Re: [Freesurfer] PVE correction tool on Freesurfer 6

[Lee Subin Kristine]

Hi Doug,


Thanks a lot for the page! It was very helpful.


I have a few questions about one of the commands and a question for one of the 
output files.


1) mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz 
--default-seg-merge --auto-mask PSF .01 --mgx .01 --o gtmpvc.output

(a) For the psf flag, do I have to know exactly the FWHM of the point-spread 
function of the scanner or would a default value of 6 work for all? I am using 
PET images from multiple centers and thus each image are from different 
scanners, and I'm not sure how I would find the fwhm for each scanner.

(b) For the mgx flag, is the GM threshold .01 an optimal threshold referring to 
the p-value?(am new to PVEcorrection and asking out of curiosity) What is the 
difference if I enter .01 versus I don't enter it?


2) From the gtm.stats.dat output file, the 5th column(number of PET voxels in 
the ROI) of, for example, the ctx-lh-precuneus and ctx-rh-precuneus are 1744 
and 1805 respectively. However, in the ?h.aparc.stats files from recon-all, the 
4th column(gray matter volume) of lh-precuneus and rh-precuneus are 5928 and 
6125 respectively. I am confused because I thought the number of PET voxels 
should be equal to the number of GM voxels in the ROI?

Also, for output files such as gtm.nii.gz or nopvc.nii.gz, what programs can I 
open them with? It doesn't seem it is openned with mricron or gedit.


Thank you again in adavnce for your help.


Best,

Subin


보낸 사람: Douglas N Greve  대신 
freesurfer-boun...@nmr.mgh.harvard.edu 
보낸 날짜: 2016년 7월 8일 금요일 오전 2:53:31
받는 사람: freesurfer@nmr.mgh.harvard.edu
제목: Re: [Freesurfer] PVE correction tool on Freesurfer 6

Hi Subin, I just created this page this morning
http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
do you want to take a look and see if it answers your questions. As for
#2, yes you still need to run gtmseg.

On 06/26/2016 07:45 AM, Lee Subin Kristine wrote:
>
> Hello,
>
> I am trying to use PVE correction on preprocessed PET data downloaded
> from the Alzheimer's Disease Neuroimaging Initiative(ADNI) database.
> I have a couple of questions:
>
>
> 1) I am using the co-registered, averaged image of the dynamic images,
> and it seems from your answers here
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43435.html)
> that
> for static PET images, #3~5 will be different. Could you explain how I
> would need to enter the command differently?
>
> 2) I already have segmentations of my MRI images obtained via
> FreeSurfer(v.5.2)'s cortical parcellation. Would I still have to do
> procedure #1 (gtmeseg --s subject) ? I did try using xcerebralseg
> because it seemed from the help command that in my case where I
> already have some FS segmentations that I should use this one:
>
> /You can use your own segmentation or a modified FS segmentation. //
> //It will be easiest if you modify apas+head.mgz to insert your//
> //segmentations. apas+head.mgz is created by gtmseg but you can//
> //create it with //
> /
> /xcerebralseg --s $subject --o $SUBJECTS_DIR/$subject/mri/apas+head.mgz/
>
> However when I do try I got the following error:
>
> /ERROR: could not open
> /usr/local/freesurfer/subjects/002_S_4213/stats/002_S_4213/mri/apas+head.stats
> for writing//
> //Errno: No such file or directory/
>
>
>
> Thanks a lot in advance,
>
> Regards,
> Subin
>
>
>
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--
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] TRACULA group stats visualization

[Derek Pisner]

Hi Anastasia,

All subjects had both time-points (for DWI and T1-weighted recons). The recons 
were run following the standard longitudinal pipeline for FS.

Would it matter that I ran the pipeline piecemeal (i.e. separate configuration 
files for each subject--see attached example)? In case you are wondering, I did 
it this way in order to run the pipeline in parallel (i.e. by subject) on our 
cluster...

Another consideration is that we did preprocessing outside of TRACULA (i.e. 
using FSL's tools directly so that we could apply a fieldmap, use new EDDY with 
TOPUP, as well as apply a denoising algorithm). We then setup the folder 
structure and filenames to begin TRACULA at the trac-all -intra stage, which we 
have done successfully in the past when not using the longitudinal pipeline 
(i.e. single-subject analyses)

Still, I have a feeling that none of these customizations should have made any 
difference as our merged outputs look excellent for both timepoints, for all 
subjects... Any other thoughts about what might be causing this?

