date:20181119

Re: [Freesurfer] How to automate recon-all command for multiple subjects

2018-11-19 Thread Vivek Sharma

External Email - Use Caution

I have a folder, lets name xyz which contains .nii file. Now I want to run
recon-all for all the files in that folder. Please let me know how I can do
that.

On Tue, Nov 20, 2018 at 11:40 AM Vivek Sharma 
wrote:

> I'm trying to run this code but it's not working. What should be $i in
> the code?
> On Mon, Nov 19, 2018 at 9:15 PM Bruce Fischl 
> wrote:
>
>> or you could do that all on a single line:
>>
>> recon-all -i $SUBJECTS_DIR/$i/ -s $i -all
>>
>> cheers
>> Bruce
>>
>> On Mon, 19 Nov 2018,
>> Alex Hanganu
>> wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > HI Vivek,
>> > you probably need 2 steps, first registration, second recon-all.
>> Something
>> > like:
>> >
>> > ...
>> > do
>> >recon-all -i $SUBJECTS_DIR/$i/ -s $i
>> >recon-all -all -subjid $i
>> >
>> >
>> > I didn't check if the scrips runs. That's the general structure.
>> >
>> > Best,
>> > Alex
>> >
>> > Le lun. 19 nov. 2018, à 06 h 26, Vivek Sharma <
>> vivek.sharma1...@gmail.com> a
>> > écrit :
>> >
>> >   External Email - Use Caution
>> >
>> >   Hi,
>> > I'm using freesurfer to generate head surfaces using MRI file.
>> > I want to execute recon-all command for number of subjects, but unable
>> > to run it.
>> > The script I'm using is:
>> >
>> > for i in `cat *subs.txt*`
>> > do
>> > recon-all -s $i -all -qcache
>> > done
>> >
>> > subs.txt contains the name of folder that contains .nii file.
>> > The scripts ends with the following error:
>> >
>> > ERROR: no run data found in
>> > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri. Make sure to
>> > have a volume called 001.mgz in
>> > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri/orig.
>> > If you have a second run of data call it 002.mgz, etc.
>> > See also:
>> > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
>> > Linux cblhost 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26
>> > 18:10:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>> >
>> > Please let me know how I can run recon-all for multiple subjects.
>> > Thank you.
>> >
>> > --
>> > Vivek Sharma
>> > Mobile: +919953582034
>> > Skype: vivek.sharma1015
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> >___
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>
>
>
> --
> Vivek Sharma
> Mobile: +919953582034
> Skype: vivek.sharma1015
>


-- 
Vivek Sharma
Mobile: +919953582034
Skype: vivek.sharma1015
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Re: [Freesurfer] How to automate recon-all command for multiple subjects

2018-11-19 Thread Vivek Sharma

External Email - Use Caution

I'm trying to run this code but it's not working. What should be $i in the
code?
On Mon, Nov 19, 2018 at 9:15 PM Bruce Fischl 
wrote:

> or you could do that all on a single line:
>
> recon-all -i $SUBJECTS_DIR/$i/ -s $i -all
>
> cheers
> Bruce
>
> On Mon, 19 Nov 2018,
> Alex Hanganu
> wrote:
>
> >
> > External Email - Use Caution
> >
> > HI Vivek,
> > you probably need 2 steps, first registration, second recon-all.
> Something
> > like:
> >
> > ...
> > do
> >recon-all -i $SUBJECTS_DIR/$i/ -s $i
> >recon-all -all -subjid $i
> >
> >
> > I didn't check if the scrips runs. That's the general structure.
> >
> > Best,
> > Alex
> >
> > Le lun. 19 nov. 2018, à 06 h 26, Vivek Sharma <
> vivek.sharma1...@gmail.com> a
> > écrit :
> >
> >   External Email - Use Caution
> >
> >   Hi,
> > I'm using freesurfer to generate head surfaces using MRI file.
> > I want to execute recon-all command for number of subjects, but unable
> > to run it.
> > The script I'm using is:
> >
> > for i in `cat *subs.txt*`
> > do
> > recon-all -s $i -all -qcache
> > done
> >
> > subs.txt contains the name of folder that contains .nii file.
> > The scripts ends with the following error:
> >
> > ERROR: no run data found in
> > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri. Make sure to
> > have a volume called 001.mgz in
> > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri/orig.
> > If you have a second run of data call it 002.mgz, etc.
> > See also:
> > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
> > Linux cblhost 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26
> > 18:10:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
> >
> > Please let me know how I can run recon-all for multiple subjects.
> > Thank you.
> >
> > --
> > Vivek Sharma
> > Mobile: +919953582034
> > Skype: vivek.sharma1015
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
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-- 
Vivek Sharma
Mobile: +919953582034
Skype: vivek.sharma1015
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Re: [Freesurfer] Tracula Question-How the threshold in final merged tracts are defined?

