subject:"\[Freesurfer\] ERROR\: input\(s\) cannot have multiple frames\!"

Re: [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all

2021-08-03 Thread Bahrani, Ahmed A.

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-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Tuesday, August 3, 2021 9:26 AM
To: 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_CtHzn4d_6hBEuO3ZWQUgAnSWkO3E9qzZZrIqyej4JAVVzPdvW5iOXjGRRWYGeANpAodjc6jG79stflXvsXT0OWMDmWIK1qL8676vNOKc8DrBgJqGtoXjvaIzozG4leYit5HqAj76nrWbnaLM3kJ_XJTNpecG5pBVwUMGmmj98fZpiSF3Wjz68CZkKEF0JxVVxtM22nXj1Rm5azd8Pm4PvLBoKpZq5o2rIY2ExdmXof5g/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting<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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Fischl, Bruce 
<mailto:bfis...@mgh.harvard.edu>
Sent: 03 August 2021 03:56:31
To: freesurfer@nmr.mgh.harvard.edu<mailto: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 multi

Re: [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all

2021-08-03 Thread Douglas N. Greve

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-boun...@nmr.mgh.harvard.edu 
 on behalf of Fischl, Bruce 


*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-boun...@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 ; Jacky LEE 
*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 : cyfr...@hku.hk <mailto:cyfr...@hku.hk>

Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam 
Road, Hong Kong



___
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The information in this e-mail is intended only for the person to whom it is 
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Re: [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all

2021-08-02 Thread Frank Chau

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/1x3qv0aS51XJZ0WhLEKzibrZlVCLHeCZ6fKtPNfkMrRcbufSfEzgMR6L4Z83clZT6yoDkC1SC2TcwCQ1CmH5bjDYS307N2lPGlEMqaFxkhlON664USaf7wm-rYvZD1PdnBFUqk34qxJYdEBCwIrIk4eWdmIyPoNsKCQlNg6QRNIQuCWgXupp_1_paHiS5DskWDrNsTXjaZmpjTyTuEQBGEhwrj8HJ9E9AhTSnvJYMQgCDHhUk5hpr6BKf7r38LOVd55215Eypj-tg08IGyPxN2w/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
---


Regards


Frank


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fischl, Bruce 

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-boun...@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 ; Jacky LEE 
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 : cyfr...@hku.hk<mailto:cyfr...@hku.hk>





Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, 
Hong Kong
___
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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all

2021-08-02 Thread Fischl, Bruce

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-boun...@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 ; Jacky LEE 
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 : cyfr...@hku.hk<mailto:cyfr...@hku.hk>





Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, 
Hong Kong
___
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Freesurfer@nmr.mgh.harvard.edu
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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 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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continue to communicate over unencrypted e-mail.

[Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all

2021-08-02 Thread Frank Chau

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 : cyfr...@hku.hk



Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, 
Hong Kong
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

2021-01-28 Thread Douglas N. Greve


Run
mri_concat input.mgz --rms --o 001.mgz
then pass 001.mgz to recon-all


On 1/28/2021 3:13 AM, 南修司郎 wrote:


External Email - Use Caution

Hello FreeSurfer Developers,
I'm attempting to recon-all a subject, but i got the following error.
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz 
has 4 frames


I checked mri_info, and the dimensions are 256 x 256 x 176 x 4.
I asked the radiation technologist to change the dimensions to 256 x 
256 x 176, but he told me it's impossible because of the multi echo 
sequence.


I'd appreciate if someone help me out with this and resolve this error.

Shujiro Minami M.D., Ph.D.
Dpt. of Otolaryngology National Tokyo Medical Center
2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan
E-mail shujiromin...@me.com 

1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform:Ubuntu 18.04.5 LTS (GNU/Linux 5.4.0-1034-gcp x86_64)
3) uname -a: Linux instance-1 5.4.0-1034-gcp #37~18.04.1-Ubuntu SMP Wed Jan 6 
19:44:48 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached

User: shujirominami  Machine: instance-1  Platform: Linux  PlatformVersion: 
5.4.0-1034-gcp  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  
ProgramVersion: $Name: stable6 $  TimeStamp: 2021/01/27-10:28:02-GMT  
BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_relabel_hypointensities.c,v 
1.13 2015/05/15 18:44:10 nicks Exp $  User: shujirominami  Machine: instance-1  
Platform: Linux  PlatformVersion: 5.4.0-1034-gcp  CompilerName: GCC  
CompilerVersion: 40400
###
GCADIR /usr/local/freesurfer/average
GCA RB_all_2016-05-10.vc700.gca
GCASkull RB_all_withskull_2016-05-10.vc700.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /usr/local/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
###
/home/shujirominami/freesurfer/subjects/todai_test

  mri_convert /home/shujirominami/NIFTI/todai_test.nii.gz 
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz

mri_convert.bin /home/shujirominami/NIFTI/todai_test.nii.gz 
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/shujirominami/NIFTI/todai_test.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, 0, 1)
k_ras = (1, 0, 0)
writing to 
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz...
#
#@# MotionCor Wed Jan 27 10:29:57 UTC 2021
Found 1 runs
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz has 4 frames
If this is a multi-frame MEMPRAGE image,
use mri_concat --rms to combine echo frames.
Linux instance-1 5.4.0-1034-gcp #37~18.04.1-Ubuntu SMP Wed Jan 6 19:44:48 UTC 
2021 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s todai_test exited with ERRORS at Wed Jan 27 10:30:01 UTC 2021

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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[Freesurfer] ERROR: input(s) cannot have multiple frames!

2021-01-28 Thread 南修司郎

   External Email - Use Caution


Hello FreeSurfer Developers,
I'm attempting to recon-all a subject, but i got the following error.
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz has 4 frames


I checked mri_info, and the dimensions are 256 x 256 x 176 x 4.

I asked the radiation technologist to change the dimensions to 256 x 256 x 176, 
but he told me it's impossible because of the multi echo sequence.



I'd appreciate if someone help me out with this and resolve this error.