Kind regards,
-Derek

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu]
Sent: Tuesday, July 12, 2016 1:45 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA group stats visualization

Hi Derek - Indeed this looks not to be in MNI coordinates, and I haven't
been able to replicate the problem in our own longitudinal data. Did you
by any chance have any subjects that had only a single time point?

a.y

On Thu, 7 Jul 2016, Derek Pisner wrote:

> Sure thing. fmajor mean.txt file is attached.
>
>
> Thanks a bunch,
> -Derek
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Thursday, July 07, 2016 4:48 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] TRACULA group stats visualization
>
> Hi Derek - this is strange. The dev and 5.3 version of freeview should
> display them differently. Can you send me one of those mean.txt files?
>
> a.y
>
> On Wed, 6 Jul 2016, Derek Pisner wrote:
>
>> Hi Anastasia,
>>
>> This occurs for me on both stable and dev versions of freview and trac-all 
>> -stat
>>
>> -Derek
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
>> [ayend...@nmr.mgh.harvard.edu]
>> Sent: Monday, July 04, 2016 12:47 AM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] TRACULA group stats visualization
>>
>> Hi Derek - Are you by any chance using the dev version of freeview?
>>
>> a.y
>>
>> On Fri, 1 Jul 2016, Derek Pisner wrote:
>>
>>> Dear Anastasia,
>>> I am running into an issue with the trac-all -stat option on our 
>>> longitudinal TRACULA data.
>>>
>>> Everything runs smoothly through all earlier stages, and I checked 
>>> individual subjects' merged outputs in freeview with -tv mode. Everything 
>>> looks fine.
>>>
>>> Also, then when I run trac-all -c dmric_config -stat, everything finishes 
>>> without error.
>>>
>>> But then when I open the results with the command:
>>> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w 
>>> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt
>>>
>>> I get the image seen in the attached .png file. Any idea what might be 
>>> causing this?
>>>
>>> Many thanks in advance for you help.
>>>
>>> Best,
>>> Derek
>>>
>>>
>>>
>>>
>>
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>>
>>
>>
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>
>
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> 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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#!/bin/tcsh
set workingDIR = "/data/blt/TRACULA"
set SUBJECTS_DIR = $workingDIR/diffusion_recons
setenv SUBJECTS_DIR $workingDIR/diffusion_recons

setenv FREESURFER_HOME /usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh

set dtroot =  $workingDIR/tractography_output

set subjlist = ( BL01_1 \
BL01_2 )

set baselist= ( BL01_1 \
BL01_2 )

set dcmlist = ( 

Re: [Freesurfer] FreesurferNHP

[Matt Glasser]

We haven¹t yet released our NHP pipeline yet, mainly because the software
support requirements are a bit higher and so it has made more sense to
work with people as a part of collaborations.  This is more of a question
for the HCP Users list or an off-list inquiry because the FreeSurfer group
doesn¹t have anything to do with the FreeSurferNHP pipeline.

Peace,

Matt.

On 7/12/16, 9:17 AM, "Moeller, Sebastian"
 wrote:

>Hi Peter,
>
>> On Jul 12, 2016, at 14:42 , Lauro, Peter  wrote:
>> 
>> Hello,
>> 
>> I'm trying to reconstruct cortical surfaces from non-human primate
>>MRIs. I tried following the instructions/scripts listed here
>>(https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData), but I was unable
>>to make it work (I¹m also running FS 5.3).
>
>   What went wrong?
>
>Best Regards
>   Sebastian
>
>> I noticed on the Washington-Pipelines github FAQ page listed a
>>FreesurferNHP pipeline
>>(https://github.com/Washington-University/Pipelines/wiki/FAQ#9-what-if-i-
>>want-to-process-non-human-primate-nhp-data-with-the-hcp-pipelines), but
>>it hasn't been released yet.
>> 
>> Do you know when this pipeline will be available? Alternatively, is
>>there another way I can obtain the pipeline scripts and template volumes?
>> 
>> Thank you,
>> Pete Lauro
>> 
>> ___
>> 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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Re: [Freesurfer] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message

[Anastasia Yendiki]

Hi Knut Jørgen - Can you please send your entire trac-all.log? Thanks!

a.y

On Mon, 11 Jul 2016, Knut J Bjuland wrote:



 


flirt.fsl -ref
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/refvol.fslregister.nii
-in
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/movvol.fslregister.nii
-bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90
-searchrz -90 90 -verbose 0 -omat
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/reg.init.dat.fsl.mat
-init
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/fslmat0.trans.mat
-schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch

terminate called after throwing an instance of
'NEWMAT::SingularException'

Abort (core dumped) 

ERROR: flirt





Fedora 24


glibc-2.23.1-8.fc24.x86_64

gcc-6.1.1-3.fc24.x86_64


libstdc++-6.1.1-3.fc24.x86_64

ldd /usr/local/freesurfer/bin/flirt.fsl 

    linux-vdso.so.1 (0x7ffe8b6c8000)

    libz.so.1 => /lib64/libz.so.1 (0x7feaeba06000)

    libstdc++.so.6 => /lib64/libstdc++.so.6
(0x7feaeb67e000)

    libm.so.6 => /lib64/libm.so.6 (0x7feaeb374000)

    libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x7feaeb15d000)

    libc.so.6 => /lib64/libc.so.6 (0x7feaead9a000)

    /lib64/ld-linux-x86-64.so.2 (0x557ba6f46000)







Knut Jørgen Bjuland


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Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - This may be a bug that was fixed at some point. Can you send me 
the scripts/trac-all.local-copy from one of your subjects? Thanks!


a.y

On Mon, 11 Jul 2016, Anri WATANABE wrote:


Hi Anastasia,There is an error in .log files of left corticospinal tract in cvs 
template and I attached one
of file. In addition .log files of right corticospinal tract in cvs template 
doesn't exist. 
Thanks in advance.

Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-07 20:12 GMT+09:00 Anastasia Yendiki :

  Hi Anri - Is there an error in the stats/*.log files for the different 
tracts?

  a.y

  On Tue, 5 Jul 2016, Anri WATANABE wrote:

Dear Anastasia, 

I use TRACULA to obtain diffusion measures at each voxel in a 
certain pathway for
group analysis, but
there aren't stats/*.path.mean.txt files. I found .log files
(_PP.avg33_mni_bbr.log) which exist
1 file per 1 tract, except corticospinal tract which has 2 .log 
files.

Command: trac-all –stat –c 
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

Error log: Loading output reference volume from
/Applications/freesurfer/subjects/cvs_avg35

corRead(): can't open file 
/Applications/freesurfer/subjects/cvs_avg35/COR-.info

ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35


I attached dmrirc.example (configuration file) and 
/scripts/trac-all.log.


Thanks in advance,
Anri





**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-06-03 9:51 GMT+09:00 Anri WATANABE :
      Hi, Anastasia.
There aren't any .log files but text files like 
lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt.
I guess text
files complete all pathways and measures.


**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-06-02 3:03 GMT+09:00 Anastasia Yendiki 
:

      Thanks, Anri. So the previous steps seem to have run fine. 
Are there any .log
files
      created in the stats/ folder, which is created by trac-all 
-stat?

      On Wed, 1 Jun 2016, Anri WATANABE wrote:

            Hi Anastasia, This is a /scripts/trac-all.log 
of one subject of
            the group.

            Thanks,
            Anri

            
**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
            
**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural University of 
Medicine
            
**

            2016-05-31 22:55 GMT+09:00 Anastasia Yendiki
            :

                  Hi Anri - Can you also send your log file 
(scripts/trac-all.log)?
            I'll need to see what
                  exactly was running when the error occurred. 
Thanks!

                  a.y

                  On Sat, 28 May 2016, Anri WATANABE wrote:

                        Hello Anastasia,sorry for few information 
and let me tell
you
            command and
                        error log.
                        Command: trac-all –stat –c
            $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

Re: [Freesurfer] TRACULA tract group comparison p-values

[Anastasia Yendiki]

Hi Barbara - Unfortunately we are very limited right now in our options 
for point set overlay display. I guess there's nothing that would be more 
suitable for displaying values that go all the way from negative to 
positive (which is what I suspect you have).

I'll submit this request to freeview headquarters :) Hopefully we can get 
it in there quickly. Thanks for your patience!

a.y

On Sun, 10 Jul 2016, Barbara Kreilkamp wrote:

> Dear Anastasia,
>
> Thank you, yes that was exactly what I was attempting to do. Would you
> be able to assist me with this following question as well please?
>
> How would I be able to use a different colormap under point sets please?
> I can only find "solid color" and "heatmap" but for example a
> blue-yellow-to-red colormap would suit my needs more.
>
> Thank you,
>
> Best wishes,
>
> Barbara
>
>
> On 07/07/2016 13:52, Anastasia Yendiki wrote:
>> Hi Barbara - I don't believe that freeview has an option to show colorbars
>> for heat maps that are loaded onto waypoints (if that's what you're
>> trying to display). We should definitely add it in the future.
>>
>> Best,
>> a.y
>>
>> On Wed, 6 Jul 2016, Barbara Kreilkamp wrote:
>>
>>> Dear Freesurfers,
>>>
>>> I am looking for a way to add a colorbar to my p-value tract cores
>>> generated through TRACULA.
>>>
>>> When I load up the images as described in the tutorial here
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
>>>
>>> I only get a colorbar from 0 to 28.5 which cannot reflect pvalues, and
>>> there is no option to select my textfile with the p-values unfortunately.
>>>
>>> Would you please help?
>>>
>>> Thanks ever so,
>>>
>>> Barbara
>>>
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>>>
>>>
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>>
>>
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>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
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Re: [Freesurfer] Fwd: TRACULA stat extraction issue

[Anastasia Yendiki]

Hi Shashwath - Unfortunately this is not possible right now, so you'd have 
to add those extra columns after you run it.


a.y

On Fri, 8 Jul 2016, Shashwath Meda wrote:


Hi Anastasia - Yes thats what i figured, however the way our pipeline system is 
setup this was the most
straightfoward way of doing it. Anyways i did figure out how to extract the 
average values in a more
convoluted fashion so we are all set with that. However,  im trying to do the 
same with the trac-all -stat
command now to extract pathbyvoxel stats and am having issues. I see that while 
assimilating group level
info, the program automatically rejects or doesnt ouput a column for the 
subject that has failed, is there
a quick and dirty fix to the code that will enable me to output all subjects 
data even if its failed (maybe
replace the values with NaN or somethign similar for failed subjects?). Please 
let me know.
Thanks
Shashwath

On Mon, Jul 4, 2016 at 3:25 AM, Anastasia Yendiki 
 wrote:

  Hi Shashwath - It looks like you have modified the directory structure of 
the output files.
  Normally the dpath/ directory is right under the directory with subject's 
name. From your file
  of inputs, it looks like you've created some other subdirectories and now 
dpath/ is a few
  levels down the hierarchy. I'd recommend reverting to the original 
structure that the commands
  expect.

  Best,
  a.y

  On Fri, 10 Jun 2016, Shashwath Meda wrote:

Dear Group -  I seem to have run into an issue when attempting to 
assimilate the
averaged pathway information from TRACULA into a group table. I have
attached my input list of paths and my output table for one of the 
tracts.
The below is the command that i have used but as you can see the 
values in my final
table are all from one subject (just replicated) despite my input 
list
having paths from different subjects, Has anyone encountered a 
similar situation?

tractstats2table --load-pathstats-from-file 
fmajor_PP_avg33_mni_bbr.txt --overall
--tablefile fmajor_PP_avg33_mni_bbr.table


--
Best,
Shashwath



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--
Best,
Shashwath

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Re: [Freesurfer] TRACULA group stats visualization

[Anastasia Yendiki]

Hi Derek - Indeed this looks not to be in MNI coordinates, and I haven't 
been able to replicate the problem in our own longitudinal data. Did you 
by any chance have any subjects that had only a single time point?

a.y

On Thu, 7 Jul 2016, Derek Pisner wrote:

> Sure thing. fmajor mean.txt file is attached.
>
>
> Thanks a bunch,
> -Derek
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Thursday, July 07, 2016 4:48 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] TRACULA group stats visualization
>
> Hi Derek - this is strange. The dev and 5.3 version of freeview should
> display them differently. Can you send me one of those mean.txt files?
>
> a.y
>
> On Wed, 6 Jul 2016, Derek Pisner wrote:
>
>> Hi Anastasia,
>>
>> This occurs for me on both stable and dev versions of freview and trac-all 
>> -stat
>>
>> -Derek
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
>> [ayend...@nmr.mgh.harvard.edu]
>> Sent: Monday, July 04, 2016 12:47 AM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] TRACULA group stats visualization
>>
>> Hi Derek - Are you by any chance using the dev version of freeview?
>>
>> a.y
>>
>> On Fri, 1 Jul 2016, Derek Pisner wrote:
>>
>>> Dear Anastasia,
>>> I am running into an issue with the trac-all -stat option on our 
>>> longitudinal TRACULA data.
>>>
>>> Everything runs smoothly through all earlier stages, and I checked 
>>> individual subjects' merged outputs in freeview with -tv mode. Everything 
>>> looks fine.
>>>
>>> Also, then when I run trac-all -c dmric_config -stat, everything finishes 
>>> without error.
>>>
>>> But then when I open the results with the command:
>>> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w 
>>> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt
>>>
>>> I get the image seen in the attached .png file. Any idea what might be 
>>> causing this?
>>>
>>> Many thanks in advance for you help.
>>>
>>> Best,
>>> Derek
>>>
>>>
>>>
>>>
>>
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Re: [Freesurfer] Freeview question

[pfotiad]

Yes, that worked Thank you.

> Have you tried rebooting your computer?
>
> Best,
> Ruopeng
>
>> On Jul 12, 2016, at 3:14 PM, pfot...@nmr.mgh.harvard.edu wrote:
>>
>> Hello FS Community,
>> Lately, whenever I am trying to use freeview I get the following error
>> message:
>>
>> freeview.bin: error while loading shared libraries:
>> libvtkverdict.so.5.6:
>> cannot open shared object file: No such file or directory
>> Exit 127
>>
>> The error started showing up after the cluster went down. I was
>> wondering
>> whether there was a way to fix this since I don't have admin privileges
>> (and hence can't sudo).
>>
>> Thanks in advance,
>> Panos
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>>
>
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>
>

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Re: [Freesurfer] Freeview question

[Ruopeng Wang]

Have you tried rebooting your computer?

Best,
Ruopeng

> On Jul 12, 2016, at 3:14 PM, pfot...@nmr.mgh.harvard.edu wrote:
> 
> Hello FS Community,
> Lately, whenever I am trying to use freeview I get the following error
> message:
> 
> freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6:
> cannot open shared object file: No such file or directory
> Exit 127
> 
> The error started showing up after the cluster went down. I was wondering
> whether there was a way to fix this since I don't have admin privileges
> (and hence can't sudo).
> 
> Thanks in advance,
> Panos
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> 

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[Freesurfer] Slight rotation when viewing brainmask.mgz in Freeview - why and is this a cause for concern?