2018-11-19 Thread Yendiki, Anastasia

Hi June - Circling back to this to see if it was resolved. If you're just using 
the publicly available data, there should be 3x96 directions, with 3 different 
b-values. Which set of 96 are you using?


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of June Kang 

Sent: Saturday, November 3, 2018 7:35:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Question-How the threshold in final merged 
tracts are defined?


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It’s just huge data collected from general population. Some data can have 
motion artifact, but I couldn’t find any special points in the protocol.

http://protocols.humanconnectome.org/HCP/3T/imaging-protocols.html

J.


On Nov 4, 2018, at 4:21 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi June - Not in principle, any number of directions > 30 should be compatible. 
Is there anything else that's different about this data, e.g., SNR, motion, 
population with more morphological variability, etc.?

a.y

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of June Kang mailto:cn...@korea.ac.kr>>
Sent: Saturday, November 3, 2018 12:24:54 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Question-How the threshold in final merged 
tracts are defined?

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Thanks, Professor Anastasia,

I am testing HCP data with 96 directions.
There are really frequent failure for right cingulum-angular bundle and right 
uncinate fasciculus (more than 25%), which not happened with my own 
64-direction data with Siemens Trio.

Is there any known issue or recommended modification of the pipeline for HCP 
data or data with more directions?

Bests,
J.


On Nov 2, 2018, at 10:44 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

They are not random, they are 20% of the maximum value. If you want to generate 
stats at a different threshold, you can find the dmri_pathstats command line in 
trac-all.log and add the --pthr option (the default 20% would be --pthr .2).

On Nov 1, 2018 9:01 PM, June Kang mailto:cn...@korea.ac.kr>> 
wrote:
External Email - Use Caution

In the visualization step of Tracula processing, freeview -tv 
merged_avg33_mni_bbr shows some tracts with very high threshold (i.e. 171), 
which make them look like the reconstruction-failed ones.
The tracts failed to reconstruction usually show threshold of 300 (not 
changeable) with tiny rounded cylinder shape.
In successfully reconstructed tracts with very high threshold, it looks ok, 
when I adjust threshold to the similar value from contralateral one.

Is there any reason for this extremely high threshold? or it’s just randomly 
set values?

Bests,
J.


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Re: [Freesurfer] Bonferroni correction of 2spaces or 3spaces

2018-11-19 Thread YAN Chao-Gan

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Dear Douglas,

Thanks a lot for your reply! That's very clear!