Shujiro Minami M.D., Ph.D.
Dpt. of Otolaryngology National Tokyo Medical Center
2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan
E-mail shujiromin...@me.com



1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Ubuntu 18.04.5 LTS (GNU/Linux 5.4.0-1034-gcp x86_64)
3) uname -a: Linux instance-1 5.4.0-1034-gcp #37~18.04.1-Ubuntu SMP Wed Jan 6 
19:44:48 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached

User: shujirominami  Machine: instance-1  Platform: Linux  PlatformVersion: 5.4.0-1034-gcp  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/01/27-10:28:02-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $  User: shujirominami  Machine: instance-1  Platform: Linux  PlatformVersion: 5.4.0-1034-gcp  CompilerName: GCC  CompilerVersion: 40400 
###

GCADIR /usr/local/freesurfer/average
GCA RB_all_2016-05-10.vc700.gca
GCASkull RB_all_withskull_2016-05-10.vc700.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /usr/local/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
###
/home/shujirominami/freesurfer/subjects/todai_test

 mri_convert /home/shujirominami/NIFTI/todai_test.nii.gz /home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz 

mri_convert.bin /home/shujirominami/NIFTI/todai_test.nii.gz /home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from /home/shujirominami/NIFTI/todai_test.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, 0, 1)
k_ras = (1, 0, 0)
writing to 
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz...
#
#@# MotionCor Wed Jan 27 10:29:57 UTC 2021
Found 1 runs
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz has 4 frames
If this is a multi-frame MEMPRAGE image,
use mri_concat --rms to combine echo frames.
Linux instance-1 5.4.0-1034-gcp #37~18.04.1-Ubuntu SMP Wed Jan 6 19:44:48 UTC 
2021 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s todai_test exited with ERRORS at Wed Jan 27 10:30:01 UTC 2021

To report a problem, see 
http://secure-web.cisco.com/1g-5Sw5A-mJK27f9rxSEw4DBgjmZ7KTng5JrfBIPRNQPlEHCK_2tvxt6c4VAFY8M8aXtgjW2wRrVh3lfJWDAObul-ChFw-EgshQxXF7xs8ftorKmKNZOxjPgprRtx6IFZh7BtQIjHj7f0sY7N_qnq-JqdGk-bpGnLlwWT-920Eo3Yp0LBOUU9rTr0sKsCENdJx2LNXqNo969fGvFq3oi1kRepC601NZSMwau1HPSNnCotMYa8YmNLmOhpelXErfVeAzYpgXP0ZLg2ZBwxKf1sCA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
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Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

2020-06-29 Thread Douglas N. Greve

How did you generate 102.mgz? It looks like it was created by a pretty 
old version of FS.


On 6/28/2020 5:41 PM, Fischl, Bruce wrote:


And how did you generate the volumes? I wouldn’t name them 001.mgz, 
that will end up being confusing. Maybe something like sub.001.mgz 
might be better, since otherwise we might overwrite some of them


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Angela Favaro

*Sent:* Sunday, June 28, 2020 4:53 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

*External Email - Use Caution *

Yes, I am sure

Now I tried to use Freesurfer 6.0 again for that volume and both 
recon-all and mri_info  worked:


recon-all -all -s subj102

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/angelafavaro/Desktop/prova

Actual FREESURFER_HOME /Applications/freesurfer

Darwin MacBookiAngela2 16.7.0 Darwin Kernel Version 16.7.0: Sun Jun  2 
20:26:31 PDT 2019; root:xnu-3789.73.50~1/RELEASE_X86_64 x86_64


#

#@# MotionCor Sun Jun 28 22:44:04 CEST 2020

Found 1 runs

/Users/angelafavaro/Desktop/prova/subj102/mri/orig/102.mgz

Checking for (invalid) multi-frame inputs...

WARNING: only one run found. This is OK, but motion

correction cannot be performed on one run, so I'll

copy the run to rawavg and continue.

….

…..



mri_info subj102/mri/orig/102.mgz

Volume information for subj102/mri/orig/102.mgz

        type: MGH

  dimensions: 256 x 256 x 256

voxel sizes: 1.00, 1.00, 1.00

        type: UCHAR (0)

        fov: 256.000

        dof: 0

      xstart: -128.0, xend: 128.0

      ystart: -128.0, yend: 128.0

      zstart: -128.0, zend: 128.0

          TR: 2250.00 msec, TE: 3.03 msec, TI: 900.00 msec, flip 
angle: 9.00 degrees


    nframes: 1

    PhEncDir: UNKNOWN

    FieldStrength: 0.00

ras xform present

  xform info: x_r =  -1., y_r =   0., z_r = -0., c_r =    
-2.5219


            : x_a =   0., y_a =  -0., z_a = 1., c_a =    
10.8637


            : x_s =  -0., y_s =  -1., z_s = -0., c_s =   
-32.3759


talairach xfm : 
/Users/angelafavaro/Desktop/aachen_free/subj102/mri/transforms/talairach.xfm


Orientation   : LIA

Primary Slice Direction: coronal

voxel to ras transform:

            -1.   0.  -0.   125.4781

              0.  -0.   1.  -117.1363

            -0.  -1.  -0.    95.6241

              0.   0.   0.     1.

voxel-to-ras determinant -1

ras to voxel transform:

            -1.  -0.  -0.   125.4781

              0.  -0.  -1.    95.6241

              0.   1.  -0.   117.1363

            -0.  -0.  -0.     1.

Il giorno 28 giu 2020, alle ore 20:45, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> ha scritto:

Are you sure 102.mgz is from our analysis previously? We typically
name the volumes 001.mgz, 002.mgz, etc….

*From:*freesurfer-boun...@nmr.mgh.harvard.edu

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>*On Behalf
Of*Angela Favaro
*Sent:*Sunday, June 28, 2020 1:49 PM
*To:*Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:*Re: [Freesurfer] ERROR: input(s) cannot have multiple
frames!

*External Email - Use Caution *

Sure!

thank you for any help!

Angela

angelafavaro% recon-all -all -s subj102

Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b

Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b

INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/Aachen

Actual FREESURFER_HOME /Applications/freesurfer/7.1.0

-rw-rw-r-- 1 angelafavaro  staff  143379 Jun 28 13:46
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log

Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct
17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64

#

#@# MotionCor Sun Jun 28 19:40:10 CEST 2020

Found 1 runs

/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz

Checking for (invalid) multi-frame inputs...

ERROR: input(s) cannot have multiple frames!

