the —conform flag, but still get this error:
Any ideas? And, BTW, I had to set the environmental variable HDF_USE_FILE_LOCKING to FALSE to get the tool running. Perhaps a tip to add to the wiki, if not people can now see it here.
Thanks for your great work! Cheers, Markus
Markus Handal Sneve, Ph.D. Center for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Markus,
This bug has been fixedhttps://github.com/freesurfer/freesurfer/commit/ca8ad3faab3a0a2f5e64b22c81232421fe2e53f2 in the dev branch of Freesurfer (FS). You can get the changes in your local copy of FS by either git checkout the mri_sclimbic_seg/mri_sclimbic_seg file into the appropriate subfolder (<FS_install_dir>/python/scripts/mri_sclimbic_seg) where you installed FS or you could simply edit the mri_sclimbic_seg file at that location as in the bug fixhttps://github.com/freesurfer/freesurfer/commit/ca8ad3faab3a0a2f5e64b22c81232421fe2e53f2.
Best, Avnish ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Markus Handal Sneve m.h.sneve@psykologi.uio.no Sent: Wednesday, September 21, 2022 5:17 PM To: Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_sclimbic_seg: --conform not conforming?
External Email - Use Caution
Hi,
I’m testing mri_sclimbic_seg in the new FS version (7.3.2). My structurals are 0.8mm isotropic, so I’m adding the —conform flag, but still get this error:
[cid:6758653C-0371-4C06-8D50-100648474ED0]
Any ideas? And, BTW, I had to set the environmental variable HDF_USE_FILE_LOCKING to FALSE to get the tool running. Perhaps a tip to add to the wiki, if not people can now see it here.
Thanks for your great work! Cheers, Markus
Markus Handal Sneve, Ph.D. Center for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo
I've also attached a new mri_sclimbic_seg. You can copy it to $FREESURFER/python/scripts/mri_sclimbic_seg
On 9/23/2022 10:52 AM, Kumar, Avnish wrote:
Hi Markus,
This bug has beenfixed https://github.com/freesurfer/freesurfer/commit/ca8ad3faab3a0a2f5e64b22c81232421fe2e53f2in the dev branch of Freesurfer (FS). You can get the changes in your local copy of FS by either/git checkout/the /mri_sclimbic_seg/mri_sclimbic_seg /file into the appropriate subfolder (<FS_install_dir>//python/scripts/mri_sclimbic_seg/) where you installed FS or you could simply edit the /mri_sclimbic_seg/ file at that location as in thebug fix https://github.com/freesurfer/freesurfer/commit/ca8ad3faab3a0a2f5e64b22c81232421fe2e53f2.
Best, Avnish
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Markus Handal Sneve m.h.sneve@psykologi.uio.no *Sent:* Wednesday, September 21, 2022 5:17 PM *To:* Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] mri_sclimbic_seg: --conform not conforming?
External Email - Use Caution
Hi,
I’m testing mri_sclimbic_seg in the new FS version (7.3.2). My structurals are 0.8mm isotropic, so I’m adding the —conform flag, but still get this error:
Any ideas? And, BTW, I had to set the environmental variable HDF_USE_FILE_LOCKING to FALSE to get the tool running. Perhaps a tip to add to the wiki, if not people can now see it here.
