Re: [Freesurfer] FSGD File Formatting Error

looks like you created the fsgd file under windows? There are a bunch of carriage returns (look like ^M in the file). Try using a simple text editor under linux.

On 11/27/15 2:32 PM, Shady El Damaty wrote:

Hi Freesurfers,

I'm having some issues running mri_glmfit using a simple custom GLM file. I've double checked to make sure the subject session file passed to isxconcat-sess is the same as the fsgd file and also checked the formatting corresponds with what is posted online however I keep getting the same error:

ERROR: gdfReadV1: Input line 1, subjid = A02217-w2

Found 43 variables, expected. 1

FSGDF Format Error: file = /Users/seldamat/Dropbox/Projects/ADS/data/ads.emostroop.marketing/new.exposure.fsgd, tag=Input

ERROR: cannot find glm-exposure

​My fsgd file is attached. Please any help would be greatly appreciated on this time sensitive matter.

Thank you, Shady​

On Thu, Nov 26, 2015 at 12:00 PM, <freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:

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Today's Topics:

   1. voxel value scaling (Rockers, Elijah D.)
   2. Re: voxel value scaling (Douglas Greve)
   3. Re: voxel value scaling (Rockers, Elijah D.)
   4. Re: Error - extracting percent signal (Douglas Greve)
   5. Re: bring volumes to fsaverage space (Andrew Bock)
   6. FS v.6.0 (Th?c Trinh)
   7. recon-all with more than 10 inputs (???)
   8. Re: Multiple comparisons to confirm atrophy (Anderson M.
Winkler)
   9. report a bug (salvatoreandrea.92@libero.it
<mailto:salvatoreandrea.92@libero.it>)


----------------------------------------------------------------------

Message: 1
Date: Wed, 25 Nov 2015 17:08:28 +0000
From: "Rockers, Elijah D." <edrockers@houstonmethodist.org
<mailto:edrockers@houstonmethodist.org>>
Subject: [Freesurfer] voxel value scaling
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: <5655EB0C.1000309@houstonmethodist.org
<mailto:5655EB0C.1000309@houstonmethodist.org>>
Content-Type: text/plain; charset="utf-8"

I am interested in finding a way to apply a slope scaling factor
to the
voxel values in a NIfTI image.

I have done this in MATLAB and PMOD so far, but for some reason both
methods change the origin or otherwise distort the dimensions of the
image and render it impossible for me to process further.

Something that simply scales the values without touching the
header (or
at least as little as possible) would be great. Is anything like this
out there?

Thanks,

Eli

Houston Methodist. Leading Medicine.

Ranked by U.S.News & World Report as one of America's "Best
Hospitals" in 11 specialties. Named to FORTUNE? Magazine's "100
Best Companies to Work For?" list 10 years in a row. Designated as
a Magnet hospital for excellence in nursing. Visit us at
houstonmethodist.org <http://houstonmethodist.org>. Follow us at
twitter.com/MethodistHosp <http://twitter.com/MethodistHosp> and
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------------------------------

Message: 2
Date: Wed, 25 Nov 2015 12:54:23 -0500
From: Douglas Greve <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] voxel value scaling
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID: <5655F5CF.8050907@nmr.mgh.harvard.edu
<mailto:5655F5CF.8050907@nmr.mgh.harvard.edu>>
Content-Type: text/plain; charset=utf-8; format=flowed

You can use  fscalc, something like
fscalc input.nii mul 10 -o output.nii
I think you can use fslmaths as well

On 11/25/15 12:08 PM, Rockers, Elijah D. wrote:
> I am interested in finding a way to apply a slope scaling factor
to the
> voxel values in a NIfTI image.
>
> I have done this in MATLAB and PMOD so far, but for some reason both
> methods change the origin or otherwise distort the dimensions of the
> image and render it impossible for me to process further.
>
> Something that simply scales the values without touching the
header (or
> at least as little as possible) would be great. Is anything like
this
> out there?
>
> Thanks,
>
> Eli
>
> Houston Methodist. Leading Medicine.
>
> Ranked by U.S.News & World Report as one of America's "Best
Hospitals" in 11 specialties. Named to FORTUNE? Magazine's "100
Best Companies to Work For?" list 10 years in a row. Designated as
a Magnet hospital for excellence in nursing. Visit us at
houstonmethodist.org <http://houstonmethodist.org>. Follow us at
twitter.com/MethodistHosp <http://twitter.com/MethodistHosp> and
www.facebook.com/HoustonMethodist
<http://www.facebook.com/HoustonMethodist>.
>
> ***CONFIDENTIALITY NOTICE*** This e-mail is the property of
Houston Methodist Hospital and/or its relevant affiliates and may
contain restricted and privileged material for the sole use of the
intended recipient(s). Any review, use, distribution or disclosure
by others is strictly prohibited. If you are not the intended
recipient (or authorized to receive for the recipient), please
contact the sender and delete all copies of the message. Thank you.
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------------------------------

Message: 3
Date: Wed, 25 Nov 2015 18:01:37 +0000
From: "Rockers, Elijah D." <edrockers@houstonmethodist.org
<mailto:edrockers@houstonmethodist.org>>
Subject: Re: [Freesurfer] voxel value scaling
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: "Pascual, Maria B." <BPascual@houstonmethodist.org
<mailto:BPascual@houstonmethodist.org>>, "Xue,  Zhong"
        <ZXue@houstonmethodist.org <mailto:ZXue@houstonmethodist.org>>
Message-ID: <5655F781.6000609@houstonmethodist.org
<mailto:5655F781.6000609@houstonmethodist.org>>
Content-Type: text/plain; charset="utf-8"

Great thank you!