/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz has 
frames

Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct
17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64

recon-all -s subj102 exited with ERRORS at Sun Jun 28 19:40:11
CEST 2020

For more details, see the log file
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log

To report a problem,
seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Then I copied 102.mgz in a differe

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

2020-06-28 Thread Angela Favaro

External Email - Use Caution

What is an offlist? 
I am running a longitudinal analysis and in the SUBJECTS directory there are 
now the following folders 

I had this problem only with subj102 (subj102/mri/orig/102.mgz)

subj001
subj001.long.template18
subj003
subj003.long.template17
subj004
subj004.long.template16
subj005
subj006
subj006.long.template14
subj007
subj007.long.template13
subj008
subj008.long.template12
subj009
subj009.long.template11
subj010
subj010.long.template10
subj011
subj011.long.template9
subj012
subj013
subj013.long.template7
subj014
subj014.long.template6
subj015
subj015.long.template5
subj016
subj016.long.template4
subj017
subj017.long.template3
subj018
subj018.long.template2
subj019
subj019.long.template1
subj020
subj020.long.template19
subj021
subj021.long.template20
subj023
subj023.long.template21
subj024
subj027
subj027.long.template23
subj029
subj029.long.template24
subj031
subj031.long.template25
subj034
subj034.long.template27
subj035
subj035.long.template28
subj036
subj038
subj038.long.template30
subj041
subj041.long.template31
subj042
subj042.long.template32
subj043
subj043.long.template33
subj044
subj045
subj047
subj049
subj049.long.template37
subj058
subj058.long.template38
subj060
subj060.long.template39
subj101
subj101.long.template40
subj102
subj103
subj103.long.template42
subj104
subj104.long.template43
subj105
subj105.long.template44
subj106
subj106.long.template45
subj107
subj107.long.template46
subj108
subj108.long.template47
subj109
subj110
subj110.long.template49
subj111
subj112
subj112.long.template51
subj113
subj113.long.template52
subj114
subj114.long.template53
subj115
subj115.long.template54
subj116
subj116.long.template55
subj117
subj117.long.template56
subj201
subj201.long.template4
subj202
subj202.long.template2
subj203
subj203.long.template6
subj204
subj204.long.template1
subj205
subj205.long.template3
subj206
subj206.long.template5
subj207
subj207.long.template7
subj208
subj208.long.template12
subj209
subj209.long.template9
subj210
subj210.long.template10
subj211
subj212
subj212.long.template11
subj213
subj213.long.template13
subj214
subj215
subj215.long.template16
subj216
subj216.long.template14
subj217
subj217.long.template17
subj218
subj218.long.template18
subj220
subj221
subj221.long.template21
subj222
subj222.long.template19
subj224
subj224.long.template20
subj225
subj225.long.template24
subj226
subj226.long.template28
subj227
subj227.long.template25
subj229
subj229.long.template23
subj230
subj230.long.template27
subj231
subj231.long.template29
subj232
subj233
subj233.long.template32
subj234
subj235
subj235.long.template33
subj236
subj236.long.template37
subj237
subj238
subj239
subj239.long.template31
subj241
subj241.long.template38
subj242
subj242.long.template39
subj301
subj301.long.template49
subj302
subj302.long.template53
subj303
subj303.long.template44
subj304
subj304.long.template55
subj305
subj305.long.template45
subj306
subj306.long.template54
subj307
subj308
subj308.long.template42
subj309
subj309.long.template51
subj310
subj310.long.template52
subj311
subj312
subj313
subj313.long.template47
subj314
subj314.long.template46
subj315
subj315.long.template40
subj316
subj316.long.template43
subj317
subj317.long.template56
subject_list.txt
subject_list_all 2.txt
subject_list_long.txt
subject_list_long1.txt
subject_list_long2.txt
subject_list_long3.txt
template1
template10
template11
template12
template13
template14
template15
template16
template17
template18
template19
template2
template20
template21
template22
template23
template24
template25
template26
template27
template28
template29
template3
template30
template31
template32
template33
template34
template35
template36
template37
template38
template39
template4
template40
template41
template42
template43
template44
template45
template46
template47
template48
template49
template5
template50
template51
template52
template53
template54
template55
template56
template6
template7
template8
template9___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

2020-06-28 Thread Fischl, Bruce

And how did you generate the volumes? I wouldn’t name them 001.mgz, that will 
end up being confusing. Maybe something like sub.001.mgz might be better, since 
otherwise we might overwrite some of them

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Angela Favaro
Sent: Sunday, June 28, 2020 4:53 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

External Email - Use Caution
Yes, I am sure
Now I tried to use Freesurfer 6.0 again for that volume and both recon-all and 
mri_info  worked:

recon-all -all -s subj102
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/angelafavaro/Desktop/prova
Actual FREESURFER_HOME /Applications/freesurfer
Darwin MacBookiAngela2 16.7.0 Darwin Kernel Version 16.7.0: Sun Jun  2 20:26:31 
PDT 2019; root:xnu-3789.73.50~1/RELEASE_X86_64 x86_64
#
#@# MotionCor Sun Jun 28 22:44:04 CEST 2020
Found 1 runs
/Users/angelafavaro/Desktop/prova/subj102/mri/orig/102.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
….
…..

mri_info subj102/mri/orig/102.mgz
Volume information for subj102/mri/orig/102.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: UCHAR (0)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2250.00 msec, TE: 3.03 msec, TI: 900.00 msec, flip angle: 9.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =  -0., c_r =-2.5219
  : x_a =   0., y_a =  -0., z_a =   1., c_a =10.8637
  : x_s =  -0., y_s =  -1., z_s =  -0., c_s =   -32.3759

talairach xfm : 
/Users/angelafavaro/Desktop/aachen_free/subj102/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.  -0.   125.4781
0.  -0.   1.  -117.1363
   -0.  -1.  -0.95.6241
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   125.4781
0.  -0.  -1.95.6241
0.   1.  -0.   117.1363
   -0.  -0.  -0. 1.

Il giorno 28 giu 2020, alle ore 20:45, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> ha scritto:

Are you sure 102.mgz is from our analysis previously? We typically name the 
volumes 001.mgz, 002.mgz, etc….

