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

[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>>
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


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

[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___
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[Freesurfer] Question about run FreeSurfer

[Alexandra Trujillo]

External Email - Use Caution

Hello,

I'm Alexandra, postgraduate student in Argentina.
I would like install and run FreeSurfer in Linux, I'm following the
instructions of '
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall' and I
obtained this output (correctly):
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/local/fsl
But, when I test have this output:
bash: /usr/local/freesurfer/bin/freeview: /bin/tcsh: intérprete erróneo: No
existe el archivo o el directorio
and,
No se ha encontrado la orden «freeview»

I need to know how open the freeview GUI to view a .mgz or .nii.gz file.
Thanks for your answers.

Cordialy,

Alexandra T.
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Re: [Freesurfer] SNR covariate in cortical thickness & volumetrics between groups analyses

[John Anderson]

External Email - Use Caution

Dear Dr Greve and Matt, your valable responses and explanations are highly 
appreciated!! Thank you so much!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Glasser, Matthew 

Sent: Sunday, August 5, 2018 6:01 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] SNR covariate in cortical thickness & volumetrics 
between groups analyses

If you have only two protocols “high quality” and “low quality", you could 
presumably include a protocol variable as a covariate of no interest, thereby 
removing any effects that correlate with protocol.  For this to work ideally, 
you would have similar numbers of low and high quality protocols across your 
comparison groups.  I agree with Doug that SNR will generally tend to make 
results more variable, but not necessarily in a specific direction.

Matt.
From:  on behalf of Douglas Greve 

Reply-To: Freesurfer support list 
Date: Sunday, August 5, 2018 at 4:48 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] SNR covariate in cortical thickness & volumetrics 
between groups analyses

I thought I answered this question last week. See my rsponse below

I don't think it is correct conceptually.  By including SNR as a covariate, you 
are saying that you expect the thickness to increase with higher SNR and 
decrease with lower SNR. This does not make sense to me. It sounds like you are 
trying to do a mixed effects analysis where you weight by the SNR. Still, 
mathematically, this is not a true mixed effect analysis (which requires 
estimates of the within and between subject noise). `

On 8/3/18 10:57 AM, John Anderson wrote:

‐‐‐ Original Message ‐‐‐
On August 5, 2018 1:04 PM, John Anderson  wrote:

>> Dear FS experts,
>> I would like to inquire about including SNR as a covariate for the between 
>> groups comparison in cortical thickness. Is this procedure valid? I have 
>> some T1 images of low quality and the majority are high in quality. I 
>> reviewed the segmentation and the cortical surfaces and fixed manually as 
>> possible. I don't want to exclude images from the data sets, so I am 
>> thinking of regressing out SNR.
>> It seems that the command "mri_segstats" can report SNR for every ROI in the 
>> brain. Is it correct to include whole brain SNR covariate for between group 
>> comparisons (cortical thickness and volumetric analyses).
>> If yes, do I need to include actual SNR values in the FSGD file or the 
>> demeaned values ?
>>
>> We appreciate your guidance!
>> John___
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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 Partners Compliance HelpLine at
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Re: [Freesurfer] SNR covariate in cortical thickness & volumetrics between groups analyses

[Glasser, Matthew]

External Email - Use Caution

If you have only two protocols “high quality” and “low quality", you could 
presumably include a protocol variable as a covariate of no interest, thereby 
removing any effects that correlate with protocol.  For this to work ideally, 
you would have similar numbers of low and high quality protocols across your 
comparison groups.  I agree with Doug that SNR will generally tend to make 
results more variable, but not necessarily in a specific direction.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas Greve 
mailto:dgr...@mgh.harvard.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Sunday, August 5, 2018 at 4:48 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] SNR covariate in cortical thickness & volumetrics 
between groups analyses

I thought I answered this question last week. See my rsponse below

I don't think it is correct conceptually.  By including SNR as a covariate, you 
are saying that you expect the thickness to increase with higher SNR and 
decrease with lower SNR. This does not make sense to me. It sounds like you are 
trying to do a mixed effects analysis where you weight by the SNR. Still, 
mathematically, this is not a true mixed effect analysis (which requires 
estimates of the within and between subject noise). `

On 8/3/18 10:57 AM, John Anderson wrote:

External Email - Use Caution

Daer FS experts,
I would like to inquire about including SNR as a covariate for the between 
groups cpmparison in cortical thickness. Is this procedure correct 
mathematically? Do I need to demean the SNA values before including it 
covariates? Finally, do you recommend any quality parameters other than SNR to 
be included covariate?

