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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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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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] 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.