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Angela Favaro
Sent: Sunday, June 28, 2020 1:49 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

External Email - Use Caution
Sure!
thank you for any help!
Angela

angelafavaro% recon-all -all -s subj102
Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/Aachen
Actual FREESURFER_HOME /Applications/freesurfer/7.1.0
-rw-rw-r--  1 angelafavaro  staff  143379 Jun 28 13:46 
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 
PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
#
#@# MotionCor Sun Jun 28 19:40:10 CEST 2020
Found 1 runs
/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz has  frames
Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 
PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64

recon-all -s subj102 exited with ERRORS at Sun Jun 28 19:40:11 CEST 2020

For more details, see the log file 
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Then I copied 102.mgz in a different folder. I also copied in this folder the 
files 102.mgz (renamed 1023.mgz), orig.mgz and rawavg.mgz from a previous 
(successful) analysis with Freesurfer 6.0

angelafavaro% mri_info 102.mgz
mri_info(77526,0x11d011dc0) malloc: can't allocate region
*** mach_vm_map(size=8386104309919531008) failed (error code=3)
mr

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

2020-06-28 Thread Fischl, Bruce

Hmmm, can you send us the volume offlist?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Angela Favaro
Sent: Sunday, June 28, 2020 4:53 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

External Email - Use Caution
Yes, I am sure
Now I tried to use Freesurfer 6.0 again for that volume and both recon-all and 
mri_info  worked:

recon-all -all -s subj102
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/angelafavaro/Desktop/prova
Actual FREESURFER_HOME /Applications/freesurfer
Darwin MacBookiAngela2 16.7.0 Darwin Kernel Version 16.7.0: Sun Jun  2 20:26:31 
PDT 2019; root:xnu-3789.73.50~1/RELEASE_X86_64 x86_64
#
#@# MotionCor Sun Jun 28 22:44:04 CEST 2020
Found 1 runs
/Users/angelafavaro/Desktop/prova/subj102/mri/orig/102.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
….
…..

mri_info subj102/mri/orig/102.mgz
Volume information for subj102/mri/orig/102.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: UCHAR (0)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2250.00 msec, TE: 3.03 msec, TI: 900.00 msec, flip angle: 9.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =  -0., c_r =-2.5219
  : x_a =   0., y_a =  -0., z_a =   1., c_a =10.8637
  : x_s =  -0., y_s =  -1., z_s =  -0., c_s =   -32.3759

talairach xfm : 
/Users/angelafavaro/Desktop/aachen_free/subj102/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.  -0.   125.4781
0.  -0.   1.  -117.1363
   -0.  -1.  -0.95.6241
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   125.4781
0.  -0.  -1.95.6241
0.   1.  -0.   117.1363
   -0.  -0.  -0. 1.

Il giorno 28 giu 2020, alle ore 20:45, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> ha scritto:

Are you sure 102.mgz is from our analysis previously? We typically name the 
volumes 001.mgz, 002.mgz, etc….

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Angela Favaro
Sent: Sunday, June 28, 2020 1:49 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

External Email - Use Caution
Sure!
thank you for any help!
Angela

angelafavaro% recon-all -all -s subj102
Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/Aachen
Actual FREESURFER_HOME /Applications/freesurfer/7.1.0
-rw-rw-r--  1 angelafavaro  staff  143379 Jun 28 13:46 
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 
PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
#
#@# MotionCor Sun Jun 28 19:40:10 CEST 2020
Found 1 runs
/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz has  frames
Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 
PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64

recon-all -s subj102 exited with ERRORS at Sun Jun 28 19:40:11 CEST 2020

For more details, see the log file 
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Then I copied 102.mgz in a different folder. I also copied in this folder the 
files 102.mgz (renamed 1023.mgz), orig.mgz and rawavg.mgz from a previous 
(successful) analysis with Freesurfer 6.0

angelafavaro% mri_info 102.mgz
mri_info(77526,0x11d011dc0) malloc: can't allocate region
*** mach_vm_map(size=8386104309919531008) failed (error code=3)
mri_info(77526,0x11d011dc0) malloc: *** set a breakpoint in malloc_error_break 
to debug
error: Cannot allocate memory
error: znzTAGskip: tag=1768777043, failed t

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

2020-06-28 Thread Angela Favaro

External Email - Use Caution

Yes, I am sure
Now I tried to use Freesurfer 6.0 again for that volume and both recon-all and 
mri_info  worked:

recon-all -all -s subj102
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/angelafavaro/Desktop/prova
Actual FREESURFER_HOME /Applications/freesurfer
Darwin MacBookiAngela2 16.7.0 Darwin Kernel Version 16.7.0: Sun Jun  2 20:26:31 
PDT 2019; root:xnu-3789.73.50~1/RELEASE_X86_64 x86_64
#
#@# MotionCor Sun Jun 28 22:44:04 CEST 2020
Found 1 runs
/Users/angelafavaro/Desktop/prova/subj102/mri/orig/102.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
….
…..

mri_info subj102/mri/orig/102.mgz
Volume information for subj102/mri/orig/102.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: UCHAR (0)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2250.00 msec, TE: 3.03 msec, TI: 900.00 msec, flip angle: 9.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =  -0., c_r =-2.5219
  : x_a =   0., y_a =  -0., z_a =   1., c_a =10.8637
  : x_s =  -0., y_s =  -1., z_s =  -0., c_s =   -32.3759

talairach xfm : 
/Users/angelafavaro/Desktop/aachen_free/subj102/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.  -0.   125.4781
0.  -0.   1.  -117.1363
   -0.  -1.  -0.95.6241
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   125.4781
0.  -0.  -1.95.6241
0.   1.  -0.   117.1363
   -0.  -0.  -0. 1.