Best,

Chao-Gan


On Tue, Nov 20, 2018 at 10:12 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

>
>
> On 11/16/18 7:34 PM, YAN Chao-Gan wrote:
>
> External Email - Use Caution
> Dear freesurfer experts,
>
> I have a pretty naive question but would like to confirm.
>
> When we use --3spaces option in multiple comparison correction, does that
> mean we set the Cluster-wise threshold (cwp, not Cluster Defining Threshold
> or Cluster Forming Threshold) to 0.5/3=0.0167 for lh. Similar cwp at 0.0167
> for rh and subcortical?
>
> Correct.
>
>
> In addition, if we use "--cortex" to restrict the calculation on cortex
> only, where can we find the corresponding mask or label file for cortex?
>
> Load the ?h.cortex.label in fsaverage
>
>
> Thanks,
>
> Chao-Gan
>
> --
> Chao-Gan YAN, Ph.D.
> Professor, Principal Investigator
> Deputy Director, Magnetic Resonance Imaging Research Center
> Institute of Psychology, Chinese Academy of Sciences
> 16 Lincui Road, Chaoyang District, Beijing 100101, China
> -
> Initiator
> DPABI 
> , DPARSF
> , PRN  and The R-fMRI
> Network  (RFMRI.ORG )
> http://rfmri.org/yan
> http://scholar.google.com/citations?user=lJQ9B58J
>
>
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>
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-- 
Chao-Gan YAN, Ph.D.
Professor, Principal Investigator
Deputy Director, Magnetic Resonance Imaging Research Center
Institute of Psychology, Chinese Academy of Sciences
16 Lincui Road, Chaoyang District, Beijing 100101, China
-
Initiator
DPABI 
, DPARSF
, PRN  and The R-fMRI Network
 (RFMRI.ORG )
http://rfmri.org/yan
http://scholar.google.com/citations?user=lJQ9B58J
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Re: [Freesurfer] Bonferroni correction of 2spaces or 3spaces

2018-11-19 Thread Greve, Douglas N.,Ph.D.



On 11/16/18 7:34 PM, YAN Chao-Gan wrote:

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Dear freesurfer experts,

I have a pretty naive question but would like to confirm.

When we use --3spaces option in multiple comparison correction, does that mean 
we set the Cluster-wise threshold (cwp, not Cluster Defining Threshold or 
Cluster Forming Threshold) to 0.5/3=0.0167 for lh. Similar cwp at 0.0167 for rh 
and subcortical?
Correct.

In addition, if we use "--cortex" to restrict the calculation on cortex only, 
where can we find the corresponding mask or label file for cortex?
Load the ?h.cortex.label in fsaverage

Thanks,

Chao-Gan

--
Chao-Gan YAN, Ph.D.
Professor, Principal Investigator
Deputy Director, Magnetic Resonance Imaging Research Center
Institute of Psychology, Chinese Academy of Sciences
16 Lincui Road, Chaoyang District, Beijing 100101, China
-
Initiator
DPABI,
  DPARSF, PRN 
and The R-fMRI Network (RFMRI.ORG)
http://rfmri.org/yan
http://scholar.google.com/citations?user=lJQ9B58J



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Re: [Freesurfer] Gray Matter Manual Edit Reverting

2018-11-19 Thread Bruce Fischl


Hi David

does this not work in freeview? Can you describe to Ruopeng (ccd) exactly 
what you tried?


cheers
Bruce
On Mon, 19 Nov 2018, David S Lee wrote:



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Hello Experts, 
I am currently using FreeSurfer version 6.0 to make manual edits to T1w images. 
In an earlier
version 5.3,  when GM has been erroneously removed, I used the "clone tool" to 
bring back voxels
based on the original T1w. However, this tool seems to be not working in 6.0. 
Would you be able to
help me troubleshoot this? If there is a better alternative to revert GM 
removal, please let me
know!

Thank you for your help.

--
David S. Lee
Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115  

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Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

2018-11-19 Thread Greve, Douglas N.,Ph.D.