Thanks for your great work! Cheers, Markus
Markus Handal Sneve, Ph.D. Center for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Doug, Avnish
Implemented the bug fix, but then another error appeared during conforming:
[cid:5D6A862E-5ECF-41F9-97A7-D4DFE7C72060]
Thanks again! Markus
On 25 Sep 2022, at 18:52, Douglas N. Greve <dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU> wrote:
I've also attached a new mri_sclimbic_seg. You can copy it to $FREESURFER/python/scripts/mri_sclimbic_seg
On 9/23/2022 10:52 AM, Kumar, Avnish wrote: Hi Markus,
This bug has been fixedhttps://secure-web.cisco.com/1X10gTeCVThYC4m1v9phgKHGG6GTlwNAH-iZaHczKIBzJ2LsvDtaSfnJWPyEtETch5EjwuM7CvZsddSwHtNPR8Vi-AW4-J8xqJ23_2ZeT215LgIp3UD-xIbfzN3LQTxxF4JsmNcJeh11w6nnjI-RxyK3_GPuFmTNDoyk6tVALxPSlTg1zP8Q1enIcE6E2wjRid6yVCSAiUUHtwBAZOmcc_COO1RX6xRQKP0WANLMSXyGYR_nU6i_K2CVKW6wm_C9L_evAM1MuEpc2T7ZsYuAl8xvymuFw30FXP2iB2l4rR7L3iQW0EGr4DTke61qLDVuR/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fcommit%2Fca8ad3faab3a0a2f5e64b22c81232421fe2e53f2 in the dev branch of Freesurfer (FS). You can get the changes in your local copy of FS by either git checkout the mri_sclimbic_seg/mri_sclimbic_seg file into the appropriate subfolder (<FS_install_dir>/python/scripts/mri_sclimbic_seg) where you installed FS or you could simply edit the mri_sclimbic_seg file at that location as in the bug fixhttps://secure-web.cisco.com/1X10gTeCVThYC4m1v9phgKHGG6GTlwNAH-iZaHczKIBzJ2LsvDtaSfnJWPyEtETch5EjwuM7CvZsddSwHtNPR8Vi-AW4-J8xqJ23_2ZeT215LgIp3UD-xIbfzN3LQTxxF4JsmNcJeh11w6nnjI-RxyK3_GPuFmTNDoyk6tVALxPSlTg1zP8Q1enIcE6E2wjRid6yVCSAiUUHtwBAZOmcc_COO1RX6xRQKP0WANLMSXyGYR_nU6i_K2CVKW6wm_C9L_evAM1MuEpc2T7ZsYuAl8xvymuFw30FXP2iB2l4rR7L3iQW0EGr4DTke61qLDVuR/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fcommit%2Fca8ad3faab3a0a2f5e64b22c81232421fe2e53f2.
Best, Avnish ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Markus Handal Sneve m.h.sneve@psykologi.uio.nomailto:m.h.sneve@psykologi.uio.no Sent: Wednesday, September 21, 2022 5:17 PM To: Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_sclimbic_seg: --conform not conforming?
External Email - Use Caution Hi,
I’m testing mri_sclimbic_seg in the new FS version (7.3.2). My structurals are 0.8mm isotropic, so I’m adding the —conform flag, but still get this error:
<PastedGraphic-2.png>
Any ideas? And, BTW, I had to set the environmental variable HDF_USE_FILE_LOCKING to FALSE to get the tool running. Perhaps a tip to add to the wiki, if not people can now see it here.
Thanks for your great work! Cheers, Markus
Markus Handal Sneve, Ph.D. Center for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1HsgwU0_RCUfDwcbKtj8RkVSHRIk8cQ3EvlmwpmK0a0m7f-...
<mri_sclimbic_seg.txt>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1HsgwU0_RCUfDwcbKtj8RkVSHRIk8cQ3EvlmwpmK0a0m7f-... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/14j6aufKawj7OZF6YrDRMkDgzXG-GpndPRvnsbmFuRG2DOY...https://secure-web.cisco.com/14j6aufKawj7OZF6YrDRMkDgzXG-GpndPRvnsbmFuRG2DOYkrq0wTpP4TYmtzFAtJp-181-4hi6ujJiqZZ6pGPJTCna_LH0HYFl0kCxjICuSSPkF3T9o2kWVk6MQ-UKuULWb1b8effGGREjbNeMjjXRVRFvxq-vte9CpWiRA4jIJzs_d_p7erV4NFM7614UQ6VdEo13YkcDducnEHi1L0ydJAeE3B_VGIlmOnwpYPzNB2hCEXiFf8fneYW_7l-AvofrQDHmzn-QQP4cN4OxZD7pELClU0JHiPdsFIj09yToY4CcNIg7e_zHUEfJz1BeNS/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
freesurfer@nmr.mgh.harvard.edu
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Kumar, Avnish -
Markus Handal Sneve