​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> wrote:

Send Freesurfer mailing list submissions to
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To subscribe or unsubscribe via the World Wide Web, visit
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."

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)

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

Message: 1
Date: Wed, 25 Nov 2015 17:08:28 +0000
From: "Rockers, Elijah D." <edrockers@houstonmethodist.org>
Subject: [Freesurfer] voxel value scaling
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <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. Follow us at twitter.com/MethodistHosp and 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.

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

Message: 2
Date: Wed, 25 Nov 2015 12:54:23 -0500
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] voxel value scaling
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <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. Follow us at twitter.com/MethodistHosp and 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.
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

Message: 3
Date: Wed, 25 Nov 2015 18:01:37 +0000
From: "Rockers, Elijah D." <edrockers@houstonmethodist.org>
Subject: Re: [Freesurfer] voxel value scaling
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: "Pascual, Maria B." <BPascual@houstonmethodist.org>, "Xue, Zhong"
<ZXue@houstonmethodist.org>
Message-ID: <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. 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
>> 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=
>>
>>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 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=
>
>
> 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
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=CwIGaQ&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=8n4cujoxKHxZUqyKPLhWvF6CDwsoST3qE1-UpVBy2Jc&s=E96MBu1BATGeDba1qAxIrp_OkpdkgP2OFa1TsirPb3M&e= . 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.

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

Message: 4
Date: Wed, 25 Nov 2015 13:03:39 -0500
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Error - extracting percent signal
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <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
> 150 South Huntington Ave D11-103
> Boston, MA 02130
> OFFICE:(857) 364-2130
>
>
>
> _______________________________________________
> Freesurfer mailing list
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Message: 5
Date: Wed, 25 Nov 2015 14:50:35 -0500
From: Andrew Bock <bock.andrew@gmail.com>
Subject: Re: [Freesurfer] bring volumes to fsaverage space
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: lzollei@nmr.mgh.harvard.edu
Message-ID:
<CAMaODrE+=z8eOqYc8eq1mNjCEfr1dnMOnVbyYAx2gim9nnJtPA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi all,

I am receiving the same error, using the same version of Freesurfer (
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0).

Was a solution found?

Andrew

On Mon, Nov 2, 2015 at 3:31 AM, Shani Ben Amitay <shani.holzer@gmail.com>
wrote:

> Dear Lilla and freesurfers,
>
> I hvae tried to rub the mri_CVS_register and got the following error:
> VolumeMorph load - failed to open input stream.
> I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> Any idea how to fix this>
> Log file atttached
> Thanks!
>
> Shani
>
> On Fri, Oct 30, 2015 at 11:17 PM, Lilla Zollei <
> lzollei@nmr.mgh.harvard.edu> wrote:
>
>>
>> Hi Shani,
>>
>> Sure. You can do
>>
>> mri_cvs_register --help
>>
>> and that should give you lots of information.
>>
>> Alternatively you can also go to
>> https://surfer.nmr.mgh.harvard.edu/fswiki/mri_cvs_register
>>
>> and read through the presentation that we give at the FS course:
>> http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.registration.ppt
>>
>> Best, Lilla
>>
>>
>> On Fri, 30 Oct 2015, Shani Ben Amitay wrote:
>>
>>
>>> Hello
>>> Can you please direct me to more information about the CVS.
>>> Thanks!
>>> Shani
>>>
>>> ?????? 30 ????' 2015 14:39, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu>
>>> ???:
>>> Hi Shani
>>>
>>> you can use mri_vol2vol with the talairach.m3z. Alternatively, you
>>> can run CVS which will give you more accurate cortical matching and use the
>>> transform that it produces.
>>>
>>> cheers
>>> Bruce
>>> On Fri, 30 Oct 2015, Shani Ben Amitay wrote:
>>>
>>> Dear freesurfers,
>>> I would like to know what will be the best way to bring
>>> volumes in the
>>> individual subject's space to the fsaverage space.
>>>
>>> Thanks,
>>> Shani
>>>
>>>
>>> _______________________________________________
>>> 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.
>>>
>>>
>>>
>> _______________________________________________
>> 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.
>>
>>
>
> _______________________________________________
> 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.
>
>
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Message: 6
Date: Thu, 26 Nov 2015 11:58:54 +0700
From: Th?c Trinh <thuctrinh187@gmail.com>
Subject: [Freesurfer] FS v.6.0
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CALnr=xuGwAo55B5u1k+0N6mvMy+U2EbTCVMNqo9NcXq6=Uz_Uw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hello Freesurfer experts,

I used recon-all command for all my subject by FS v.5.3. But now I decide
to upgrade to FS v.6 to eliminate some segmentation errors. The pial errors
still appear on the new output of FS v.6 Can I replace the braimask.mgz of
FS v.6 by the brainmask.mgz of FS v.5.3 (that been already fixed) to fixed
all the pial errors,

Have a nice day,
Trinh
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Message: 7
Date: Thu, 26 Nov 2015 13:10:54 +0800
From: ??? <dongnandi1@163.com>
Subject: [Freesurfer] recon-all with more than 10 inputs
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <003e01d12808$d4910be0$7db323a0$@163.com>
Content-Type: text/plain; charset="gb2312"

Dear freesurfer exports,

I am trying to recon more than 10 T1 scans from a single subject, but
something went wrong.