I can' tell what is going wrong there. Can you run it with --debug as 
the first option and send the output? BTW, the MC correction for LGI is 
probably not very accurate. I would recommend using permutation. See 
here 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsClusterSummaryV6.0Perm


On 11/19/18 7:17 AM, C.P.E. Rollins wrote:
>  External Email - Use Caution
>
> Dear Freesurfer Developers,
>
> I'm trying to run mri_glmfit-sim to correct for multiple comparisons but
> am receiving the following error:
>
> cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt
> dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C
> contrast_dods.txt
> SURFACE: fsaverage lh
> log file is lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
>
> cd /home/cper2/BeneMin/Freesurfer
> /applications/freesurfer/freesurfer_6.0.0/bin/mri_glmfit-sim
> --glmdir lh.5.lgi_MAN_new.glmdir --cache 2 neg --cwp 0.05 --2spaces
>
> $Id: mri_glmfit-sim,v 1.66 2016/11/16 20:52:22 greve Exp $
> Fri Nov 16 09:38:40 GMT 2018
> Linux wbic-gate-2 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14)
> x86_64 GNU/Linux
> cper2
> setenv SUBJECTS_DIR /home/cper2/BeneMin/Freesurfer
> FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0
>
> Original mri_glmfit command line:
> cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt
> dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C
> contrast_dods.txt
>
> DoSim = 0
> UseCache = 1
> DoPoll = 0
> DoPBSubmit = 0
> DoBackground = 0
> DiagCluster = 0
> gd2mtx = dods
> fwhm = 26.134985
> CSD
> /applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/neg/th20/mc-z.csd
> mri_surfcluster --in lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh
> --mask lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.mgh
> --sum
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.summary
> --ocn
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.mgh
> --annot aparc --cwpvalthresh 0.05 --o
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.masked.mgh
> --no-fixmni --csd
> /applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/neg/th20/mc-z.csd
> --csdpdf
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.pdf.dat --vwsig
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.voxel.mgh
> --vwsigmax
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.voxel.max.dat
> --oannot
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.annot
> --bonferroni 2 --surf white
> Creating CDFs from CSD files
> csd->threshsign = -1
> thsign = neg, id = -1
> version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $
> hemi   = lh
> srcid  = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh
> srcsubjid  = fsaverage
> srcsurf= white
> srcframe   = 0
> thsign = neg
> thmin  = 2
> thmax  = -1
> fdr= -1
> minarea= 0
> Bonferroni  = 2
> xfmfile= talairach.xfm
> nth = -1
> outid=
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.masked.mgh
> MGH
> ocnid=
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.mgh MGH
> sumfile  =
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.summary
> subjectsdir= /home/cper2/BeneMin/Freesurfer
> FixMNI = 0
> Found 149955 vertices in mask
> Found 149955 vertices in mask
> Found 149955 points in clabel.
> - XFM matrix (RAS2RAS) ---
> /home/cper2/BeneMin/Freesurfer/fsaverage/mri/transforms/talairach.xfm
>1.0   0.0   0.0   0.0;
>0.0   1.0   0.0   0.0;
>0.0   0.0   1.0   0.0;
>0.0   0.0   0.0   1.0;
> MRISread(?): could not open file
> No such file or directory
> 
> Reading source surface
> /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white
> mri_surfcluster.bin: could not read surface
> /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white
> No such file or directory
>
> However, the files
> /home/cper2/BeneMin/Freesurfer/fsaverage/mri/transforms/talairach.xfm
> and /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white both exist
> and I can read them looking at the permissions.
>
> I was wondering if you might have any advice for this.
>
> Many thanks,
> Colleen
>
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Re: [Freesurfer] Extra-axial CSF and TCV GM

2018-11-19 Thread Greve, Douglas N.,Ph.D.



On 11/19/18 7:34 AM, Crocetti, Deana wrote:

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Hi Folks,

1) Can I derive a measure of extra-axial CSF.  I realize this must be generated 
in order to create the boundary between the skull and dura but not sure if this 
is saved in as one of the labels.
Do you mean extra cerebral CSF? We don't have a great way to do this now 
(though it is coming). The SPM segmentation will generate skull and CSF 
segmenations, so you can try that.