[Reema Jayakar]

Hello FS developers/users,

When viewing brainmask.mgz in Freeview, for some subjects the brain is
slightly (~10-20 degrees) rotated. By looking at the raw data, I see that
their head position in the scanner was slightly skewed.

I thought  that brainmask.mgz is created after Talairach transformation and
normalization has been completed. I took this to mean that the
brainmask.mgz file has been registered to an atlas. If so, shouldn't the
brainmask.mgz files for all subjects appear with 0 rotation in freeview?
Should I be concerned that this is not the case for my dataset?

Thanks for your help!
Reema

-- 
*Reema Jayakar, M.A.*
Doctoral Candidate - Clinical Neuropsychology
Health Resources and Services Administration (HRSA) Fellow
Department of Psychology
Georgia State University
Email: rjayak...@student.gsu.edu
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[Freesurfer] Freeview question

[pfotiad]

Hello FS Community,
Lately, whenever I am trying to use freeview I get the following error
message:

freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6:
cannot open shared object file: No such file or directory
Exit 127

The error started showing up after the cluster went down. I was wondering
whether there was a way to fix this since I don't have admin privileges
(and hence can't sudo).

Thanks in advance,
Panos
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[Freesurfer] Visually inspecting subcortical segmentations + what command should be run to apply manual fixes to aseg.mgz voxels?

[Reema Jayakar]

Hello FS developers/users,

I have a two part question regarding subcortical segmentation:

1) To visually inspect if segmentation accurately captures structure
boundaries (e.g., amygdala) I am using the norm.mgz file and overlaying it
with the aseg.mgz file in Freeview.
Is this correct? Or should I be using brainmask.mgz (instead of norm.mgz)?
Also, Freeview gives me some options - "Resample to standard RAS space" and
"Apply registration file". Where can I find information about whether or
not to use these options?

2) If I manually edit the boundaries of the amygdala (either by erasing
voxels or using the color brush to add voxels), what command should I use
to re-run such that the corrections are applied to my aseg.stats output?
The command I found on the wiki page says to use recon-all
-autorecon-2-noaseg -subjid . My understanding was that the
-noaseg flag will skip all the subcortical segmentation steps and that is
not what I want. What I want is for FS to re-run subcortical segmentation
such that it reflects the voxel editing I did in Freeview.

This is the first time I am doing something like this so any help you can
provide or pointing me to the right resource would be great!

Thank you!
Reema

-- 
*Reema Jayakar, M.A.*
Doctoral Candidate - Clinical Neuropsychology
Health Resources and Services Administration (HRSA) Fellow
Department of Psychology
Georgia State University
Email: rjayak...@student.gsu.edu
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Re: [Freesurfer] mri_glmfit-sim

[greve]

There were bugs in AlphaSim (not FSL randomise); these do not affect FS
because FS is an independent implementation.

FS does not use random field theory (RFT) but monte carlo simulation. The
MC simulation does assume that the smoothing kernel is gaussian, so
violations of that assumption will result in inaccurate results from the
MC simulation. The PNAS paper found that the actual kernel had a heavier
tail than gaussian resulting in larger clusters than expected and so more
false positives.

I am in the process of doing similar analyses on thickness data. I'll will
report when I have finalized them.


> Dear Freesurfers,
> As freesurfer mri_glmfit-sim is based on AlphaSim & FSL randomise, I would
> like to know if the results I’m getting are affected by recently found
> bugs/violations in RFT assumptions, e.g.
> http://www.pnas.org/content/early/2016/06/27/1602413113.full.pdf.
>
> Thank you in advance!
> Lauri Tuominen
>
>
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[Freesurfer] CVS question

[Michael Zeineh]

Hi,

I want to compare two populations using CVS so I can cross-register multimodal 
maps (e.g. ASL, FA, QSM) for volumetric comparisons.

I’ve gotten CVS to work very well registering one subject to another, it really 
is impressive

However, using the --mni option, it doesn’t work so well, perhaps because the 
atlas is so averaged together and smoothed out, the images look highly warped.

I know I can pick a subject at random, and register everything to that, but 
that may induce some biases. The following website suggests I might try simply 
creating my own atlas (under the answers to Nov 2014 course questions): 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers 


Seems like they register 40 subjects with each other for multiple iterations, 
average the brain together, then run recon-all on that. How does one actually 
do that, however? i.e. 1st round, register everyone to subject 1 … then what? 
Seems like somehow you would want a registration intermediate point somehow?

Any help would be great, thank you!

