External Email - Use Caution Hello Elizabeth,
thanks again for reporting this issue. A new version 2.0.1 that hopefully fixes everything is now available on our github platform https://secure-web.cisco.com/15PjI_RM0czhby0YUc6YQAjaxySjo5XDO6Z_9EdsUUjLEmBbW0_sQMGL33vM1dyZCRngtxUacqswXwRAzx-f2-5p7yNc86UOfMrGz8MvbJyH7nOw-gAxfFgmPhYfx00ISvl2Ic5L98Dq48yYt5XI862hKSD8wFyjPbIvK_4UjBk27-6ynXyoTA5zdokSlDI8jQX6iwMEYS6z3wa7RzH_lE-U8qhRZlSoCDZAEUQYJG6w2Y5yiEgGLL-YCFIMeHuvWuwbLcPx7anC0gTdM-0p7X_SVL7EwyowOQgjL9utlse8niOcO0ZpEx6cfeuyDEI_L/https%3A%2F%2Fgithub.com%2FDeep-MI%2Ffsqc, and can be downloaded/installed from there or via pip. Best regards, Kersten On Tue, 2023-10-17 at 17:51 +0200, Diers, Kersten wrote: > Hello, > > and thanks for the confirmation. > > Then I'll try to make the toolbox run with these image dimensions / > resolutions also; will take approximately one week, I guess. > > Best regards, > > Kersten > > On Mon, 2023-10-16 at 21:15 +0000, Elizabeth Haris wrote: > > CAUTION: This email originated from outside of DZNE. Do not click > > links or open attachments unless you recognize the sender and know > > the content is safe. > > ACHTUNG: Dies ist eine externe E-Mail, bitte seien Sie vorsichtig > > beim Anklicken von Links oder Öffnen von Anhängen > > > > External Email - Use Caution > > Hi Kersten, > > > > Ah yes, that would be it. I am using data from a 7T scanner, so > > wanted it to be processed at the best resolution possible, hence > > using the -cm command. > > > > Many thanks, > > Elizabeth > > > > From:freesurfer-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Diers, > > Kersten /DZNE <kersten.di...@dzne.de> > > Date: Tuesday, 17 October 2023 at 12:12 am > > To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] [WARNING: ATTACHMENT(S) MAY CONTAIN > > MALWARE]Re: Stools error query > > External Email - Use Caution > > Hello Elizabeth, > > > > thank you for giving the new version of the toolbox a try as well. > > > > Since the error persists: my suspicion is that not all of your > > images have the canonical ("FreeSurfer - conformed") dimensions of > > 256 x 256 x 256 voxels, maybe because they were processed with > > FreeSurfer's high-resolution processing variant / the recon-all ... > > -cm ... command? > > > > If that's indeed the case, I will try to update the toolbox to be > > able to deal with images that have dimensions different from 256 > > x 256 x 256. > > > > Best regards, > > > > Kersten > > > > On Sun, 2023-10-15 at 23:37 +0000, Elizabeth Haris wrote: > > > CAUTION: This email originated from outside of DZNE. Do not click > > > links or open attachments unless you recognize the sender and > > > know the content is safe. > > > ACHTUNG: Dies ist eine externe E-Mail, bitte seien Sie vorsichtig > > > beim Anklicken von Links oder Öffnen von Anhängen > > > > > > External Email - Use Caution > > > Hi Kersten, > > > > > > I ran the fsqc, but am still getting the same error for 45 of my > > > 72 participants (outlined below). I’ve attached the logfile and > > > the csv output if that helps. > > > > > > Starting fsqc for subject 630 at 2023-10-16 10:09 AEDT > > > Computing white and gray matter SNR for orig.mgz ... > > > ERROR: SNR computation failed for 630 > > > Reason: index 256 is out of bounds for axis 2 with size 256 > > > Computing white and gray matter SNR for norm.mgz ... > > > ERROR: SNR computation failed for 630 > > > Reason: index 256 is out of bounds for axis 2 with size 256 > > > > > > Thanks, > > > Elizabeth > > > > > > From:freesurfer-boun...@nmr.mgh.harvard.edu > > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Diers, > > > Kersten /DZNE <kersten.di...