2) To generate a measure for Total Cerebral Volume Gray Matter would I combine 
the following labels?   lhCortex + rhCortex + SubCortGray + CerebellumGM
See here https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats

Thank you,
Deana

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Re: [Freesurfer] FDR correction

2018-11-19 Thread Greve, Douglas N.,Ph.D.

High p-values (i,e close to 1) mean non-significance. I don't know how 
to do a power analysis with FDR.

On 11/19/18 1:16 PM, Laura Ferrero wrote:
>  External Email - Use Caution
>
> Hi,
> I performed an statistical analysis comparing autism group with control group 
> using volume/area and thickness measures. I found significant differences in 
> some regions but they were not significant after FDR correction. The majority 
> of p-values are really high and only some of them are small, I would like to 
> know is that can affect the result. Additionally, I read that it is 
> interesting to do a power analysis to know the amount of difference that can 
> be detected based on the sample size and I would like to know if it is a good 
> approach to follow trying to explain why some results were not significant 
> after multiple comparison correction.
> Thank you,
> Laura
>
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Re: [Freesurfer] Map image in MNI onto fsaverage

2018-11-19 Thread Greve, Douglas N.,Ph.D.

You can follow the instructions here for the case where you are not using 
kinetic modeling. You don't need to do the PVC either
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
This command in particular, you just need to generate the registration and 
supply you input as the --mov

mri_vol2vol --mov subctxgm.nii.gz --reg aux/bbpet2anat.lta
--tal --talres 2  --o subctxgm.mni305.2mm.sm00.nii.gz

It can be used genericall

On 11/19/18 1:14 PM, john Anderson wrote:

External Email - Use Caution

Dear Freesurfer experts,
I have the mean PET images for a number of subjects in MNI152 space. For 
visualization purposes, I would like to map this mean image onto brain surface. 
How can I do it. I appreciate any suggestion you may provide.
Thanks!
John







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Re: [Freesurfer] Pial edition and Intensity Normalization / Control points

2018-11-19 Thread Bruce Fischl

1. Yes, this should be fine. Frequently control points help the pial 
surface


cheers
Bruce
On Mon, 19 Nov 2018, Rosalia Dacosta Aguayo wrote:



External Email - Use Caution

Dear Free Surfer team,

I have edited the pial surface and I am running: -autorecon-pial. This process 
is taking its time.
Then I will look for intensity normalization and control points. Then I will 
have to run  recon-all
-autorecon2-cp -autorecon3.

I wonder if:

1. Is there any way to do pial and normalization/control points at the same 
time, so I only have to
run the process one time (speed in it up).
2. Is there any other change I should consider when editing?



Best regards,
Rosalia


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Re: [Freesurfer] Error tkmedit

2018-11-19 Thread Bruce Fischl


Hi Rosalia

tkmedit is deprecated - can you try freeview? Also, check to make sure 
that your SUBJECTS_DIR is set properly (it looks like it is 
/home/ms_naroa/subjects and it probably should be 
~/Escritorio/subjects_controls)


cheers
Bruce


On Mon, 19 Nov 2018, Rosalia Dacosta Aguayo wrote:



External Email - Use Caution

Dear Free Surfer experts,

I am trying to load my brainmask and the T1 to make editions but I have a 
problem I do not know how
to solve.
I would much appreciate your helping here.
Best regards,
Rosalia

Problem:
ms_naroa@neuroimagen1:~/Escritorio/subjects_controls$ ls
001  006  013  021  027  031  035  039  047  fsaverage
002  008  014  023  028  032  036  040  betn_controls    NN
004  009  015  024  029  033  037  043  correct_errors
005  010  017  026  030  034  038  046  Errors_list.ods
ms_naroa@neuroimagen1:~/Escritorio/subjects_controls$ tkmedit 002 brainmask.mgz 
-aux T1.mgz
ERROR: cannot find subject 002 in /home/ms_naroa/subjects or it is not readable 
by you

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[Freesurfer] Gray Matter Manual Edit Reverting

2018-11-19 Thread David S Lee

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Hello Experts,

I am currently using FreeSurfer version 6.0 to make manual edits to T1w
images. In an earlier version 5.3,  when GM has been erroneously removed, I
used the "clone tool" to bring back voxels based on the original T1w.
However, this tool seems to be not working in 6.0. Would you be able to
help me troubleshoot this? If there is a better alternative to revert GM
removal, please let me know!