Michael Zeineh, M.D.-Ph.D.
Assistant Professor, Dept. of Radiology
Stanford University
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[Freesurfer] Beta-Zero Correction - No Phase File

[Afzal, Afsana]

Hi,

I'm working with a dataset that outputs only one file (not two separate mag and 
phase files) for the fieldmap. The data was also collected on non-Siemens 
scanners: Philips Ingenia and GE SIGNA HDx (not sure if this is the reason the 
fieldmaps are unpacking differently). I've attached the .dat file for one of 
the fieldmaps in this email.

If there a way to separate out the mag and phase from the single fieldmap file 
so I can use epidewarp.fsl?

Thanks,

Afsana

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078


b0map-infodump.dat
Description: b0map-infodump.dat
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Re: [Freesurfer] tcsh update

[Z K]

On ubuntu it would be something like:

   sudo apt-get update tcsh



On 07/11/2016 01:55 PM, shi yao wang wrote:
> Dear FS experts:
> I am running FS in local computer and showing following error message
> and program stopped at recon-all
>
> WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
>
> Do I need to update tcsh? and how can I do it.
>
> thanks
> Lawrence
>
>
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[Freesurfer] mri_convert WARNING: files are not found to be different and cannot be sorted

[Olivia Walton Stanley]

Hello all,

I have run mri_convert on a series of dicoms and received the following error 
for several of my images. As with the previous bug report for this I have run 
mri_info on my dicom series and it’s output is below. My main concern is since 
these dicoms are being jumbled up and I am not sure what that warning means. Is 
it the dicom header it is comparing? Can you elaborate or put me on track to 
debug this error?

Thanks,

Olivia

mri_info is below:

mri_info 500/Image_SLC0_CON0_PHS0_REP1_SET0_AVE0_2.dcm 
Getting Series No 
Scanning Directory 
INFO: Found 9218 files in 500
INFO: Scanning for Series Number 3076
INFO: found 4608 files in series
INFO: loading series header info.

INFO: sorting.
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC0_CON0_PHS0_REP13_SET0_AVE0_2.dcm
File2: 500/Image_SLC0_CON0_PHS0_REP1_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC0_CON0_PHS0_REP25_SET0_AVE0_2.dcm
File2: 500/Image_SLC0_CON0_PHS0_REP2_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC0_CON0_PHS0_REP37_SET0_AVE0_2.dcm
File2: 500/Image_SLC0_CON0_PHS0_REP3_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC0_CON0_PHS0_REP49_SET0_AVE0_2.dcm
File2: 500/Image_SLC0_CON0_PHS0_REP4_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC0_CON0_PHS0_REP5_SET0_AVE0_2.dcm
File2: 500/Image_SLC0_CON0_PHS0_REP61_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC0_CON0_PHS0_REP6_SET0_AVE0_2.dcm
File2: 500/Image_SLC0_CON0_PHS0_REP73_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC0_CON0_PHS0_REP7_SET0_AVE0_2.dcm
File2: 500/Image_SLC0_CON0_PHS0_REP85_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC10_CON0_PHS0_REP1_SET0_AVE0_2.dcm
File2: 500/Image_SLC10_CON0_PHS0_REP20_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC10_CON0_PHS0_REP2_SET0_AVE0_2.dcm
File2: 500/Image_SLC10_CON0_PHS0_REP32_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC10_CON0_PHS0_REP4_SET0_AVE0_2.dcm
File2: 500/Image_SLC10_CON0_PHS0_REP56_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC10_CON0_PHS0_REP3_SET0_AVE0_2.dcm
File2: 500/Image_SLC10_CON0_PHS0_REP44_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC10_CON0_PHS0_REP5_SET0_AVE0_2.dcm
File2: 500/Image_SLC10_CON0_PHS0_REP68_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC10_CON0_PHS0_REP6_SET0_AVE0_2.dcm
File2: 500/Image_SLC10_CON0_PHS0_REP80_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC11_CON0_PHS0_REP0_SET0_AVE0_2.dcm
File2: 500/Image_SLC11_CON0_PHS0_REP10_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC10_CON0_PHS0_REP7_SET0_AVE0_2.dcm
File2: 500/Image_SLC10_CON0_PHS0_REP92_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC11_CON0_PHS0_REP1_SET0_AVE0_2.dcm
File2: 500/Image_SLC11_CON0_PHS0_REP22_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC11_CON0_PHS0_REP3_SET0_AVE0_2.dcm
File2: 500/Image_SLC11_CON0_PHS0_REP46_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC11_CON0_PHS0_REP4_SET0_AVE0_2.dcm
File2: 500/Image_SLC11_CON0_PHS0_REP58_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC11_CON0_PHS0_REP6_SET0_AVE0_2.dcm
File2: 500/Image_SLC11_CON0_PHS0_REP82_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC11_CON0_PHS0_REP7_SET0_AVE0_2.dcm
File2: 500/Image_SLC11_CON0_PHS0_REP94_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC11_CON0_PHS0_REP5_SET0_AVE0_2.dcm
File2: 500/Image_SLC11_CON0_PHS0_REP70_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC11_CON0_PHS0_REP2_SET0_AVE0_2.dcm
File2: 500/Image_SLC11_CON0_PHS0_REP34_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC11_CON0_PHS0_REP106_SET0_AVE0_2.dcm
File2: 500/Image_SLC11_CON0_PHS0_REP8_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 500/Image_SLC10_CON0_PHS0_REP104_SET0_AVE0_2.dcm
File2: 500/Image_SLC10_CON0_PHS0_REP8_SET0_AVE0_2.dcm
WARNING: files are not found to be different and cannot be sorted
File1: 

