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Hello, I’m trying to reconstruct an old pipeline that I don’t completely understand (so sorry if this is very elementary or out of date), and one step is to convert the freesurfer T1 segmentation ribbon.mgz to .nii format using mri_convert.
Through freesurfer interface I see the T1 and the segmentation are fine; but mri_convert seems to fail on looking for the T1:
The command (from inside Matlab) is: mri_convert --reslice_like /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz /Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii
Output looks like: mri_convert --reslice_like /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz /Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii reading from /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) reading template info from volume /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii... error: niiRead(): error opening file /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii*****
It is failing to read the T1 and then it does not save the output file. But the input files (T1.nii and ribbon.mgz) are all where they should be. What could I be doing wrong?
thanks, -Andrew
Can you load /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii in freeview? Maybe run ls -l on it?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Andrew Sent: Friday, July 30, 2021 1:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] niiRead: error opening file, through mri_convert
External Email - Use Caution Hello, I’m trying to reconstruct an old pipeline that I don’t completely understand (so sorry if this is very elementary or out of date), and one step is to convert the freesurfer T1 segmentation ribbon.mgz to .nii format using mri_convert.
Through freesurfer interface I see the T1 and the segmentation are fine; but mri_convert seems to fail on looking for the T1:
The command (from inside Matlab) is: mri_convert --reslice_like /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz /Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii Output looks like: mri_convert --reslice_like /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz /Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii reading from /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) reading template info from volume /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii... error: niiRead(): error opening file /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii*****
It is failing to read the T1 and then it does not save the output file. But the input files (T1.nii and ribbon.mgz) are all where they should be. What could I be doing wrong?
thanks, -Andrew
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Bruce, thank you for this response. In fact I had the T1 path wrong despite having read it over and over 20 times.. listing directory contents indeed revealed my error… -andrew
On Jul 30, 2021, at 13:38, Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Can you load /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii in freeview? Maybe run ls -l on it?
From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Andrew Sent: Friday, July 30, 2021 1:44 PM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] niiRead: error opening file, through mri_convert
External Email - Use CautionHello, I’m trying to reconstruct an old pipeline that I don’t completely understand (so sorry if this is very elementary or out of date), and one step is to convert the freesurfer T1 segmentation ribbon.mgz to .nii format using mri_convert.
Through freesurfer interface I see the T1 and the segmentation are fine; but mri_convert seems to fail on looking for the T1:
The command (from inside Matlab) is: mri_convert --reslice_like /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz /Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii
Output looks like: mri_convert --reslice_like /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz /Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii reading from /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) reading template info from volume /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii... error: niiRead(): error opening file /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii*****
It is failing to read the T1 and then it does not save the output file. But the input files (T1.nii and ribbon.mgz) are all where they should be. What could I be doing wrong?
thanks, -Andrew _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1c0lmlF_zpC_h2i8RgbD2UTu3XUfSBquo0-Jtr6xERlpksK... https://secure-web.cisco.com/1c0lmlF_zpC_h2i8RgbD2UTu3XUfSBquo0-Jtr6xERlpksKBDKN0G2mmK5utiVaxelmaYH-I-s3RGz9KDKYEj5s9KlfMxrUdnca2mcxdy6hA1EnP0b1WAkFuuZI5liauHLi4maNLoThdpQm4hAc54Cn7ZhuP-q4HeDF61ng5ofXCmjSfxL-rnwXVXXLUTRq-OG9XpdjVdKckokqqJgW3ZBuT3MrYd47gmk_6eOERu5C8ic3aeIcWGdndo-zq3NNDRY2Pts6tQCwSjbWKJ3qDt7w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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 http://secure-web.cisco.com/1Llqh66rQvsMufa7YCZb28LQ5gI2FTSPEEyTNjho9XbkAyK-... http://secure-web.cisco.com/1Llqh66rQvsMufa7YCZb28LQ5gI2FTSPEEyTNjho9XbkAyK-isOl4-cUGkPV1AFvR2Sc3IW6U5Jt7ima1jYQZRNcwhhJDkn6ucIjQWE6E81hcPeLLXg4cTpwAQ-6_IErSRn8vDpkEFQlQYVzk2igBiroXk-BAWkAB4xzJhmi34CJWLHdnkk_-BPsjdqy07ubmAv9QQmnsx850-W_mWXMVOYnE9P_nAZ1lVSMKS29UgOC3dfL0olNV161h5TAC5lAg2P3TF52sW3bm638D1f3jKg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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.
I’m glad to hear it worked out. We have all done this…. Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Andrew Sent: Monday, August 2, 2021 12:07 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] niiRead: error opening file, through mri_convert
External Email - Use Caution Bruce, thank you for this response. In fact I had the T1 path wrong despite having read it over and over 20 times.. listing directory contents indeed revealed my error… -andrew
On Jul 30, 2021, at 13:38, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote:
Can you load /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii in freeview? Maybe run ls -l on it?
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 Andrew Sent: Friday, July 30, 2021 1:44 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] niiRead: error opening file, through mri_convert
External Email - Use Caution Hello, I’m trying to reconstruct an old pipeline that I don’t completely understand (so sorry if this is very elementary or out of date), and one step is to convert the freesurfer T1 segmentation ribbon.mgz to .nii format using mri_convert.
Through freesurfer interface I see the T1 and the segmentation are fine; but mri_convert seems to fail on looking for the T1:
The command (from inside Matlab) is: mri_convert --reslice_like /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz /Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii Output looks like: mri_convert --reslice_like /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz /Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii reading from /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) reading template info from volume /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii... error: niiRead(): error opening file /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii*****
It is failing to read the T1 and then it does not save the output file. But the input files (T1.nii and ribbon.mgz) are all where they should be. What could I be doing wrong?
thanks, -Andrew _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1c0lmlF_zpC_h2i8RgbD2UTu3XUfSBquo0-Jtr6xERlpksKBDKN0G2mmK5utiVaxelmaYH-I-s3RGz9KDKYEj5s9KlfMxrUdnca2mcxdy6hA1EnP0b1WAkFuuZI5liauHLi4maNLoThdpQm4hAc54Cn7ZhuP-q4HeDF61ng5ofXCmjSfxL-rnwXVXXLUTRq-OG9XpdjVdKckokqqJgW3ZBuT3MrYd47gmk_6eOERu5C8ic3aeIcWGdndo-zq3NNDRY2Pts6tQCwSjbWKJ3qDt7w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1Llqh66rQvsMufa7YCZb28LQ5gI2FTSPEEyTNjho9XbkAyK-isOl4-cUGkPV1AFvR2Sc3IW6U5Jt7ima1jYQZRNcwhhJDkn6ucIjQWE6E81hcPeLLXg4cTpwAQ-6_IErSRn8vDpkEFQlQYVzk2igBiroXk-BAWkAB4xzJhmi34CJWLHdnkk_-BPsjdqy07ubmAv9QQmnsx850-W_mWXMVOYnE9P_nAZ1lVSMKS29UgOC3dfL0olNV161h5TAC5lAg2P3TF52sW3bm638D1f3jKg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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
-
Andrew -
Fischl, Bruce