External Email - Use Caution
Dear Freesurfer experts,
I tried to run Recon-all on a T1 series .nii file. A error occurred: "ERROR: input(s) cannot have multiple frames!". I tried to google the method of converting multi frame dicom to single frame dicom. I found software of "dicom2" stated that it could perform the conversion but their manual guide are too hard for me to understand. May I know there are any easier method to perform the conversion? Thank you.
Regards
Frank
---------------------------
FRANK C Y CHAU
Research assistant
Division of Neurology
Department of Medicine
Tel: +852 6340 2553
Fax: 2872 5828
E-mail : cyfrank@hku.hkmailto:cyfrank@hku.hk
Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong
Hi Frank
Do you know why there are multiple frames? What kind of MRI acquisition are you trying to use as input? Most standard T1-weighted series only have a single frame Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Frank Chau Sent: Monday, August 2, 2021 3:49 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Jacky Lee cylee10@gmail.com; Jacky LEE lcy339@ha.org.hk Subject: [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all
External Email - Use Caution
Dear Freesurfer experts,
I tried to run Recon-all on a T1 series .nii file. A error occurred: "ERROR: input(s) cannot have multiple frames!". I tried to google the method of converting multi frame dicom to single frame dicom. I found software of "dicom2" stated that it could perform the conversion but their manual guide are too hard for me to understand. May I know there are any easier method to perform the conversion? Thank you.
Regards
Frank
---------------------------
FRANK C Y CHAU
Research assistant
Division of Neurology
Department of Medicine
Tel: +852 6340 2553
Fax: 2872 5828
E-mail : cyfrank@hku.hkmailto:cyfrank@hku.hk
Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong
External Email - Use Caution
Dear Bruce,
I have briefly read a article about multiple frames DICOM. As my understanding, it can reduce the amount of data repetition and decreases the time required to read and parse DICOM studies.
Yes, I want to use T1-weighted series as input. I have converted a DICOM series, which the name of the series is "SAG T1 MPRAGE (INC UPPERCX AS MUCH)", to Nifti format. When I input the Nifti T1 file. The multiple frames error occurred.
Below are log record:
--------------------------------------------------------------------------------------- PFCs-MacBook-Pro:T1 PFC$ recon-all -all -i 101.nii -s 101 Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /Users/PFC/SPM12/T1 Actual FREESURFER_HOME /Applications/freesurfer Darwin PFCs-MacBook-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Mon May 3 20:41:19 PDT 2021; root:xnu-4903.278.68~1/RELEASE_X86_64 x86_64 /Users/PFC/SPM12/T1/101 \n mri_convert /Users/PFC/SPM12/T1/101.nii /Users/PFC/SPM12/T1/101/mri/orig/001.mgz \n mri_convert.bin /Users/PFC/SPM12/T1/101.nii /Users/PFC/SPM12/T1/101/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Users/PFC/SPM12/T1/101.nii... TR=7.24, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.135649, -0.98975, -0.0446586) j_ras = (0.0870012, -0.0330015, 0.995661) k_ras = (0.98693, 0.138946, -0.0816328) writing to /Users/PFC/SPM12/T1/101/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sat Jul 31 18:01:46 HKT 2021 Found 1 runs /Users/PFC/SPM12/T1/101/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /Users/PFC/SPM12/T1/101/mri/orig/001.mgz has 2 frames Darwin PFCs-MacBook-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Mon May 3 20:41:19 PDT 2021; root:xnu-4903.278.68~1/RELEASE_X86_64 x86_64
recon-all -s 101 exited with ERRORS at Sat Jul 31 18:01:48 HKT 2021
For more details, see the log file /Users/PFC/SPM12/T1/101/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1x3qv0aS51XJZ0WhLEKzibrZlVCLHeCZ6fKtPNfkMrRcbufS... ---------------------------------------------------------------------------------------
Regards
Frank
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce BFISCHL@MGH.HARVARD.EDU Sent: 03 August 2021 03:56:31 To: freesurfer@nmr.mgh.harvard.edu Cc: Jacky Lee; Jacky LEE Subject: Re: [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all
Hi Frank
Do you know why there are multiple frames? What kind of MRI acquisition are you trying to use as input? Most standard T1-weighted series only have a single frame Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Frank Chau Sent: Monday, August 2, 2021 3:49 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Jacky Lee cylee10@gmail.com; Jacky LEE lcy339@ha.org.hk Subject: [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all
External Email - Use Caution
Dear Freesurfer experts,
I tried to run Recon-all on a T1 series .nii file. A error occurred: "ERROR: input(s) cannot have multiple frames!". I tried to google the method of converting multi frame dicom to single frame dicom. I found software of "dicom2" stated that it could perform the conversion but their manual guide are too hard for me to understand. May I know there are any easier method to perform the conversion? Thank you.