Re: [Freesurfer] FreesurferNHP

[Moeller, Sebastian]

Hi Peter,

> On Jul 12, 2016, at 14:42 , Lauro, Peter  wrote:
> 
> Hello,
> 
> I'm trying to reconstruct cortical surfaces from non-human primate MRIs. I 
> tried following the instructions/scripts listed here 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData), but I was unable to 
> make it work (I’m also running FS 5.3).

What went wrong?

Best Regards
Sebastian

> I noticed on the Washington-Pipelines github FAQ page listed a FreesurferNHP 
> pipeline 
> (https://github.com/Washington-University/Pipelines/wiki/FAQ#9-what-if-i-want-to-process-non-human-primate-nhp-data-with-the-hcp-pipelines),
>  but it hasn't been released yet.
> 
> Do you know when this pipeline will be available? Alternatively, is there 
> another way I can obtain the pipeline scripts and template volumes?
> 
> Thank you,
> Pete Lauro
> 
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> 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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Re: [Freesurfer] Regarding: Concatenating hippocampal to generate sig.mgh

[Bruce Fischl]

Hi Sampada

why not just take the volume of the hippocampus from the aseg.stats?  Why 
do you want an mgz? You just want one number per subject, right?


Bruce


On Tue, 12 Jul 2016, Dr Sampada Sinha wrote:


Dear Bruce, 

Thanks for you for your response. I am trying to  generate an average
hippocampal volume and its correlation with HAM-D score in early and late
onset depression (eod vs lod). One way I tried to do it was by binarizing
and concatanating the hippocampal volumes and then run mri_glmfit. But, I am
stuck at glm_fit and would be grateful if you can let me know how to proceed
from here. How do I run the glm_fit between eod and lod patients? Secondly,
after running glm_fit how do I calculate the significance from sig.mgh?

Appreciate all your help. 

Thanks and regards,

Sampada

On Sun, Jul 10, 2016 at 7:15 PM, Bruce Fischl 
wrote:
  Hi Sampada

  can you elaborate a bit? What are you trying to achieve? Do you
  want an
  average hippocampus? Average maps of subfields? What hypothesis
  are you
  trying to test? The individual subject data is not resampled to
  a common
  coordinate system, so just averaging them as is won't produce
  anything
  interested.

  cheers
  Bruce

  On Sun, 10 Jul 2016, Dr
  Sampada Sinha wrote:

  > Dear freesurfer experts,
  > Will you please let me know if it's possible to get one
  average mgz image
  > file by concatenating the hippocampal volumes of different
  subjects using
  > dev version? Since, I already have the hippocampal subfields
  mgz volume
  > files, I intend to run the glmfit later on between two groups
  to get sig.mgh
  > files.
  >
  > Thanks and regards?
  >
  > Sampada
  >
  >
  > --
  > Sampada
  > Pre-doctoral student
  > Department of Geriatric Mental Health (DGMH)
  > King George Medical University
  > Lucknow-226003
  > India
  >
  >
  >
  >
  >
  >
  >
  >
  >
  >
  >
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--
Sampada
Pre-doctoral student
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003
India









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[Freesurfer] FreesurferNHP

[Lauro, Peter]

Hello,

I'm trying to reconstruct cortical surfaces from non-human primate MRIs. I
tried following the instructions/scripts listed here (
https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData), but I was unable to
make it work (I'm also running FS 5.3). I noticed on the
Washington-Pipelines github FAQ page listed a FreesurferNHP pipeline (
https://github.com/Washington-University/Pipelines/wiki/FAQ#9-what-if-i-want-to-process-non-human-primate-nhp-data-with-the-hcp-pipelines),
but it hasn't been released yet.

Do you know when this pipeline will be available? Alternatively, is there
another way I can obtain the pipeline scripts and template volumes?

