External Email - Use Caution Ahh great, thank you!
From: Douglas N. Greve<mailto:dgr...@mgh.harvard.edu> Sent: Monday, June 8, 2020 11:43 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] samseg with subfields {Disarmed} Actually, I don't think there is an example. You can run samseg without it running samseg2recon, but once you specify --s, it will run samseg2recon On 6/8/2020 11:22 AM, Sneha Pandya wrote: External Email - Use Caution Ahh perfect, thank you Doug 😊 Can you share an example case when we might have to run samseg2recon post running samseg? Thanks, Sneha From: Douglas N. Greve<mailto:dgr...@mgh.harvard.edu> Sent: Monday, June 8, 2020 11:20 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] samseg with subfields {Disarmed} Oh, sorry, that way of running recon-all will run samseg2recon. Sorry, I lost track of what you are asking On 6/8/2020 10:45 AM, Sneha Pandya wrote: External Email - Use Caution Hi Doug, What do you mean it did not do anything different? What is your samseg command? * Our samseg command was as follow: samseg --t1w /home/ubuntu/T1.nii --sd /home/ubuntu --s subjID --refmode t1w --threads 4 –parallel * Once this command ran successfully it created these o/p folders: coreg, input, mri, scripts * samseg.log file under scripts folder ended with following lines: Started at Fri Jun 5 12:49:50 EDT 2020 Ended at Fri Jun 5 12:51:57 EDT 2020 Samseg2recon-Run-Time-Sec 127 Samseg2recon-Run-Time-Hours 0.04 samseg2recon Done Started at Fri Jun 5 12:27:43 EDT 2020 Ended at Fri Jun 5 12:51:57 EDT 2020 Samseg-Run-Time-Min 24.23 Samseg-Run-Time-Hours 0.40 Thank you, Sneha From: Douglas N. Greve<mailto:dgr...@mgh.harvard.edu> Sent: Monday, June 8, 2020 10:08 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] samseg with subfields {Disarmed} On 6/5/2020 4:47 PM, Sneha Pandya wrote: External Email - Use Caution Thank you Doug. it is not run by default * When I ran “samseg2recon –s subject” after running samseg, it did not do anything different, am I missing anything? What do you mean it did not do anything different? What is your samseg command? * Yes, a lot of file names changed. You should look at the seg.stats file * We did not get seg.stats as an output file when we ran 2019 dev version. We just got samseg.stats under subject/mri/samseg folder. In that case which file should we consider, or something went wrong if it did not generate this file. the samseg.stats file has been renamed to seg.stats Besides, when we ran samseg in 2019 we had used mri/T1.mgz file as an input. Will this be a problem based on your suggestion in MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65310.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_freesurfer-40nmr.mgh.harvard.edu_msg65310.html&d=DwMD-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=AEsux002jQ5JzIPYIcsXKAuQmrt-1dubP8ZVldIiOrE&m=un8Achn1Kt93JCywHWWuT6jklJQN9oHoIkuwkrPoxZs&s=qZGTSXTP2Z20WAcwAP2PqaGmpK9af6Is_k_VrittVlk&e=> * Should we rerun our subjects with orig.mgz or with raw dicom or nifti file? Use the orig.mgz, not the T1.mgz. file format is unimportant * Thank you, Sneha From: Douglas N. Greve<mailto:dgr...@mgh.harvard.edu> Sent: Friday, June 5, 2020 4:05 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] samseg with subfields {Disarmed} On 6/5/2020 3:54 PM, Sneha Pandya wrote: External Email - Use Caution Dear Dough, Is samseg2recon run by default when we run just samseg command? After samseg is completed it displays towards the end samseg2recon run time in sec and hours, right before computation time of samseg as below. If it is called by samseg command itself there would be no need to run samseg2recon separately after samseg command right unless it is doing something in addition? Started at Fri Jun 5 12:49:50 EDT 2020 Ended at Fri Jun 5 12:51:57 EDT 2020 Samseg2recon-Run-Time-Sec 127 Samseg2recon-Run-Time-Hours 0.04 samseg2recon Done Started at Fri Jun 5 12:27:43 EDT 2020 Ended at Fri Jun 5 12:51:57 EDT 2020 Samseg-Run-Time-Min 24.23 Samseg-Run-Time-Hours 0.40 it is not run by default. I had ran few subjects with samseg from Freesurfer dev version in Oct of 2019 and compared it with samseg version from Freesurfer v7.1.0 and realized that some file names are different. Samseg from dev version I ran in 2019 created file t1w_biasCorrected.nii, t1w_biasField.nii, t1w_crispSegmentation.nii names under saubject/mri/samseg directory and Freesurfer v7.1.0 creates mode01_bias_corrected.mgz, mode01_bias_field.mgz, seg.mgz files. I assume these files should be comparable across these two versions right? Also, I do not see seg.stats file when I ran with dev version in 2019. Which stat file am I suppose to consider in lieu of seg.stats file when I ran with 2019 dev version? Yes, a lot of file names changed. You should look at the seg.stats file Besides, when we ran samseg in 2019 we had used mri/T1.mgz file as an input. Will this be a problem based on your suggestion in MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65310.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_freesurfer-40nmr.mgh.harvard.edu_msg65310.html&d=DwMD-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=AEsux002jQ5JzIPYIcsXKAuQmrt-1dubP8ZVldIiOrE&m=un8Achn1Kt93JCywHWWuT6jklJQN9oHoIkuwkrPoxZs&s=qZGTSXTP2Z20WAcwAP2PqaGmpK9af6Is_k_VrittVlk&e=> Thank you, Sneha From: Douglas N. Greve<mailto:dgr...@mgh.harvard.edu> Sent: Tuesday, May 5, 2020 11:38 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] samseg with subfields In theory it is possible, though I don't know if it is better or worse. You can run samseg, then run samseg2recon (this creates a folder that looks like it was created by recon-all), then run subfields on that folder On 5/5/2020 10:45 AM, Sneha Pandya wrote: External Email - Use Caution Dear experts, I want to revisit if anyone has ran subfield analysis just by running samseg? If it is possible is it as reliable as from running regular routine with “-all” recon-all flag? Thank you, Sneha From: Sneha Pandya Sent: Thursday, April 30, 2020 4:15 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: samseg with subfields Dear experts, Is it possible to run subfield analysis (hippcampal subfields, amygdalar, thalamic nuclei, and brainstem structures) when we only run samseg on our dataset? 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