> Il giorno 28 giu 2020, alle ore 20:45, Fischl, Bruce 
>  ha scritto:
> 
> Are you sure 102.mgz is from our analysis previously? We typically name the 
> volumes 001.mgz, 002.mgz, etc….
>  
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Angela Favaro
> Sent: Sunday, June 28, 2020 1:49 PM
> To: Freesurfer support list  <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!
>  
> External Email - Use Caution
> 
> Sure! 
> thank you for any help!
> Angela
>  
> angelafavaro% recon-all -all -s subj102
> Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/Aachen
> Actual FREESURFER_HOME /Applications/freesurfer/7.1.0
> -rw-rw-r--  1 angelafavaro  staff  143379 Jun 28 13:46 
> /Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
> Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 
> 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
> #
> #@# MotionCor Sun Jun 28 19:40:10 CEST 2020
> Found 1 runs
> /Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz
> Checking for (invalid) multi-frame inputs...
> ERROR: input(s) cannot have multiple frames!
> /Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz has  frames
> Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 
> 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
>  
> recon-all -s subj102 exited with ERRORS at Sun Jun 28 19:40:11 CEST 2020
>  
> For more details, see the log file 
> /Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
> To report a problem, see 
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>  
>  
> Then I copied 102.mgz in a different folder. I also copied in this folder the 
> files 102.mgz (renamed 1023.mgz), orig.mgz and rawavg.mgz from a previous 
> (successful) analysis with Freesurfer 6.0
>  
> angelafavaro% mri_info 102.mgz 
> mri_info(77526,0x11d011dc0) malloc: can't allocate region
> *** mach_vm_map(size=8386104309919531008) failed (error code=3)
> mri_info(77526,0x11d011dc0) malloc: *** set a breakpoint in 
> malloc_

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

2020-06-28 Thread Angela Favaro

External Email - Use Caution

For this dataset, I named cases 001.mgz 002.mgz ...
and controls 101.mgz 102.mgz... 

But the error message also appear when I rename that volume... 

⁣Ottieni BlueMail per Android 

Il giorno 28 giu 2020, 20:46, alle ore 20:46, "Fischl, Bruce" 
 ha scritto:
>Are you sure 102.mgz is from our analysis previously? We typically name
>the volumes 001.mgz, 002.mgz, etc
>
>From: freesurfer-boun...@nmr.mgh.harvard.edu
> On Behalf Of Angela Favaro
>Sent: Sunday, June 28, 2020 1:49 PM
>To: Freesurfer support list 
>Subject: Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!
>
>
>External Email - Use Caution
>Sure!
>thank you for any help!
>Angela
>
>angelafavaro% recon-all -all -s subj102
>Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
>Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
>INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/Aachen
>Actual FREESURFER_HOME /Applications/freesurfer/7.1.0
>-rw-rw-r--  1 angelafavaro  staff  143379 Jun 28 13:46
>/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
>Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17
>16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
>#
>#@# MotionCor Sun Jun 28 19:40:10 CEST 2020
>Found 1 runs
>/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz
>Checking for (invalid) multi-frame inputs...
>ERROR: input(s) cannot have multiple frames!
>/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz has  frames
>Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17
>16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
>
>recon-all -s subj102 exited with ERRORS at Sun Jun 28 19:40:11 CEST
>2020
>
>For more details, see the log file
>/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
>To report a problem, see
>http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>Then I copied 102.mgz in a different folder. I also copied in this
>folder the files 102.mgz (renamed 1023.mgz), orig.mgz and rawavg.mgz
>from a previous (successful) analysis with Freesurfer 6.0
>
>angelafavaro% mri_info 102.mgz
>mri_info(77526,0x11d011dc0) malloc: can't allocate region
>*** mach_vm_map(size=8386104309919531008) failed (error code=3)
>mri_info(77526,0x11d011dc0) malloc: *** set a breakpoint in
>malloc_error_break to debug
>error: Cannot allocate memory
>error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes!
>
>angelafavaro% mri_info 1023.mgz
>mri_info(77711,0x1125ffdc0) malloc: can't allocate region
>*** mach_vm_map(size=8386104309919531008) failed (error code=3)
>mri_info(77711,0x1125ffdc0) malloc: *** set a breakpoint in
>malloc_error_break to debug
>error: Cannot allocate memory
>error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes!
>
>mri_info rawavg.mgz
>mri_info(77716,0x11438bdc0) malloc: can't allocate region
>*** mach_vm_map(size=8386104309919531008) failed (error code=3)
>mri_info(77716,0x11438bdc0) malloc: *** set a breakpoint in
>malloc_error_break to debug
>error: Cannot allocate memory
>error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes!
>
>
>mri_info orig.mgz
>Volume information for orig.mgz
>  type: MGH
>dimensions: 256 x 256 x 256
>   voxel sizes: 1.00, 1.00, 1.00
>  type: UCHAR (0)
>   fov: 256.000
>   dof: 0
>xstart: -128.0, xend: 128.0
>ystart: -128.0, yend: 128.0
>zstart: -128.0, zend: 128.0
>TR: 2250.00 msec, TE: 3.03 msec, TI: 900.00 msec, flip angle: 9.00
>degrees
>   nframes: 1
>   PhEncDir: UNKNOWN
>   FieldStrength: 0.00
>ras xform present
>xform info: x_r =  -1., y_r =   0., z_r =  -0., c_r =   
>-2.5219
> : x_a =   0., y_a =  -0., z_a =   1., c_a =10.8637
> : x_s =  -0., y_s =  -1., z_s =  -0., c_s =   -32.3759
>
>talairach xfm :
>/Users/angelafavaro/Desktop/aachen_free/subj102/mri/transforms/talairach.xfm
>Orientation   : LIA
>Primary Slice Direction: coronal
>
>voxel to ras transform:
>   -1.   0.  -0.   125.4781
>0.  -0.   1.  -117.1363
>   -0.  -1.  -0.95.6241
>0.   0.   0. 1.
>
>voxel-to-ras determinant -1
>
>ras to voxel transform:
>   -1.  -0.  -0.   125.4781
>0.  -0.  -1.95.6241
>0.   1.  -0.   117.1363
>   -0.  -0.  -0. 1.
>
>
>
&

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

2020-06-28 Thread Fischl, Bruce

Are you sure 102.mgz is from our analysis previously? We typically name the 
volumes 001.mgz, 002.mgz, etc

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Angela Favaro
Sent: Sunday, June 28, 2020 1:49 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

External Email - Use Caution
Sure!
thank you for any help!
Angela

angelafavaro% recon-all -all -s subj102
Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/Aachen
Actual FREESURFER_HOME /Applications/freesurfer/7.1.0
-rw-rw-r--  1 angelafavaro  staff  143379 Jun 28 13:46 
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 
PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
#
#@# MotionCor Sun Jun 28 19:40:10 CEST 2020
Found 1 runs
/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz has  frames
Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 
PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64

recon-all -s subj102 exited with ERRORS at Sun Jun 28 19:40:11 CEST 2020

For more details, see the log file 
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Then I copied 102.mgz in a different folder. I also copied in this folder the 
files 102.mgz (renamed 1023.mgz), orig.mgz and rawavg.mgz from a previous 
(successful) analysis with Freesurfer 6.0

angelafavaro% mri_info 102.mgz
mri_info(77526,0x11d011dc0) malloc: can't allocate region
*** mach_vm_map(size=8386104309919531008) failed (error code=3)
mri_info(77526,0x11d011dc0) malloc: *** set a breakpoint in malloc_error_break 
to debug
error: Cannot allocate memory
error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes!

