subject:"\[Freesurfer\] mysterious fsgd format error \(not the end of line problem\)"

Re: [Freesurfer] mysterious fsgd format error (not the end of line problem)

2016-03-06 Thread Joseph Dien

never mind!  It turned out I was forgetting to run a script to move copies of 
the fixed fsgd files into their final locations.  Once I did so the files I 
posted worked fine.  Sorry for the false alarm and thanks for getting back to 
me!

Joe

> On Mar 3, 2016, at 12:18, Douglas N Greve  wrote:
> 
> I cannot replicate the error. What version of FS are you using? What 
> happens if you run
>  mri_glmfit --fsgd RPA-acc.fsgd
> or
> mri_glmfit --fsgd RPA-accGT.fsgd
> 
> 
> 
> On 02/29/2016 09:38 PM, Joseph Dien wrote:
>> Hi,
>>I’m having an fsgd error that has totally stumped me.  I’m trying to run 
>> the following command to compute the second level statistics:
>> 
>> mri_glmfit --surf fsaverage lh --y ces.nii.gz --wls cesvar.nii.gz  --nii.gz 
>> --fsgd RPA-accGT.fsgd --glmdir conVinc_normAcc.wls --C main.mtx --C 
>> normAcc.mtx
>> 
>> I get the error message:
>> 
>> Reading source surface /Volumes/Data2/RP1/freesurfer/fsaverage/surf/lh.white
>> gdfReadHeader: reading RPA-accGT.fsgd
>> FSGDF Format Error: file = RPA-accGT.fsgd, tag=Title
>> 
>> I used the utility flip to make sure the file was in UNIX format (with 
>> linefeeds).
>> I then double-checked by reading in the binary codes with Matlab’s fread and 
>> directly checking the ASCII numbers, which are indeed ASCII 10 (linefeed).
>> 
>> Here is the contents of the fsgd file.
>> 
>> GroupDescriptorFile 1
>> Title RP1
>> Class Main
>> Variables LogoAcc NormAcc OrthAcc PhonAcc
>> InputRPA903  Main0.750.790.770.62
>> InputRPA906  Main0.810.810.830.74
>> InputRPA907  Main0.871   0.840.83
>> InputRPA908  Main0.910.930.950.89
>> InputRPA909  Main0.740.950.720.72
>> InputRPA910  Main0.850.960.810.79
>> InputRPA912  Main0.750.780.730.73
>> InputRPA914  Main0.7 0.850.830.81
>> InputRPA915  Main0.850.890.750.83
>> InputRPA916  Main0.840.920.870.72
>> InputRPA917  Main0.830.930.920.83
>> InputRPA918  Main0.870.910.790.85
>> InputRPA919  Main0.860.960.910.88
>> InputRPA920  Main0.840.920.870.84
>> InputRPA921  Main0.870.920.880.85
>> InputRPA922  Main0.8 0.9 0.9 0.72
>> 
>> What’s really driving me to distraction is that a previous version of this 
>> file (with a different set of participants) works fine.  I’m attaching both. 
>>  RPA-accGT.fsgd does not work and RPA-acc.fsgd does work.  Using Matlab’s 
>> fread, the first 85 characters (first four lines) of both files are 
>> identical.
>> 
>> I’m running on OS X 10.11.3.  I’m using FSFAST 5.20.  Matlab 2015b.
>> 
>> Any help would be greatly appreciated!
>> 
>> Joe
>> 
>> 
>> 
>> 
>> 
>> Joseph Dien, PhD
>> Senior Research Scientist
>> Maryland Neuroimaging Center
>> University of Maryland, College Park
>> E-mail: jdie...@mac.com
>> Cell Phone: 202-297-8117
>> http://joedien.com
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 
> 
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> 
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 
> 
> 
> ___
> 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.



Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com

Re: [Freesurfer] mysterious fsgd format error (not the end of line problem)

2016-03-03 Thread Douglas N Greve

I cannot replicate the error. What version of FS are you using? What 
happens if you run
  mri_glmfit --fsgd RPA-acc.fsgd
or
mri_glmfit --fsgd RPA-accGT.fsgd



On 02/29/2016 09:38 PM, Joseph Dien wrote:
> Hi,
> I’m having an fsgd error that has totally stumped me.  I’m trying to run 
> the following command to compute the second level statistics:
>
> mri_glmfit --surf fsaverage lh --y ces.nii.gz --wls cesvar.nii.gz  --nii.gz 
> --fsgd RPA-accGT.fsgd --glmdir conVinc_normAcc.wls --C main.mtx --C 
> normAcc.mtx
>
> I get the error message:
>
> Reading source surface /Volumes/Data2/RP1/freesurfer/fsaverage/surf/lh.white
> gdfReadHeader: reading RPA-accGT.fsgd
> FSGDF Format Error: file = RPA-accGT.fsgd, tag=Title
>
> I used the utility flip to make sure the file was in UNIX format (with 
> linefeeds).
> I then double-checked by reading in the binary codes with Matlab’s fread and 
> directly checking the ASCII numbers, which are indeed ASCII 10 (linefeed).
>
> Here is the contents of the fsgd file.
>
> GroupDescriptorFile 1
> Title RP1
> Class Main
> Variables LogoAcc NormAcc OrthAcc PhonAcc
> Input RPA903  Main0.750.790.770.62
> Input RPA906  Main0.810.810.830.74
> Input RPA907  Main0.871   0.840.83
> Input RPA908  Main0.910.930.950.89
> Input RPA909  Main0.740.950.720.72
> Input RPA910  Main0.850.960.810.79
> Input RPA912  Main0.750.780.730.73
> Input RPA914  Main0.7 0.850.830.81
> Input RPA915  Main0.850.890.750.83
> Input RPA916  Main0.840.920.870.72
> Input RPA917  Main0.830.930.920.83
> Input RPA918  Main0.870.910.790.85
> Input RPA919  Main0.860.960.910.88
> Input RPA920  Main0.840.920.870.84
> Input RPA921  Main0.870.920.880.85
> Input RPA922  Main0.8 0.9 0.9 0.72
>
> What’s really driving me to distraction is that a previous version of this 
> file (with a different set of participants) works fine.  I’m attaching both.  
> RPA-accGT.fsgd does not work and RPA-acc.fsgd does work.  Using Matlab’s 
> fread, the first 85 characters (first four lines) of both files are identical.
>
> I’m running on OS X 10.11.3.  I’m using FSFAST 5.20.  Matlab 2015b.
>
> Any help would be greatly appreciated!
>
> Joe
>
>
>
> 
>
> Joseph Dien, PhD
> Senior Research Scientist
> Maryland Neuroimaging Center
> University of Maryland, College Park
> E-mail: jdie...@mac.com
> Cell Phone: 202-297-8117
> http://joedien.com
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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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
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] mysterious fsgd format error (not the end of line problem)

