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Dear FreeSurfer Developers,
I am now working on the analysis of MRI images with the voxel resolution less than 0.2mm3. I read your webpage about submillimeter reconstruction, https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard...., which said Freesurfer 6.0 works well for voxel sizes 0.75 mm3, and inputs with 0.5 mm3 voxels or below will have a brainmask failure (we are working on it!). So I am writing to ask for your help about the reconstruction with freesurfer. I would like to know, have you solved the higher resolution problem in the new version v6.0? Could I use it to analyze the cortical thickness of these MRI images now? If not, is there any other way to help processing these MRI images and we could run freesurfer step by step for evaluation? Look forward to your timely help! Thanks a lot in advance! yours sincerely, Rui
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Dear Rui,
there is no hard limit to resolution. Your data should have a decent quality (no motion artifacts, high SNR, high contrast, isotropic resolution) and the suggestions of the submillimeter reconstruction should give good results. I have run FreeSurfer on 250 µm human data with reasonable, but improvable results. Still working on it.
From my experience skull stripping seems to fail using data with higher resolution than 0.7 mm. Therefore, I suggest you to follow the first steps of the guideline: https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon to create a low resolution brainmask, upsampling, and applying it on your high resolution data. Apart from that everything should run smoothly.
Expect it to run for a few weeks, especially the topological fixation and autorecon3 will take time.
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Nian Rui Gesendet: Donnerstag, 18. Oktober 2018 00:50 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Ask for your help about freesurfer submillimeter reconstruction! Priorität: Hoch
External Email - Use Caution Dear FreeSurfer Developers,
I am now working on the analysis of MRI images with the voxel resolution less than 0.2mm3. I read your webpage about submillimeter reconstruction, https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard...., which said Freesurfer 6.0 works well for voxel sizes 0.75 mm3, and inputs with 0.5 mm3 voxels or below will have a brainmask failure (we are working on it!). So I am writing to ask for your help about the reconstruction with freesurfer. I would like to know, have you solved the higher resolution problem in the new version v6.0? Could I use it to analyze the cortical thickness of these MRI images now? If not, is there any other way to help processing these MRI images and we could run freesurfer step by step for evaluation? Look forward to your timely help! Thanks a lot in advance! yours sincerely, Rui
External Email - Use Caution
Dear FreeSurfer Developers,
I am now working on the analysis of MRI images with freesurfer. I read your webpage about submillimeter reconstruction, https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard..... However, I found, when I set the expert.opt wrongly, I cannot update it again. Every time I try to update it with the following command,
recon-all -all -s 172332recon -hires -i 172332_3T_T1w_MPR1.nii.gz_result.nrrd.nii.gz -expert /fileserver/projects/Nian/New3DEDSR20181006/result/1/expert.opt
The system will show the error as follows,
INFO: hi-res volumes are conformed to the min voxel size ERROR: cannot find /fileserver/projects/Nian/New3DEDSR20181006/result/1/expert.opt Linux chai 3.10.0-862.14.4.el7.x86_64 #1 SMP Wed Sep 26 15:12:11 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 172332recon exited with ERRORS at Fri Oct 19 18:12:40 EDT 2018 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I already deleted all the previous produced files and directory and killed and cleared opt with the commands shown in your website, it still did not work. Could you help me with it? Look forward to your timely help! Thanks a lot in advance! yours sincerely,
________________________________ 发件人: Nian Rui 发送时间: 2018年10月18日 6:50 收件人: freesurfer@nmr.mgh.harvard.edu 主题: Ask for your help about freesurfer submillimeter reconstruction!
Dear FreeSurfer Developers,
I am now working on the analysis of MRI images with the voxel resolution less than 0.2mm3. I read your webpage about submillimeter reconstruction, https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard...., which said Freesurfer 6.0 works well for voxel sizes 0.75 mm3, and inputs with 0.5 mm3 voxels or below will have a brainmask failure (we are working on it!). So I am writing to ask for your help about the reconstruction with freesurfer. I would like to know, have you solved the higher resolution problem in the new version v6.0? Could I use it to analyze the cortical thickness of these MRI images now? If not, is there any other way to help processing these MRI images and we could run freesurfer step by step for evaluation? Look forward to your timely help! Thanks a lot in advance! yours sincerely, Rui
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Could you send the output of the following command, please:
ls -l /fileserver/projects/Nian/New3DEDSR20181006/result/1/expert.opt
Tim
On October 20, 2018 at 12:22 AM Nian Rui nianrui_80@hotmail.com wrote:
External Email - Use CautionDear FreeSurfer Developers,
I am now working on the analysis of MRI images with freesurfer. I read your webpage about submillimeter reconstruction, https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard..... However, I found, when I set the expert.opt wrongly, I cannot update it again. Every time I try to update it with the following command,
recon-all -all -s 172332recon -hires -i 172332_3T_T1w_MPR1.nii.gz_result.nrrd.nii.gz -expert /fileserver/projects/Nian/New3DEDSR20181006/result/1/expert.opt
The system will show the error as follows,
INFO: hi-res volumes are conformed to the min voxel size ERROR: cannot find /fileserver/projects/Nian/New3DEDSR20181006/result/1/expert.opt Linux chai 3.10.0-862.14.4.el7.x86_64 #1 SMP Wed Sep 26 15:12:11 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 172332recon exited with ERRORS at Fri Oct 19 18:12:40 EDT 2018 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I already deleted all the previous produced files and directory and killed and cleared opt with the commands shown in your website, it still did not work. Could you help me with it? Look forward to your timely help! Thanks a lot in advance! yours sincerely,
发件人: Nian Rui 发送时间: 2018年10月18日 6:50 收件人: freesurfer@nmr.mgh.harvard.edu 主题: Ask for your help about freesurfer submillimeter reconstruction!
Dear FreeSurfer Developers,
I am now working on the analysis of MRI images with the voxel resolution less than 0.2mm3. I read your webpage about submillimeter reconstruction, https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard...., which said Freesurfer 6.0 works well for voxel sizes 0.75 mm3, and inputs with 0.5 mm3 voxels or below will have a brainmask failure (we are working on it!). So I am writing to ask for your help about the reconstruction with freesurfer. I would like to know, have you solved the higher resolution problem in the new version v6.0? Could I use it to analyze the cortical thickness of these MRI images now? If not, is there any other way to help processing these MRI images and we could run freesurfer step by step for evaluation? Look forward to your timely help! Thanks a lot in advance! yours sincerely, Rui _______________________________________________ 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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Nian Rui -
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