angelafavaro% mri_info 1023.mgz
mri_info(77711,0x1125ffdc0) malloc: can't allocate region
*** mach_vm_map(size=8386104309919531008) failed (error code=3)
mri_info(77711,0x1125ffdc0) malloc: *** set a breakpoint in malloc_error_break 
to debug
error: Cannot allocate memory
error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes!

mri_info rawavg.mgz
mri_info(77716,0x11438bdc0) malloc: can't allocate region
*** mach_vm_map(size=8386104309919531008) failed (error code=3)
mri_info(77716,0x11438bdc0) malloc: *** set a breakpoint in malloc_error_break 
to debug
error: Cannot allocate memory
error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes!

mri_info orig.mgz
Volume information for orig.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: UCHAR (0)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2250.00 msec, TE: 3.03 msec, TI: 900.00 msec, flip angle: 9.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =  -0., c_r =-2.5219
  : x_a =   0., y_a =  -0., z_a =   1., c_a =10.8637
  : x_s =  -0., y_s =  -1., z_s =  -0., c_s =   -32.3759

talairach xfm : 
/Users/angelafavaro/Desktop/aachen_free/subj102/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.  -0.   125.4781
0.  -0.   1.  -117.1363
   -0.  -1.  -0.95.6241
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   125.4781
0.  -0.  -1.95.6241
0.   1.  -0.   117.1363
   -0.  -0.  -0. 1.

Il giorno 28 giu 2020, alle ore 17:51, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> ha scritto:

HI Angela

Can you send us the complete command line and screen output of the commands you 
ran that worked and the ones that failed?

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Angela Favaro
Sent: Sunday, June 28, 2020 8:03 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] ERROR: input(s) cannot have multiple frames!

External Email - Use Caution
Dear Freesurfer experts,
I have a problem with a T1 volume of my dataset and I a

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

2020-06-28 Thread Angela Favaro

External Email - Use Caution

Sure! 
thank you for any help!
Angela

angelafavaro% recon-all -all -s subj102
Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/Aachen
Actual FREESURFER_HOME /Applications/freesurfer/7.1.0
-rw-rw-r--  1 angelafavaro  staff  143379 Jun 28 13:46 
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 
PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
#
#@# MotionCor Sun Jun 28 19:40:10 CEST 2020
Found 1 runs
/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz has  frames
Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 
PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64

recon-all -s subj102 exited with ERRORS at Sun Jun 28 19:40:11 CEST 2020

For more details, see the log file 
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Then I copied 102.mgz in a different folder. I also copied in this folder the 
files 102.mgz (renamed 1023.mgz), orig.mgz and rawavg.mgz from a previous 
(successful) analysis with Freesurfer 6.0

angelafavaro% mri_info 102.mgz 
mri_info(77526,0x11d011dc0) malloc: can't allocate region
*** mach_vm_map(size=8386104309919531008) failed (error code=3)
mri_info(77526,0x11d011dc0) malloc: *** set a breakpoint in malloc_error_break 
to debug
error: Cannot allocate memory
error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes!

angelafavaro% mri_info 1023.mgz
mri_info(77711,0x1125ffdc0) malloc: can't allocate region
*** mach_vm_map(size=8386104309919531008) failed (error code=3)
mri_info(77711,0x1125ffdc0) malloc: *** set a breakpoint in malloc_error_break 
to debug
error: Cannot allocate memory
error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes!

mri_info rawavg.mgz
mri_info(77716,0x11438bdc0) malloc: can't allocate region
*** mach_vm_map(size=8386104309919531008) failed (error code=3)
mri_info(77716,0x11438bdc0) malloc: *** set a breakpoint in malloc_error_break 
to debug
error: Cannot allocate memory
error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes!

mri_info orig.mgz
Volume information for orig.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: UCHAR (0)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2250.00 msec, TE: 3.03 msec, TI: 900.00 msec, flip angle: 9.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =  -0., c_r =-2.5219
  : x_a =   0., y_a =  -0., z_a =   1., c_a =10.8637
  : x_s =  -0., y_s =  -1., z_s =  -0., c_s =   -32.3759

talairach xfm : 
/Users/angelafavaro/Desktop/aachen_free/subj102/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.  -0.   125.4781
0.  -0.   1.  -117.1363
   -0.  -1.  -0.95.6241
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   125.4781
0.  -0.  -1.95.6241
0.   1.  -0.   117.1363
   -0.  -0.  -0. 1.




> Il giorno 28 giu 2020, alle ore 17:51, Fischl, Bruce 
>  ha scritto:
> 
> HI Angela
>  
> Can you send us the complete command line and screen output of the commands 
> you ran that worked and the ones that failed?
>  
> Cheers
> Bruce
>  
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Angela Favaro
> Sent: Sunday, June 28, 2020 8:03 AM
> To: Freesurfer support list  <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: [Freesurfer] ERROR: input(s) cannot have multiple frames!
>  
> External Email - Use Caution
> 
> Dear Freesurfer experts, 
> I have a problem with a T1 volume of my dataset and I am not able to 
> understand it.
> This volume was correctly analyzed by Freesurfer 6.
> Whan I run recon-all with Freesurfer 7.1 the following error appear:
>  
> Checking for (invalid) multi-frame inputs...

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

2020-06-28 Thread Fischl, Bruce

HI Angela

Can you send us the complete command line and screen output of the commands you 
ran that worked and the ones that failed?

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Angela Favaro
Sent: Sunday, June 28, 2020 8:03 AM
To: Freesurfer support list 
Subject: [Freesurfer] ERROR: input(s) cannot have multiple frames!