I look forward to learn from your expertise,
Thanks,
John


On 8/5/18 1:04 PM, John Anderson wrote:

External Email - Use Caution

Dear FS experts,
I would like to inquire about including SNR as a covariate for the between 
groups comparison in cortical thickness. Is this procedure valid? I have some 
T1 images of low quality and the majority are high in quality. I reviewed the 
segmentation and the cortical surfaces and fixed manually as possible. I don't 
want to exclude images from the data sets, so I am thinking of regressing out 
SNR.
It seems that the command "mri_segstats" can report SNR for every ROI in the 
brain. Is it correct to include whole brain SNR covariate for between group 
comparisons (cortical thickness and volumetric analyses).
If yes, do I need to include actual SNR values in the FSGD file or the demeaned 
values ?

We appreciate your guidance!
John




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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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Re: [Freesurfer] SNR covariate in cortical thickness & volumetrics between groups analyses

[Douglas Greve]

I thought I answered this question last week. See my rsponse below

I don't think it is correct conceptually.  By including SNR as a 
covariate, you are saying that you expect the thickness to increase with 
higher SNR and decrease with lower SNR. This does not make sense to me. 
It sounds like you are trying to do a mixed effects analysis where you 
weight by the SNR. Still, mathematically, this is not a true mixed 
effect analysis (which requires estimates of the within and between 
subject noise). `


On 8/3/18 10:57 AM, John Anderson wrote:

External Email - Use Caution

Daer FS experts,
I would like to inquire about including SNR as a covariate for the 
between groups cpmparison in cortical thickness. Is this procedure 
correct mathematically? Do I need to demean the SNA values before 
including it covariates? Finally, do you recommend any quality 
parameters other than SNR to be included covariate?


I look forward to learn from your expertise,
Thanks,
John


On 8/5/18 1:04 PM, John Anderson wrote:


External Email - Use Caution



Dear FS experts,
I would like to inquire about including SNR as a covariate for the 
between groups comparison in cortical thickness. Is this procedure 
valid? I have some T1 images of low quality and the majority are high 
in quality. I reviewed the segmentation and the cortical surfaces and 
fixed manually as possible. I don't want to exclude images from the 
data sets, so I am thinking of regressing out SNR.
It seems that the command "mri_segstats" can report SNR for every ROI 
in the brain. Is it correct to include whole brain SNR covariate for 
between group comparisons (cortical thickness and volumetric analyses).
If yes, do I need to include actual SNR values in the FSGD file or 
the demeaned values ?


We appreciate your guidance!
John




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


___
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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 Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] SNR covariate in cortical thickness & volumetrics between groups analyses

[John Anderson]

External Email - Use Caution

> Dear FS experts,
> I would like to inquire about including SNR as a covariate for the between 
> groups comparison in cortical thickness. Is this procedure valid? I have some 
> T1 images of low quality and the majority are high in quality. I reviewed the 
> segmentation and the cortical surfaces and fixed manually as possible. I 
> don't want to exclude images from the data sets, so I am thinking of 
> regressing out SNR.
> It seems that the command "mri_segstats" can report SNR for every ROI in the 
> brain. Is it correct to include whole brain SNR covariate for between group 
> comparisons (cortical thickness and volumetric analyses).
> If yes, do I need to include actual SNR values in the FSGD file or the 
> demeaned values ?
>
> We appreciate your guidance!
> John___
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Re: [Freesurfer] Origin of freesusrfer output

[Bruce Fischl]

Hi Ritesh

you can use the vox2ras matrix to compute the RAS coordinates of any 
voxel. Just give it column,row,slice,1 indices as the input vector.


cheers
Bruce
On Sun, 
5 Aug 2018, Ritesh Mahajan wrote:



   External Email - Use Caution

Thanks Bruce.