On 11/25/2015 11:54 AM, Douglas Greve wrote:
> You can use  fscalc, something like
> fscalc input.nii mul 10 -o output.nii
> I think you can use fslmaths as well
>
> On 11/25/15 12:08 PM, Rockers, Elijah D. wrote:
>> I am interested in finding a way to apply a slope scaling
factor to the
>> voxel values in a NIfTI image.
>>
>> I have done this in MATLAB and PMOD so far, but for some reason
both
>> methods change the origin or otherwise distort the dimensions
of the
>> image and render it impossible for me to process further.
>>
>> Something that simply scales the values without touching the
header (or
>> at least as little as possible) would be great. Is anything
like this
>> out there?
>>
>> Thanks,
>>
>> Eli
>>
>> Houston Methodist. Leading Medicine.
>>
>> Ranked by U.S.News & World Report as one of America's "Best
Hospitals" in 11 specialties. Named to FORTUNE? Magazine's "100
Best Companies to Work For?" list 10 years in a row. Designated as
a Magnet hospital for excellence in nursing. Visit us at
houstonmethodist.org <http://houstonmethodist.org>. Follow us at
https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHosp&d=CwIGaQ&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=8n4cujoxKHxZUqyKPLhWvF6CDwsoST3qE1-UpVBy2Jc&s=90ErO06n0uvW3LGGzLcY8_miCTsjq_rUaK5lCHOhs34&e=
and
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.facebook.com_HoustonMethodist&d=CwIGaQ&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=8n4cujoxKHxZUqyKPLhWvF6CDwsoST3qE1-UpVBy2Jc&s=2bnJkXlkkepUmpEPsiW94Tl3NWj9KmPs6HSnQ5_Yn0c&e=
.
>>
>> ***CONFIDENTIALITY NOTICE*** This e-mail is the property of
Houston Methodist Hospital and/or its relevant affiliates and may
contain restricted and privileged material for the sole use of the
intended recipient(s). Any review, use, distribution or disclosure
by others is strictly prohibited. If you are not the intended
recipient (or authorized to receive for the recipient), please
contact the sender and delete all copies of the message. Thank you.
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
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>>
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=CwIGaQ&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=8n4cujoxKHxZUqyKPLhWvF6CDwsoST3qE1-UpVBy2Jc&s=kYq2Hf2HbvCMyTBr329UFqm1yXG1gsFkOflb6qTSjxk&e=
>>
>>
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------------------------------

Message: 4
Date: Wed, 25 Nov 2015 13:03:39 -0500
From: Douglas Greve <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Error - extracting percent signal
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID: <5655F7FB.8010801@nmr.mgh.harvard.edu
<mailto:5655F7FB.8010801@nmr.mgh.harvard.edu>>
Content-Type: text/plain; charset="windows-1252"

It looks like the ces input is from a surface-based analysis. If
you're
label is already on the surface, then no need to do the label2vol
step.
If it is in the volume, then you'll need to transfer it to the surface
with mri_label2label with the --paint option
doug

On 11/24/15 12:14 PM, Danielle Miller wrote:
> Hello freesurfer experts,
>
> I am trying to extract an average percent signal change from a
> functional roi label I created in tkmedit using fsaverage. I
followed
> previously discussed methods:
>
> 1) mri_label2vol --label <name of label> --temp
> fsaverage/mri.2mm/orig.mgz --regheader fsaverage/mri/orig.mgz --o
> <name of label mask>
>
> 2) I checked (tkmedit fsaverage orig.mgz -overlay <label mask>
> -fminmax .5 1) and the label looked fine
>
> 3) I ran mri_segstats --i ces.nii.gz --seg <label mask from above>
> --id 1 --avgwf ces.label.dat
> ces.nii.gz is the file from my group analysis (isxconcat-sess) using
> the correct contrast
> It returns with this error:
> ERROR: dimension mismatch between input volume and seg
>   input 163842 1 1
>   seg   76 76 93
>
> Is there something I am doing wrong here?
>
> Also of note I tried using the following commands:
> 1) funcroi-config -label <label mask created from above
mri_label2vol>
>  -analysis <analysis directory> -roi <name of roicfg file>
>
> 2) funcroi-sess -sf sessid - roi <roicfg file from above>
> But this returns with this error:
> ERROR: cannot find
>
/Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_001_recon/label/label_lh_ACC_correct_mask.mgz
>
>
> Any suggestions would be extremely helpful.
>
> Thanks,
> Danielle
> --
> Ph.D. Program in Behavioral Neuroscience
> Boston University School of Medicine L-815
> 72 E. Concord St
> Boston, MA 02118
>
>
> VA Boston Healthcare System Jamaica Plain
> Memory Disorders Research Center
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>
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