I have converted all T1 nifti files into mgz format into mri/orig directory
with following names: 001.mgz 002.mgz ?. 010.mgz 011.mgz? But when I run
the command:

?recon-all ?s ${subjec} ?autorecon1 ?notal?check ?clean-bm ?gcut ?
no-isrunning -noappend?,

it seems that recon-all only recognizes the files with names 01*.mgz(i.e.
0013.mgz), the 00*.mgz(i.e. 001.mgz) files failed to be processed. Once I
change the files name to ?001.mgz 002.mgz ?. 0010.mgz 0011.mgz?, the 00*.
mgz(i.e. 001.mgz) are able to be recognized, but the 001*.mgz(i.e. 0013.mgz)
files failed.

How should I deal with this to make all files recognized?

Sincerely,

Dong Haoming

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Message: 8
Date: Thu, 26 Nov 2015 07:03:47 -0200
From: "Anderson M. Winkler" <winkler@fmrib.ox.ac.uk>
Subject: Re: [Freesurfer] Multiple comparisons to confirm atrophy
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CALKxBNyz1sR8NtV-8YTL5K-v5d5DE=g74CihO=Yk1p4BCpr7Ng@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Clare,

This is something that PALM <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM>
can do. It seems we're in the same Dept. Please send me an email off-list
and we can try to have this sorted out.

All the best,

Anderson

On 19 November 2015 at 08:37, Clare Loane <clare.loane@ndcn.ox.ac.uk> wrote:

> Dear All,
>
> I have completed recon-all on my dataset of controls and patients. My
> patients have hippocampal/MTL atrophy and I would like to conduct multiple
> comparisons on the data to ensure that the atrophy is indeed focal in each
> patient and if not, identify where else atrophy is occurring in these
> patients. My hypothesis is that I do not expect atrophy elsewhere due to
> the disease type of these patients, but as this has never been
> confirmed outside of visual inspection before I wish to check this more
> robustly.
>
> I am not at all familiar with this kind of analysis and would like to ask
> some advice on how I should approach this? My initial instinct is to go
> with permutation testing. I would like to consider the whole brain (subcortical
> and surface).
>
> Are there other issues I should be taking into account?
>
> Any advice and specific information regarding the subsequent analysis in
> freesurfer would be greatly appreciated.
>
> Many thanks in advance.
>
> Clare
>
> _______________________________________________
> 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.
>
>
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Message: 9
Date: Thu, 26 Nov 2015 13:21:39 +0100 (CET)
From: "salvatoreandrea.92@libero.it" <salvatoreandrea.92@libero.it>
Subject: [Freesurfer] report a bug
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <1463619852.2181541448540499137.JavaMail.httpd@webmail-03>
Content-Type: text/plain; charset="utf-8"

Hi!
- I am using Ubuntu 14.4 (trusty).

- This is my subject directory: /home/salvatore/freesurfer/subjects

- This is the output of which recon-all (that is the tool I am trying to use): /home/salvatore/freesurfer/bin/recon-all

- The command line that I run is recon-all -s /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis -i /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis/T1.nii.gz -all

Following the error that I got after 12 hours of processing:

sysname Linux
hostname salvatore-HP-630-Notebook-PC
machine x86_64

setenv SUBJECTS_DIR /home/salvatore/freesurfer/subjects
cd /home/salvatore/freesurfer/subjects/FreeSurfer_analysis/mri
mri_ca_label -align norm.mgz transforms/talairach.m3z /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz

renormalizing sequences with structure alignment, equivalent to:
-renormalize
-renormalize_mean 0.500
-regularize 0.500
reading 1 input volumes...
reading classifier array from /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca...
reading input volume from norm.mgz...
Killed
Linux salvatore-HP-630-Notebook-PC 3.19.0-33-generic #38~14.04.1-Ubuntu SMP Fri Nov 6 18:17:28 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s FreeSurfer_analysis exited with ERRORS at gio 26 nov 2015, 12.42.40, CET

Could you please help me to fix this problem? I tried to ran it again in an other terminal, without succeding...Thank you

Best,

Salvatore

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End of Freesurfer Digest, Vol 141, Issue 43
*******************************************