Thank you for your help.

-- 
David S. Lee
Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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Re: [Freesurfer] Segmentation fault

2018-11-19 Thread Whitney, Jon

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Update -  Segmentation fault

I think I have finally found the issue.  The bvec files I uploaded actually
contained only zeroes for each bvec value, and that made it impossible for
Tracula to function properly.  This was a result of the original files we
were given having empty header data.  We have been able to locate the
original bvec values and it appears as though everything is working now.

Thanks for your help!!

On Wed, Oct 31, 2018 at 10:55 AM Whitney, Jon  wrote:

> I probably deleted the log file prior to running the path step so I could
> focus on what was going on.  I'll re-run it and give you the results when
> it finishes.
>
> Thanks!
>

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Image Analysis Engineer
ERT | 26801 Miles Rd | Cleveland, OH 44128 | USA
ert.com

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[Freesurfer] Pial edition and Intensity Normalization / Control points

2018-11-19 Thread Rosalia Dacosta Aguayo

External Email - Use Caution

Dear Free Surfer team,

I have edited the pial surface and I am running: -autorecon-pial. This
process is taking its time.
Then I will look for intensity normalization and control points. Then I
will have to run  recon-all -autorecon2-cp -autorecon3.

I wonder if:

1. Is there any way to do pial and normalization/control points at the same
time, so I only have to run the process one time (speed in it up).
2. Is there any other change I should consider when editing?



Best regards,
Rosalia
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[Freesurfer] FDR correction

2018-11-19 Thread Laura Ferrero

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Hi,
I performed an statistical analysis comparing autism group with control group 
using volume/area and thickness measures. I found significant differences in 
some regions but they were not significant after FDR correction. The majority 
of p-values are really high and only some of them are small, I would like to 
know is that can affect the result. Additionally, I read that it is interesting 
to do a power analysis to know the amount of difference that can be detected 
based on the sample size and I would like to know if it is a good approach to 
follow trying to explain why some results were not significant after multiple 
comparison correction. 
Thank you,
Laura

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[Freesurfer] Map image in MNI onto fsaverage

2018-11-19 Thread john Anderson

External Email - Use Caution

Dear Freesurfer experts,
I have the mean PET images for a number of subjects in MNI152 space. For 
visualization purposes, I would like to map this mean image onto brain surface. 
How can I do it. I appreciate any suggestion you may provide.
Thanks!
John___
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[Freesurfer] Research Associate Position: Molecular Imaging in Neurodegenerative Disease, Johns Hopkins University

2018-11-19 Thread Gwenn Smith

External Email - Use Caution

Research Associate

Molecular Brain Imaging in Neurodegenerative Disease
A full-time opening is available for a Research Associate in the Department of 
Psychiatry and Behavioral Sciences and Radiology and Radiological Sciences at 
Johns Hopkins University School of Medicine. The research program focuses on 
applying multi-modality PET and MR imaging to investigate the neurobiology of 
late life depression, mild cognitive impairment and Parkinson's disease.
Responsibilities include design and implementation of human neuroimaging 
research studies and image processing, in collaboration with the 
interdisciplinary team. The position is a great opportunity for self-motivated 
individuals to take the lead on scientific publications and presentations and 
to develop independent projects and grant submissions.
Position Requirements: Candidates should have a doctorate (Ph.D. or M.D) in 
Experimental Psychology, Neuropsychology, Neuroscience, Neurology or a 
comparable discipline.  Experience in the conduct of clinical research studies 
is required. Experience in PET or MRI image analysis is preferred.
Review of applications will begin immediately and will continue until the 
position is filled. Applicants should send their Curriculum Vitae and a 
statement of academic interests to: Gwenn S. Smith, PhD 
(gsmit...@jhmi.edu), Division of Geriatric Psychiatry 
and Neuropsychiatry, Department of Psychiatry and Behavioral Sciences, Johns 
Hopkins University School of Medicine 5300 Alpha Commons Drive, Baltimore, MD  
21224