External Email - Use Caution
Dear Freesurfer experts,
I have a problem with a T1 volume of my dataset and I am not able to understand 
it.
This volume was correctly analyzed by Freesurfer 6.
Whan I run recon-all with Freesurfer 7.1 the following error appear:

Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz has  frames
Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 
PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64

recon-all -s subj102 exited with ERRORS at Sun Jun 28 13:46:17 CEST 2020






Using Freeview I was not able to see the volume and when I tried, as suggested 
in the support list, to run mri_info:




mri_info(21013,0x11e0d7dc0) malloc: can't allocate region
*** mach_vm_map(size=8386104309919531008) failed (error code=3)
mri_info(21013,0x11e0d7dc0) malloc: *** set a breakpoint in malloc_error_break 
to debug
error: Cannot allocate memory
error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes!








When I tried to run mri_info with the file rawavg.mgz (from previous analysis 
with Freesurfer 6) the same error message appeared (and Freeview was not able 
to open it). But when I used the file orig.mgz, I obtained the below output and 
Freeview was able to open the volume. But when I tried to use the orig.mgz file 
as the input file (renamed 001.mgz) in the subj/mri/orig folder, again the 
error output appear (ERROR: input(s) cannot have multiple frames!). What is the 
problem according to you?
Thank you for any help
Angela




Volume information for orig.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: UCHAR (0)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2250.00 msec, TE: 3.03 msec, TI: 900.00 msec, flip angle: 9.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =  -0., c_r =-2.5219
  : x_a =   0., y_a =  -0., z_a =   1., c_a =10.8637
  : x_s =  -0., y_s =  -1., z_s =  -0., c_s =   -32.3759

talairach xfm : 
/Users/angelafavaro/Desktop/aachen_free/subj102/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.  -0.   125.4781
0.  -0.   1.  -117.1363
   -0.  -1.  -0.95.6241
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   125.4781
0.  -0.  -1.95.6241
0.   1.  -0.   117.1363
   -0.  -0.  -0. 1.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] ERROR: input(s) cannot have multiple frames!

2020-06-28 Thread Angela Favaro

External Email - Use Caution

Dear Freesurfer experts, 
I have a problem with a T1 volume of my dataset and I am not able to understand 
it.
This volume was correctly analyzed by Freesurfer 6.
Whan I run recon-all with Freesurfer 7.1 the following error appear:

Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz has  frames
Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 
PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64

recon-all -s subj102 exited with ERRORS at Sun Jun 28 13:46:17 CEST 2020



Using Freeview I was not able to see the volume and when I tried, as suggested 
in the support list, to run mri_info:


mri_info(21013,0x11e0d7dc0) malloc: can't allocate region
*** mach_vm_map(size=8386104309919531008) failed (error code=3)
mri_info(21013,0x11e0d7dc0) malloc: *** set a breakpoint in malloc_error_break 
to debug
error: Cannot allocate memory
error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes!




When I tried to run mri_info with the file rawavg.mgz (from previous analysis 
with Freesurfer 6) the same error message appeared (and Freeview was not able 
to open it). But when I used the file orig.mgz, I obtained the below output and 
Freeview was able to open the volume. But when I tried to use the orig.mgz file 
as the input file (renamed 001.mgz) in the subj/mri/orig folder, again the 
error output appear (ERROR: input(s) cannot have multiple frames!). What is the 
problem according to you?
Thank you for any help
Angela


Volume information for orig.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: UCHAR (0)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2250.00 msec, TE: 3.03 msec, TI: 900.00 msec, flip angle: 9.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =  -0., c_r =-2.5219
  : x_a =   0., y_a =  -0., z_a =   1., c_a =10.8637
  : x_s =  -0., y_s =  -1., z_s =  -0., c_s =   -32.3759

talairach xfm : 
/Users/angelafavaro/Desktop/aachen_free/subj102/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.  -0.   125.4781
0.  -0.   1.  -117.1363
   -0.  -1.  -0.95.6241
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   125.4781
0.  -0.  -1.95.6241
0.   1.  -0.   117.1363
   -0.  -0.  -0. 1.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

2018-08-06 Thread Bruce Fischl

and make sure that the direction cosines are correct (that is, the 
directions that freeview says are in fact the actual anatomical directions)


On Mon, 6 Aug 2018, Douglas N. Greve wrote:


You should first verify that the input is in fact a T1 of about 1mm
resolution and that there are no obvious artifacts. After that, you
should check the talairach registration (see the web page it points you to)

On 08/06/2018 04:40 PM, Renew Andrade wrote:

 External Email - Use Caution

Hello again:
I have downloaded this raw data from a database that’s the reason I’m not sure 
it is T1w but I think what they call ntdi it is. So when I run recon-all from 
this ntdi.nifti file it gives me a Talairach error.

I send you the output terminal.

Sun Aug  5 21:16:32 -05 2018
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi
/Applications/freesurfer/bin/recon-all
-all -i 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/ntdi/NIfTI/p06316_bmatrix_2500_CSD_tracked_normalized_filt_TDI.nii.gz
 -s Parkinson_p06316_ntdi
subjid Parkinson_p06316_ntdi
setenv SUBJECTS_DIR /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir
FREESURFER_HOME /Applications/freesurfer
Actual FREESURFER_HOME /Applications/freesurfer
build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  
5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
descriptors  256
memorylocked unlimited
maxproc  709

PhysMem: 6923M used (1652M wired), 1269M unused.


program versions used
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 
2017 22:24:12  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp 
$  User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 
2017 22:24:12  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve 
Exp $  User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin 
 PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by ni...@gust.nmr.mgh.harvard.edu 
(x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 
2017 22:24:12  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ 
 User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: 
 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 22:24:12  
CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: 
andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 
22:24:12  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp 
$  User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 
22:24:12  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: 
andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  
$  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 22:24:12  
CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: 
andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2018/08/06-02:16:33-GMT

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

2018-08-06 Thread Douglas N. Greve

You should first verify that the input is in fact a T1 of about 1mm 
resolution and that there are no obvious artifacts. After that, you 
should check the talairach registration (see the web page it points you to)