Thank you,
Pete Lauro
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[Freesurfer] R: Re: Recon-all error after El Capitain update

[stdp82]

This is the command and the error line.
Thanks.
Stefano


recon-all -all -i $SUBJECTS_DIR/T1_STRUCT.nii.gz -subject SUBJECTS_DIR 

#
INFO: fsaverage subject does not have perirhinal labels!
\n cd /Applications/freesurfer/subjects/subject_prova/Control89; rm -Rf 
fsaverage; cd - \n
INFO: Creating symlink to fsaverage subject...
\n cd /Applications/freesurfer/subjects/subject_prova/Control89; ln -s 
/Applications/freesurfer/subjects/fsaverage; cd - \n
\n mri_label2label --srcsubject fsaverage --srclabel 
/Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh.
BA1.label --trgsubject SUBJECTS_DIR --trglabel ./lh.BA1.label --hemi lh --
regmethod surface \n
No such file or directory
mri_label2label: could not open label file 
/Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh.
BA1.label

srclabel = 
/Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh.
BA1.label
srcsubject = fsaverage
trgsubject = SUBJECTS_DIR
trglabel = ./lh.BA1.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR/Applications/freesurfer/subjects/subject_prova/Control89
FREESURFER_HOME /Applications/freesurfer
Loading source label.
No such file or directory
ERROR reading 
/Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh.
BA1.label
Darwin iMac-di-Stefano.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 
18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64

recon-all -s SUBJECTS_DIR exited with ERRORS at Sat Jul  9 17:20:34 CEST 2016

For more details, see the log file 
/Applications/freesurfer/subjects/subject_prova/Control89/SUBJECTS_DIR/scripts/recon-
all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



>Messaggio originale
>Da: "dgw" 
>Data: 7-lug-2016 15.58
>A: , "Freesurfer support list"
>Ogg: Re: [Freesurfer] Recon-all error after El Capitain update
>
>It's hard to fully diagnose, without the command you called, but it
>looks like you have your SUBJECTS_DIR and SUBJECT variable wrong, and
>perhaps command syntax. Take another look at your command.
>
>hth
>d
>
>On Thu, Jul 7, 2016 at 2:59 AM,   wrote:
>> Hi list,
>>
>> after update with El Capitain, recon-all -all produce the error reported
>> below.
>>
>>
>> Thanks
>>
>> srclabel =
>> /Applications/freesurfer/subjects/subject_prova/subj/fsaverage/label/lh.BA1.
label
>>
>> srcsubject = fsaverage
>>
>> trgsubject = SUBJECTS_DIR
>>
>> trglabel = ./lh.BA1.label
>>
>> regmethod = surface
>>
>>
>> srchemi = lh
>>
>> trghemi = lh
>>
>> trgsurface = white
>>
>> srcsurfreg = sphere.reg
>>
>> trgsurfreg = sphere.reg
>>
>> usehash = 1
>>
>> Use ProjAbs  = 0, 0
>>
>> Use ProjFrac = 0, 0
>>
>> DoPaint 0
>>
>>
>> SUBJECTS_DIR/Applications/freesurfer/subjects/subject_prova/subj
>>
>> FREESURFER_HOME /Applications/freesurfer
>>
>> Loading source label.
>>
>> No such file or directory
>>
>> ERROR reading
>> 
/Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh.
BA1.label
>>
>> Darwin iMac-di-Stefano.local 15.5.0 Darwin Kernel Version 15.5.0:
>> root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
>>
>>
>> recon-all -s SUBJECTS_DIR exited with ERRORS
>>
>>
>> ___
>> 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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Re: [Freesurfer] Regarding: Concatenating hippocampal to generate sig.mgh

[Dr Sampada Sinha]

Dear Bruce,

Thanks for you for your response. I am trying to  generate an average
hippocampal volume and its correlation with HAM-D score in early and late
onset depression (eod vs lod). One way I tried to do it was by binarizing
and concatanating the hippocampal volumes and then run mri_glmfit. But, I
am stuck at glm_fit and would be grateful if you can let me know how to
proceed from here. How do I run the glm_fit between eod and lod patients?
Secondly, after running glm_fit how do I calculate the significance from
sig.mgh?

Appreciate all your help.

Thanks and regards,

Sampada

On Sun, Jul 10, 2016 at 7:15 PM, Bruce Fischl 
wrote:

> Hi Sampada
>
> can you elaborate a bit? What are you trying to achieve? Do you want an
> average hippocampus? Average maps of subfields? What hypothesis are you
> trying to test? The individual subject data is not resampled to a common
> coordinate system, so just averaging them as is won't produce anything
> interested.
>
> cheers
> Bruce
>
> On Sun, 10 Jul 2016, Dr
> Sampada Sinha wrote:
>
> > Dear freesurfer experts,
> > Will you please let me know if it's possible to get one average mgz image
> > file by concatenating the hippocampal volumes of different subjects using
> > dev version? Since, I already have the hippocampal subfields mgz volume
> > files, I intend to run the glmfit later on between two groups to get
> sig.mgh
> > files.
> >
> > Thanks and regards?
> >
> > Sampada
> >
> >
> > --
> > Sampada
> > Pre-doctoral student
> > Department of Geriatric Mental Health (DGMH)
> > King George Medical University
> > Lucknow-226003
> > India
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> ___
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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.
>
>


-- 
Sampada
Pre-doctoral student
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003
India
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