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Re: [Freesurfer] How to automate recon-all command for multiple subjects

2018-11-19 Thread Bruce Fischl


or you could do that all on a single line:

recon-all -i $SUBJECTS_DIR/$i/ -s $i -all

cheers
Bruce

On Mon, 19 Nov 2018, 
Alex Hanganu 
wrote:




External Email - Use Caution

HI Vivek,
you probably need 2 steps, first registration, second recon-all. Something
like:

...
do
   recon-all -i $SUBJECTS_DIR/$i/ -s $i
   recon-all -all -subjid $i


I didn't check if the scrips runs. That's the general structure.

Best,
Alex

Le lun. 19 nov. 2018, à 06 h 26, Vivek Sharma  a
écrit :

  External Email - Use Caution

  Hi,
I'm using freesurfer to generate head surfaces using MRI file.
I want to execute recon-all command for number of subjects, but unable
to run it.
The script I'm using is:

for i in `cat *subs.txt*`
do
    recon-all -s $i -all -qcache
done

subs.txt contains the name of folder that contains .nii file.
The scripts ends with the following error:

ERROR: no run data found in
/cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri. Make sure to
have a volume called 001.mgz in 
/cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
Linux cblhost 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26
18:10:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

Please let me know how I can run recon-all for multiple subjects.
Thank you.

--
Vivek Sharma
Mobile: +919953582034
Skype: vivek.sharma1015
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Re: [Freesurfer] How to automate recon-all command for multiple subjects

2018-11-19 Thread Alex Hanganu

External Email - Use Caution

HI Vivek,

you probably need 2 steps, first registration, second recon-all. Something
like:

...
do
   recon-all -i $SUBJECTS_DIR/$i/ -s $i
   recon-all -all -subjid $i


I didn't check if the scrips runs. That's the general structure.

Best,
Alex

Le lun. 19 nov. 2018, à 06 h 26, Vivek Sharma 
a écrit :

> External Email - Use Caution
>
> Hi,
> I'm using freesurfer to generate head surfaces using MRI file.
> I want to execute recon-all command for number of subjects, but unable to
> run it.
> The script I'm using is:
>
> for i in `cat *subs.txt*`
> do
> recon-all -s $i -all -qcache
> done
>
> subs.txt contains the name of folder that contains .nii file.
> The scripts ends with the following error:
>
> ERROR: no run data found in
> /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri. Make sure to
> have a volume called 001.mgz in
> /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri/orig.
> If you have a second run of data call it 002.mgz, etc.
> See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
> Linux cblhost 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26 18:10:19
> UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>
> Please let me know how I can run recon-all for multiple subjects.
> Thank you.
>
> --
> Vivek Sharma
> Mobile: +919953582034
> Skype: vivek.sharma1015
> ___
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[Freesurfer] Extra-axial CSF and TCV GM

2018-11-19 Thread Crocetti, Deana

External Email - Use Caution

Hi Folks,

1) Can I derive a measure of extra-axial CSF.  I realize this must be generated 
in order to create the boundary between the skull and dura but not sure if this 
is saved in as one of the labels.

2) To generate a measure for Total Cerebral Volume Gray Matter would I combine 
the following labels?   lhCortex + rhCortex + SubCortGray + CerebellumGM

Thank you,
Deana

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Re: [Freesurfer] loading and rendering the Amygdala nuclei only in Freeview

2018-11-19 Thread Erik O'Hanlon

External Email - Use Caution

Thanks Eugenio,


I'll do that.