On 08/06/2018 04:40 PM, Renew Andrade wrote:
>  External Email - Use Caution
>
> Hello again:
> I have downloaded this raw data from a database that’s the reason I’m not 
> sure it is T1w but I think what they call ntdi it is. So when I run recon-all 
> from this ntdi.nifti file it gives me a Talairach error.
>
> I send you the output terminal.
>
> Sun Aug  5 21:16:32 -05 2018
> /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi
> /Applications/freesurfer/bin/recon-all
> -all -i 
> /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/ntdi/NIfTI/p06316_bmatrix_2500_CSD_tracked_normalized_filt_TDI.nii.gz
>  -s Parkinson_p06316_ntdi
> subjid Parkinson_p06316_ntdi
> setenv SUBJECTS_DIR /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir
> FREESURFER_HOME /Applications/freesurfer
> Actual FREESURFER_HOME /Applications/freesurfer
> build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
> Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 
>  5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
> cputime  unlimited
> filesize unlimited
> datasize unlimited
> stacksize8192 kbytes
> coredumpsize 0 kbytes
> memoryuseunlimited
> descriptors  256
> memorylocked unlimited
> maxproc  709
>
> PhysMem: 6923M used (1652M wired), 1269M unused.
>
> 
> program versions used
> $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
> $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
> mri_convert.bin -all-info
> ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: 
> $Name: stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 
> 2017 22:24:12  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter 
> Exp $  User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: 
> Darwin  PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400
> FLIRT version 5.5
> $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
> mri_convert.bin --version
> stable6
> ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: 
> $Name: stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 
> 2017 22:24:12  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve 
> Exp $  User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: 
> Darwin  PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400
> Program nu_correct, built from:
> Package MNI N3, version 1.12.0, compiled by ni...@gust.nmr.mgh.harvard.edu 
> (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08
> ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: 
> $Name: stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 
> 2017 22:24:12  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp 
> $  User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
> PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: 
> $Name:  $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 
> 22:24:12  CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman 
> Exp $  User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: 
> Darwin  PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: 
> $Name: stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 
> 2017 22:24:12  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 
> zkaufman Exp $  User: andraderenew  Machine: Renes-MacBook-Air-2.local  
> Platform: Darwin  PlatformVersion: 17.5.0  CompilerName: GCC  
> CompilerVersion: 40400
> ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: 
> stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 
> 22:24:12  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  
> User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
> PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: 
>  $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 22:24:12  
> CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: 
> andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
> PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mri_label2label.bin  ProgramArguments: -all-info  
> ProgramVersion: $Name:  $  TimeStamp: 2018/08/06-02:16:33-GMT  
> BuildTimeStamp: Jan 19 2017

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

2018-08-06 Thread Renew Andrade

External Email - Use Caution

Hello again:
I have downloaded this raw data from a database that’s the reason I’m not sure 
it is T1w but I think what they call ntdi it is. So when I run recon-all from 
this ntdi.nifti file it gives me a Talairach error. 

I send you the output terminal. 

Sun Aug  5 21:16:32 -05 2018
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi
/Applications/freesurfer/bin/recon-all
-all -i 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/ntdi/NIfTI/p06316_bmatrix_2500_CSD_tracked_normalized_filt_TDI.nii.gz
 -s Parkinson_p06316_ntdi
subjid Parkinson_p06316_ntdi
setenv SUBJECTS_DIR /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir
FREESURFER_HOME /Applications/freesurfer
Actual FREESURFER_HOME /Applications/freesurfer
build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  
5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
descriptors  256 
memorylocked unlimited
maxproc  709 

PhysMem: 6923M used (1652M wired), 1269M unused.


program versions used
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 
2017 22:24:12  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp 
$  User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 
2017 22:24:12  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve 
Exp $  User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin 
 PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by ni...@gust.nmr.mgh.harvard.edu 
(x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 
2017 22:24:12  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ 
 User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: 
 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 22:24:12  
CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: 
andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 
22:24:12  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp 
$  User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 
22:24:12  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: 
andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  
$  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 22:24:12  
CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: 
andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 
22:24:12  CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman 
Exp $  User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin 
 PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 
22:24:12  CVS: $Id:

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

2018-08-05 Thread Glasser, Matthew

External Email - Use Caution

How about running FreeSurfer on your T1w image?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Renew Andrade 
mailto:andradere...@yahoo.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Sunday, August 5, 2018 at 9:13 PM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] ERROR: input(s) cannot have multiple frames!


External Email - Use Caution

Hello community!

I have an issue while running recon-all -all in a dpi file. What do you suggest 
as a solution?
Thank you!

Renes-MacBook-Air-2:~ andraderenew$ recon-all -all  -i 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz
   -s Parkinson_p06316_dwi_2500
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 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir
Actual FREESURFER_HOME /Applications/freesurfer
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  
5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500
\n mri_convert 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz
 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz
 \n
mri_convert.bin 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz
 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0.973179, 0.23005)
k_ras = (0, -0.23005, 0.973179)
writing to 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz...
#
#@# MotionCor Sun Aug  5 21:11:50 -05 2018
Found 1 runs
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz
 has 121 frames
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  
5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64

recon-all -s Parkinson_p06316_dwi_2500 exited with ERRORS at Sun Aug  5 
21:11:50 -05 2018

For more details, see the log file 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . 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.

[Freesurfer] ERROR: input(s) cannot have multiple frames!

2018-08-05 Thread Renew Andrade

External Email - Use Caution

Hello community!

I have an issue while running recon-all -all in a dpi file. What do you suggest 
as a solution?
Thank you!

Renes-MacBook-Air-2:~ andraderenew$ recon-all -all  -i 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz
   -s Parkinson_p06316_dwi_2500
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 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir
Actual FREESURFER_HOME /Applications/freesurfer
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  
5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500
\n mri_convert 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz
 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz
 \n
mri_convert.bin 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz
 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz
 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0.973179, 0.23005)
k_ras = (0, -0.23005, 0.973179)
writing to 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz...
#
#@# MotionCor Sun Aug  5 21:11:50 -05 2018
Found 1 runs
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz
 has 121 frames
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  
5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64

recon-all -s Parkinson_p06316_dwi_2500 exited with ERRORS at Sun Aug  5 
21:11:50 -05 2018

For more details, see the log file 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . 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.

Re: [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all

Re: [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all

Re: [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all

Re: [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all

[Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

[Freesurfer] ERROR: input(s) cannot have multiple frames!

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

[Freesurfer] ERROR: input(s) cannot have multiple frames!

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

[Freesurfer] ERROR: input(s) cannot have multiple frames!

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