Regards
Frank
---------------------------
FRANK C Y CHAU
Research assistant
Division of Neurology
Department of Medicine
Tel: +852 6340 2553
Fax: 2872 5828
E-mail : cyfrank@hku.hkmailto:cyfrank@hku.hk
Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong
But do you know why it has multiple frames? We collect multi-echo T1 MPRAGEs that will have multiple frames. We then reduce it to one frame by computing the RMS across frames (actually the scanner can output a separate RMS series). Check to see whether you got an RMS series in their. If not, check with whoever collected the data to find out why it has multiple frames.
On 8/2/2021 4:08 PM, Frank Chau wrote:
External Email - Use Caution
Dear Bruce,
I have briefly read a article about multiple framesDICOM. As my understanding, it can reduce the amount of data repetition and decreases the time required to read and parse DICOM studies.
Yes, I want to use T1-weighted seriesas input. I have converted a DICOM series, which the name of the series is "SAG T1 MPRAGE (INC UPPERCX AS MUCH)", to Nifti format. When I input the Nifti T1 file. The multiple frameserror occurred.
Below are log record:
PFCs-MacBook-Pro:T1 PFC$ recon-all -all -i101.nii -s101
Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /Users/PFC/SPM12/T1
Actual FREESURFER_HOME /Applications/freesurfer
Darwin PFCs-MacBook-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Mon May3 20:41:19 PDT 2021; root:xnu-4903.278.68~1/RELEASE_X86_64 x86_64
/Users/PFC/SPM12/T1/101
\n mri_convert /Users/PFC/SPM12/T1/101.nii /Users/PFC/SPM12/T1/101/mri/orig/001.mgz \n
mri_convert.bin /Users/PFC/SPM12/T1/101.nii /Users/PFC/SPM12/T1/101/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Users/PFC/SPM12/T1/101.nii...
TR=7.24, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.135649, -0.98975, -0.0446586)
j_ras = (0.0870012, -0.0330015, 0.995661)
k_ras = (0.98693, 0.138946, -0.0816328)
writing to /Users/PFC/SPM12/T1/101/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Jul 31 18:01:46 HKT 2021
Found 1 runs
/Users/PFC/SPM12/T1/101/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/PFC/SPM12/T1/101/mri/orig/001.mgz has 2 frames
Darwin PFCs-MacBook-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Mon May3 20:41:19 PDT 2021; root:xnu-4903.278.68~1/RELEASE_X86_64 x86_64
recon-all -s 101 exited with ERRORS at Sat Jul 31 18:01:48 HKT 2021
For more details, see the log file /Users/PFC/SPM12/T1/101/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Regards
Frank
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce BFISCHL@MGH.HARVARD.EDU *Sent:* 03 August 2021 03:56:31 *To:* freesurfer@nmr.mgh.harvard.edu *Cc:* Jacky Lee; Jacky LEE *Subject:* Re: [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all
Hi Frank
Do you know why there are multiple frames? What kind of MRI acquisition are you trying to use as input? Most standard T1-weighted series only have a single frame Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Frank Chau *Sent:* Monday, August 2, 2021 3:49 PM *To:* freesurfer@nmr.mgh.harvard.edu *Cc:* Jacky Lee cylee10@gmail.com; Jacky LEE lcy339@ha.org.hk *Subject:* [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all
* External Email - Use Caution *
Dear Freesurfer experts,
I tried to run Recon-all on a T1 series .nii file. A error occurred: "ERROR: input(s) cannot have multiple frames!". I tried to google the method of converting multi frame dicom to single frame dicom. I found software of "dicom2" stated that it could perform the conversion but their manual guide are too hard for me to understand. May I know there are any easier method to perform the conversion? Thank you.