2016-03-02 Thread Bruce Fischl

No worries, it happens to all of us
Bruce

> On Mar 2, 2016, at 12:20 AM, Joseph Dien  wrote:
> 
> Oops, never mind.  User error.  I’m too embarrassed to even explain what I 
> did.  :)
> 
> Joe
> 
>> On Feb 29, 2016, at 21:38, Joseph Dien  wrote:
>> 
>> Hi,
>>   I’m having an fsgd error that has totally stumped me.  I’m trying to run 
>> the following command to compute the second level statistics:
>> 
>> mri_glmfit --surf fsaverage lh --y ces.nii.gz --wls cesvar.nii.gz  --nii.gz 
>> --fsgd RPA-accGT.fsgd --glmdir conVinc_normAcc.wls --C main.mtx --C 
>> normAcc.mtx
>> 
>> I get the error message:
>> 
>> Reading source surface /Volumes/Data2/RP1/freesurfer/fsaverage/surf/lh.white
>> gdfReadHeader: reading RPA-accGT.fsgd
>> FSGDF Format Error: file = RPA-accGT.fsgd, tag=Title
>> 
>> I used the utility flip to make sure the file was in UNIX format (with 
>> linefeeds).
>> I then double-checked by reading in the binary codes with Matlab’s fread and 
>> directly checking the ASCII numbers, which are indeed ASCII 10 (linefeed).
>> 
>> Here is the contents of the fsgd file.
>> 
>> GroupDescriptorFile 1
>> Title RP1
>> Class Main
>> Variables LogoAcc NormAcc OrthAcc PhonAcc
>> InputRPA903  Main0.750.790.770.62
>> InputRPA906  Main0.810.810.830.74
>> InputRPA907  Main0.871   0.840.83
>> InputRPA908  Main0.910.930.950.89
>> InputRPA909  Main0.740.950.720.72
>> InputRPA910  Main0.850.960.810.79
>> InputRPA912  Main0.750.780.730.73
>> InputRPA914  Main0.7 0.850.830.81
>> InputRPA915  Main0.850.890.750.83
>> InputRPA916  Main0.840.920.870.72
>> InputRPA917  Main0.830.930.920.83
>> InputRPA918  Main0.870.910.790.85
>> InputRPA919  Main0.860.960.910.88
>> InputRPA920  Main0.840.920.870.84
>> InputRPA921  Main0.870.920.880.85
>> InputRPA922  Main0.8 0.9 0.9 0.72
>> 
>> What’s really driving me to distraction is that a previous version of this 
>> file (with a different set of participants) works fine.  I’m attaching both. 
>>  RPA-accGT.fsgd does not work and RPA-acc.fsgd does work.  Using Matlab’s 
>> fread, the first 85 characters (first four lines) of both files are 
>> identical.
>> 
>> I’m running on OS X 10.11.3.  I’m using FSFAST 5.20.  Matlab 2015b.
>> 
>> Any help would be greatly appreciated!
>> 
>> Joe
>> 
>> 
>> 
>> 
>> Joseph Dien, PhD
>> Senior Research Scientist
>> Maryland Neuroimaging Center
>> University of Maryland, College Park
>> E-mail: jdie...@mac.com
>> Cell Phone: 202-297-8117
>> http://joedien.com
>> 
>> ___
>> 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.
> 
> 
> 
> Joseph Dien, PhD
> Senior Research Scientist
> Maryland Neuroimaging Center
> University of Maryland, College Park
> E-mail: jdie...@mac.com
> Cell Phone: 202-297-8117
> http://joedien.com
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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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.

Re: [Freesurfer] mysterious fsgd format error (not the end of line problem)

2016-03-01 Thread Joseph Dien

Oops, never mind.  User error.  I’m too embarrassed to even explain what I did. 
 :)

Joe

> On Feb 29, 2016, at 21:38, Joseph Dien  wrote:
> 
> Hi,
>   I’m having an fsgd error that has totally stumped me.  I’m trying to run 
> the following command to compute the second level statistics:
> 
> mri_glmfit --surf fsaverage lh --y ces.nii.gz --wls cesvar.nii.gz  --nii.gz 
> --fsgd RPA-accGT.fsgd --glmdir conVinc_normAcc.wls --C main.mtx --C 
> normAcc.mtx
> 
> I get the error message:
> 
> Reading source surface /Volumes/Data2/RP1/freesurfer/fsaverage/surf/lh.white
> gdfReadHeader: reading RPA-accGT.fsgd
> FSGDF Format Error: file = RPA-accGT.fsgd, tag=Title
> 
> I used the utility flip to make sure the file was in UNIX format (with 
> linefeeds).
> I then double-checked by reading in the binary codes with Matlab’s fread and 
> directly checking the ASCII numbers, which are indeed ASCII 10 (linefeed).
> 
> Here is the contents of the fsgd file.
> 
> GroupDescriptorFile 1
> Title RP1
> Class Main
> Variables LogoAcc NormAcc OrthAcc PhonAcc
> Input RPA903  Main0.750.790.770.62
> Input RPA906  Main0.810.810.830.74
> Input RPA907  Main0.871   0.840.83
> Input RPA908  Main0.910.930.950.89
> Input RPA909  Main0.740.950.720.72
> Input RPA910  Main0.850.960.810.79
> Input RPA912  Main0.750.780.730.73
> Input RPA914  Main0.7 0.850.830.81
> Input RPA915  Main0.850.890.750.83
> Input RPA916  Main0.840.920.870.72
> Input RPA917  Main0.830.930.920.83
> Input RPA918  Main0.870.910.790.85
> Input RPA919  Main0.860.960.910.88
> Input RPA920  Main0.840.920.870.84
> Input RPA921  Main0.870.920.880.85
> Input RPA922  Main0.8 0.9 0.9 0.72
> 
> What’s really driving me to distraction is that a previous version of this 
> file (with a different set of participants) works fine.  I’m attaching both.  
> RPA-accGT.fsgd does not work and RPA-acc.fsgd does work.  Using Matlab’s 
> fread, the first 85 characters (first four lines) of both files are identical.
> 
> I’m running on OS X 10.11.3.  I’m using FSFAST 5.20.  Matlab 2015b.
> 
> Any help would be greatly appreciated!
> 
> Joe
> 
> 
> 
> 
> Joseph Dien, PhD
> Senior Research Scientist
> Maryland Neuroimaging Center
> University of Maryland, College Park
> E-mail: jdie...@mac.com
> Cell Phone: 202-297-8117
> http://joedien.com
> 
> ___
> 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.



Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com
Cell Phone: 202-297-8117
http://joedien.com

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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.

[Freesurfer] mysterious fsgd format error (not the end of line problem)

2016-02-29 Thread Joseph Dien

Hi,
   I’m having an fsgd error that has totally stumped me.  I’m trying to run the 
following command to compute the second level statistics:

mri_glmfit --surf fsaverage lh --y ces.nii.gz --wls cesvar.nii.gz  --nii.gz 
--fsgd RPA-accGT.fsgd --glmdir conVinc_normAcc.wls --C main.mtx --C normAcc.mtx

I get the error message:

Reading source surface /Volumes/Data2/RP1/freesurfer/fsaverage/surf/lh.white
gdfReadHeader: reading RPA-accGT.fsgd
FSGDF Format Error: file = RPA-accGT.fsgd, tag=Title

I used the utility flip to make sure the file was in UNIX format (with 
linefeeds).
I then double-checked by reading in the binary codes with Matlab’s fread and 
directly checking the ASCII numbers, which are indeed ASCII 10 (linefeed).

Here is the contents of the fsgd file.

GroupDescriptorFile 1
Title RP1
Class Main
Variables LogoAcc NormAcc OrthAcc PhonAcc
Input   RPA903  Main0.750.790.770.62
Input   RPA906  Main0.810.810.830.74
Input   RPA907  Main0.871   0.840.83
Input   RPA908  Main0.910.930.950.89
Input   RPA909  Main0.740.950.720.72
Input   RPA910  Main0.850.960.810.79
Input   RPA912  Main0.750.780.730.73
Input   RPA914  Main0.7 0.850.830.81
Input   RPA915  Main0.850.890.750.83
Input   RPA916  Main0.840.920.870.72
Input   RPA917  Main0.830.930.920.83
Input   RPA918  Main0.870.910.790.85
Input   RPA919  Main0.860.960.910.88
Input   RPA920  Main0.840.920.870.84
Input   RPA921  Main0.870.920.880.85
Input   RPA922  Main0.8 0.9 0.9 0.72

What’s really driving me to distraction is that a previous version of this file 
(with a different set of participants) works fine.  I’m attaching both.  
RPA-accGT.fsgd does not work and RPA-acc.fsgd does work.  Using Matlab’s fread, 
the first 85 characters (first four lines) of both files are identical.

I’m running on OS X 10.11.3.  I’m using FSFAST 5.20.  Matlab 2015b.

Any help would be greatly appreciated!

Joe



RPA-accGT.fsgd
Description: Binary data


RPA-acc.fsgd
Description: Binary data



Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com
Cell Phone: 202-297-8117
http://joedien.com

___
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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
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] mysterious fsgd format error (not the end of line problem)

Re: [Freesurfer] mysterious fsgd format error (not the end of line problem)

Re: [Freesurfer] mysterious fsgd format error (not the end of line problem)

Re: [Freesurfer] mysterious fsgd format error (not the end of line problem)

[Freesurfer] mysterious fsgd format error (not the end of line problem)

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