@dzne.de> > > > Date: Thursday, 12 October 2023 at 10:06 pm > > > To: freesurfer@nmr.mgh.harvard.edu > > > <freesurfer@nmr.mgh.harvard.edu> > > > Subject: Re: [Freesurfer] Stools error query > > > External Email - Use Caution > > > Hi Elizabeth, > > > > > > the qatools / fsqc tools have evolved quite a bit since their > > > inclusion in FS 7.1. > > > > > > Would it be possible for you to try their newest version, > > > available from MailScanner has detected a possible fraud attempt > > > from "secure-web.cisco.com" claiming to be > > > https://secure-web.cisco.com/15PjI_RM0czhby0YUc6YQAjaxySjo5XDO6Z_9EdsUUjLEmBbW0_sQMGL33vM1dyZCRngtxUacqswXwRAzx-f2-5p7yNc86UOfMrGz8MvbJyH7nOw-gAxfFgmPhYfx00ISvl2Ic5L98Dq48yYt5XI862hKSD8wFyjPbIvK_4UjBk27-6ynXyoTA5zdokSlDI8jQX6iwMEYS6z3wa7RzH_lE-U8qhRZlSoCDZAEUQYJG6w2Y5yiEgGLL-YCFIMeHuvWuwbLcPx7anC0gTdM-0p7X_SVL7EwyowOQgjL9utlse8niOcO0ZpEx6cfeuyDEI_L/https%3A%2F%2Fgithub.com%2FDeep-MI%2Ffsqc? > > > > > > Thanks, > > > > > > Kersten > > > > > > On Thu, 2023-10-12 at 00:23 +0000, Elizabeth Haris wrote: > > > > CAUTION: This email originated from outside of DZNE. Do not > > > > click links or open attachments unless you recognize the sender > > > > and know the content is safe. > > > > ACHTUNG: Dies ist eine externe E-Mail, bitte seien Sie > > > > vorsichtig beim Anklicken von Links oder Öffnen von Anhängen > > > > > > > > External Email - Use Caution > > > > Hi there, > > > > > > > > I am running into a problem when using qatools.py to qa my > > > > recon-all. Some of my participants process ok, but with others > > > > I get the error below. Any advice on what to do to address > > > > this? > > > > > > > > Many thanks, > > > > Elizabeth > > > > > > > > ERROR: > > > > > > > > Computing white and gray matter SNR for orig.mgz ... > > > > Traceback (most recent call last): > > > > File > > > > "/Applications/freesurfer_v7.1.0/python/scripts/qatools.py", > > > > line 17, in <module> > > > > qatoolspython.run_qatools(subjects_dir, output_dir, > > > > subjects, shape, screenshots, fornix, outlier, outlier_table) > > > > File > > > > "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/ > > > > qatoolspython.py", line 883, in run_qatools > > > > _do_qatools(subjects_dir, output_dir, subjects, shape, > > > > screenshots, fornix, outlier, outlier_table) > > > > File > > > > "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/ > > > > qatoolspython.py", line 663, in _do_qatools > > > > wm_snr_orig, gm_snr_orig = checkSNR(subjects_dir, subject, > > > > SNR_AMOUT_EROSION, ref_image="orig.mgz") > > > > File > > > > "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/ > > > > checkSNR.py", line 83, in checkSNR > > > > b_wm_data[x,y,z] = 1 > > > > IndexError: index 256 is out of bounds for axis 2 with size 256 > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > > > MailScanner has detected a possible fraud attempt from "secure- > > > > web.cisco.com" claiming to be > > > > https://secure-web.cisco.com/1fR5x7OiI-iJ2l-1fVXR55Xrs09BX51peAeelfWUR9X23d7YA8FG6TBHTcIGIN1VX_4-__gekyMMt2lt9vqJoDULdiXS8NRVhuq4VHwkDxAjlaFs-EsuWcAqv1gP9N4xBPpMZQumnSuLJxuz1yiFMzJ-76rJ-_MuFe9lv86bx38rcuRNIGs4yxGE2eEOgLDrHaRMBc1lg2NTHr3goUAPqmlQCZCcQn0mWi8kjeXJvdDIeftNQTjoLZ7YfWw2e05FMdAhCCUUvDtKgCVWU_TapksaM3XBcH39YVwgwniXpjN2KtyIW2EWFi196c5l_ppo1/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > > 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 mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > MailScanner has detected a possible fraud attempt from "secure- > > > web.cisco.com" claiming to be > > > https://secure-web.cisco.com/1fR5x7OiI-iJ2l-1fVXR55Xrs09BX51peAeelfWUR9X23d7YA8FG6TBHTcIGIN1VX_4-__gekyMMt2lt9vqJoDULdiXS8NRVhuq4VHwkDxAjlaFs-EsuWcAqv1gP9N4xBPpMZQumnSuLJxuz1yiFMzJ-76rJ-_MuFe9lv86bx38rcuRNIGs4yxGE2eEOgLDrHaRMBc1lg2NTHr3goUAPqmlQCZCcQn0mWi8kjeXJvdDIeftNQTjoLZ7YfWw2e05FMdAhCCUUvDtKgCVWU_TapksaM3XBcH39YVwgwniXpjN2KtyIW2EWFi196c5l_ppo1/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > 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 mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://secure-web.cisco.com/1fR5x7OiI-iJ2l-1fVXR55Xrs09BX51peAeelfWUR9X23d7YA8FG6TBHTcIGIN1VX_4-__gekyMMt2lt9vqJoDULdiXS8NRVhuq4VHwkDxAjlaFs-EsuWcAqv1gP9N4xBPpMZQumnSuLJxuz1yiFMzJ-76rJ-_MuFe9lv86bx38rcuRNIGs4yxGE2eEOgLDrHaRMBc1lg2NTHr3goUAPqmlQCZCcQn0mWi8kjeXJvdDIeftNQTjoLZ7YfWw2e05FMdAhCCUUvDtKgCVWU_TapksaM3XBcH39YVwgwniXpjN2KtyIW2EWFi196c5l_ppo1/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