Regards
Frank
*FRANK C Y CHAU*
Research assistant
Division of Neurology
Department of Medicine
Tel: +852 6340 2553
Fax: 2872 5828
E-mail : cyfrank@hku.hk mailto:cyfrank@hku.hk
Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Maybe for post-processing in case you have multi frames, you can merge all of them (multi-echo MPRages) and then take the RMS to get one 3D volume. Ahmed
Ahmed A. Bahrani, Ph.D., Sanders-Brown Center on Aging University of Kentucky
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Tuesday, August 3, 2021 9:26 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all
CAUTION: External Sender
But do you know why it has multiple frames? We collect multi-echo T1 MPRAGEs that will have multiple frames. We then reduce it to one frame by computing the RMS across frames (actually the scanner can output a separate RMS series). Check to see whether you got an RMS series in their. If not, check with whoever collected the data to find out why it has multiple frames.
On 8/2/2021 4:08 PM, Frank Chau wrote:
External Email - Use Caution
Dear Bruce,
I have briefly read a article about multiple frames DICOM. As my understanding, it can reduce the amount of data repetition and decreases the time required to read and parse DICOM studies.
Yes, I want to use T1-weighted series as input. I have converted a DICOM series, which the name of the series is "SAG T1 MPRAGE (INC UPPERCX AS MUCH)", to Nifti format. When I input the Nifti T1 file. The multiple frames error occurred.
Below are log record:
---------------------------------------------------------------------------------------
PFCs-MacBook-Pro:T1 PFC$ recon-all -all -i 101.nii -s 101
Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /Users/PFC/SPM12/T1
Actual FREESURFER_HOME /Applications/freesurfer
Darwin PFCs-MacBook-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Mon May 3 20:41:19 PDT 2021; root:xnu-4903.278.68~1/RELEASE_X86_64 x86_64
/Users/PFC/SPM12/T1/101
\n mri_convert /Users/PFC/SPM12/T1/101.nii /Users/PFC/SPM12/T1/101/mri/orig/001.mgz \n
mri_convert.bin /Users/PFC/SPM12/T1/101.nii /Users/PFC/SPM12/T1/101/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Users/PFC/SPM12/T1/101.nii...