Thanks Doug for clearing this. Can you please tell, how can i get back the 
first voxel of  input ?
Also, can you tell what mathematical formula or equation is used convert this 
origin ?

Thanks,
Ritesh Mahajan

- Original Message -
From: "Douglas Greve" 
To: "freesurfer" 
Sent: Friday, August 3, 2018 9:51:30 PM
Subject: Re: [Freesurfer] Origin of freesusrfer output

To add on, the origin is changed in that the "first voxel" is not the
same in the 256^3 volume as it is in the original dicom. Having said
that, all our files (eg, mgz and nifti) have a  matrix that converts a
col, row, slice into the scanner RAS, so you can always find your way
back to the dicom coordinates.

On 8/3/18 10:41 AM, Bruce Fischl wrote:

Hi Ritesh

Doug can correct any inaccuracies, but

1. Yes, unless you tell recon-all not to.
2. I'm not sure what you mean by the origin, but we do keep track of
the ras coordinates of the center of the volume after resampling (the so-called 
"cras").
3. We do keep track of the original dicom coordinates.
4. mri_info will spit out various matrices, among them the voxel to ras
transform that should take you back to scanner ras coordinates.

cheers
Bruce

On Fri, 3 Aug 2018, Ritesh
Mahajan wrote:


External Email - Use Caution

Hi Bruce,

1) Free-surfer output is always 256*256*256, regardless of any input dimensions.
2) I have a doubt, while doing this re-sampling from input dimension to 
256*256*256. Does free-surfer change the origin of image?
3) My input is an MRI dicom image, for dicom tag value (0020,0032) which gives 
me the image position(origin).
4) How can i know the origin of free-surfer output in nii format? Do 
free-surfer change this value during processing?

Can you please provide your valuable comments on this.

Thanks,
Ritesh Mahajan




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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 Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Origin of freesusrfer output

[Ritesh Mahajan]

External Email - Use Caution

Thanks Bruce.

Thanks Doug for clearing this. Can you please tell, how can i get back the 
first voxel of  input ?
Also, can you tell what mathematical formula or equation is used convert this 
origin ?

Thanks,
Ritesh Mahajan

- Original Message -
From: "Douglas Greve" 
To: "freesurfer" 
Sent: Friday, August 3, 2018 9:51:30 PM
Subject: Re: [Freesurfer] Origin of freesusrfer output

To add on, the origin is changed in that the "first voxel" is not the 
same in the 256^3 volume as it is in the original dicom. Having said 
that, all our files (eg, mgz and nifti) have a  matrix that converts a 
col, row, slice into the scanner RAS, so you can always find your way 
back to the dicom coordinates.

On 8/3/18 10:41 AM, Bruce Fischl wrote:
> Hi Ritesh
>
> Doug can correct any inaccuracies, but
>
> 1. Yes, unless you tell recon-all not to.
> 2. I'm not sure what you mean by the origin, but we do keep track of
> the ras coordinates of the center of the volume after resampling (the 
> so-called "cras").
> 3. We do keep track of the original dicom coordinates.
> 4. mri_info will spit out various matrices, among them the voxel to ras
> transform that should take you back to scanner ras coordinates.
>
> cheers
> Bruce
>
> On Fri, 3 Aug 2018, Ritesh
> Mahajan wrote:
>
>> External Email - Use Caution
>>
>> Hi Bruce,
>>
>> 1) Free-surfer output is always 256*256*256, regardless of any input 
>> dimensions.
>> 2) I have a doubt, while doing this re-sampling from input dimension to 
>> 256*256*256. Does free-surfer change the origin of image?
>> 3) My input is an MRI dicom image, for dicom tag value (0020,0032) which 
>> gives me the image position(origin).
>> 4) How can i know the origin of free-surfer output in nii format? Do 
>> free-surfer change this value during processing?
>>
>> Can you please provide your valuable comments on this.
>>
>> Thanks,
>> Ritesh Mahajan
>>
>>
>>
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