TR=7.24, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.135649, -0.98975, -0.0446586)
j_ras = (0.0870012, -0.0330015, 0.995661)
k_ras = (0.98693, 0.138946, -0.0816328)
writing to /Users/PFC/SPM12/T1/101/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Jul 31 18:01:46 HKT 2021
Found 1 runs
/Users/PFC/SPM12/T1/101/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/PFC/SPM12/T1/101/mri/orig/001.mgz has 2 frames
Darwin PFCs-MacBook-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Mon May 3 20:41:19 PDT 2021; root:xnu-4903.278.68~1/RELEASE_X86_64 x86_64
recon-all -s 101 exited with ERRORS at Sat Jul 31 18:01:48 HKT 2021
For more details, see the log file /Users/PFC/SPM12/T1/101/scripts/recon-all.log
To report a problem, see http://secure-web.cisco.com/1ARLUAXWFpvPqkvHHhdhgZfwGYwa-W5rxZHYll2077_CtHzn...https://secure-web.cisco.com/1H2C0UAM0EUoMNQV-mYoPKmXHPmnOQCgc8hmUpDAb4Tewgx2uA6bLIHyXM85tjLc1G5g3LQweJpn121jzCWWpgUVmIhVjZYAJEsMSQWkeYtg8r8y0XbVVoSTQKz7k9U-Uu8BVuYpSUAIhLXQlQxH_xTY1uIoi49a0WFi77_bmaThL844CMg9YP7PzqCRNM1TcZGAR1ioVHIFPgKTeUnaaAFQvVKIk9TZDfNYn3k5KkEfxCiTmB1CRiD0ll8IZg0ZSuaV9JZmUbeTiKNpKUaxrsw/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252FBugReporting%26data%3D04%257C01%257Cahmed.bahrani%2540uky.edu%257C69866f35c2194c96813f08d9568258f4%257C2b30530b69b64457b818481cb53d42ae%257C0%257C0%257C637635940099926429%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DFQ0AeEcwfJ%252BQfRxZvUuwN3i0P9%252BpiYV9R47tqV5hU%252Fw%253D%26reserved%3D0
---------------------------------------------------------------------------------------
Regards
Frank
________________________________ 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 Fischl, Bruce BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@MGH.HARVARD.EDU Sent: 03 August 2021 03:56:31 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Cc: Jacky Lee; Jacky LEE Subject: Re: [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all
Hi Frank
Do you know why there are multiple frames? What kind of MRI acquisition are you trying to use as input? Most standard T1-weighted series only have a single frame Bruce
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 Frank Chau Sent: Monday, August 2, 2021 3:49 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Cc: Jacky Lee cylee10@gmail.commailto:cylee10@gmail.com; Jacky LEE lcy339@ha.org.hkmailto:lcy339@ha.org.hk Subject: [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all
External Email - Use Caution
Dear Freesurfer experts,
I tried to run Recon-all on a T1 series .nii file. A error occurred: "ERROR: input(s) cannot have multiple frames!". I tried to google the method of converting multi frame dicom to single frame dicom. I found software of "dicom2" stated that it could perform the conversion but their manual guide are too hard for me to understand. May I know there are any easier method to perform the conversion? Thank you.
Regards
Frank
---------------------------
FRANK C Y CHAU
Research assistant
Division of Neurology
Department of Medicine
Tel: +852 6340 2553
Fax: 2872 5828
E-mail : cyfrank@hku.hkmailto:cyfrank@hku.hk
Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1vfQvr2PdL6N1N8uZJkC-LRXRCWwULtgVK68eCyunXgUVst...https://secure-web.cisco.com/1sq7fKFbX3YdDrWDmgZmO-9VwTw4OHoHRYY_T1tzsMrHAmCbYE8RRwg8qXEOzF8NylDqGEU6s17uyDaS_Ahuflv4GOqv73qdLQRK0ocjNufaw4-S5qXFxVvDsQFLYU6mDEE_c6sTXxKv12ZQpnARaiAPl6YgVaJ58-xiSP8JdxjeDNpqDvhhnPnW_Ska2N-fcEUavIoeA7ozsZV6qzGEQLTh19mMbGU9bOSFkVEgXh8ifUe4Y1Kt4l9gMOnRXTTlYbWuypAOQ84kYU3Y2KZsQ8A/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Cahmed.bahrani%2540uky.edu%257C69866f35c2194c96813f08d9568258f4%257C2b30530b69b64457b818481cb53d42ae%257C0%257C0%257C637635940099936423%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DI828fPbkxzmXl21huHJcbeQ0cKIbYLlTOEcu0LkM78I%253D%26reserved%3D0
freesurfer@nmr.mgh.harvard.edu
-
Bahrani, Ahmed A. -
Douglas N. Greve -
Fischl, Bruce -
Frank Chau