Much appreciated.


best regards


Erik



Postdoctoral Research Fellow
Dept. Of Psychiatry
Royal College of Surgeons in Ireland
ERC Building
Beaumont Hospital
Dublin
&
Dept. Of Psychiatry
Trinity College Institute of Neuroscience
The Llyod Institute
Trinity College Dublin
D2

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, 
Eugenio 
Sent: 16 November 2018 15:45:27
To: Freesurfer support list
Subject: Re: [Freesurfer] loading and rendering the Amygdala nuclei only in 
Freeview


External Email - Use Caution

Hi Erik,

If you render labels >7000, you shouldn’t see a rendering of the subfields – 
but they will indeed remain visible in the orthogonal views. If you want to get 
rid of them, you can use mri_threshold:

mri_threshold 
lh.hippoAmygLabels-T1-HippoAMYT1andT2FLAIR.v20.FS60.FSvoxelSpace.mgz6999  
onlyAmyg.mgz

Cheers,

/Eugenio



--

Juan Eugenio Iglesias



ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London, and

Research Affiliate

Computer Science and Artificial Intelligence Laboratory (CSAIL)

Massachusetts Institute of Technology



http://www.jeiglesias.com







From:  on behalf of Erik O'Hanlon 


Erik O'Hanlon
Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont D9 Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.com


Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022


[cid:AS_BRONZE_IIDD_65c26b0a-ea45-42c8-956e-5d84e884e4e6.png]


Reply-To: Freesurfer support list 
Date: Friday, 16 November 2018 at 08:15
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] loading and rendering the Amygdala nuclei only in Freeview



External Email - Use Caution

Hi FS Experts,



I'm trying to make some images of my amygdala nuclei in freeview and selected 
my T1 as background and then loaded up 
lh.hippoAmygLabels-T1-HippoAMYT1andT2FLAIR.v20.FS60.FSvoxelSpace.mgz image 
which loads up perfectly. I selected the "show existing labels " and the 
freesurfer colour LUT but when I select the range for 7001-7015 for amygdala 
only, the hippocampal subfields are still there. Is there a way to only load 
the amygdala nuclei. I'm sure it's something simple I'm just not doing, but I 
can't seem to get it to work.



Any pointers gladly accepted



Thanks



Erik







Erik O'Hanlon
Postdoctoral researcher

[cid:image001.png@01D47D99.7BDC9930]

RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont D9 Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.com

RCSI Homepage - Royal College of Surgeons in Ireland
www.rcsi.com
RCSI provides extensive education and training in the healthcare professions at 
undergraduate and postgraduate level. Learn about our undergraduate courses in 
medicine, pharmacy and physiotherapy, our surgical training and our range of 
postgraduate opportunities.


Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022


[cid:image002.png@01D47D99.7BDC9930]
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[Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

2018-11-19 Thread C.P.E. Rollins

External Email - Use Caution

Dear Freesurfer Developers,

I'm trying to run mri_glmfit-sim to correct for multiple comparisons but 
am receiving the following error:

cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt 
dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C 
contrast_dods.txt
SURFACE: fsaverage lh
log file is lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log

cd /home/cper2/BeneMin/Freesurfer
/applications/freesurfer/freesurfer_6.0.0/bin/mri_glmfit-sim
--glmdir lh.5.lgi_MAN_new.glmdir --cache 2 neg --cwp 0.05 --2spaces

$Id: mri_glmfit-sim,v 1.66 2016/11/16 20:52:22 greve Exp $
Fri Nov 16 09:38:40 GMT 2018
Linux wbic-gate-2 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) 
x86_64 GNU/Linux
cper2
setenv SUBJECTS_DIR /home/cper2/BeneMin/Freesurfer
FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0

Original mri_glmfit command line:
cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt 
dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C 
contrast_dods.txt

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 26.134985
CSD 
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/neg/th20/mc-z.csd
mri_surfcluster --in lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh 
--mask lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.mgh 
--sum 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.summary 
--ocn 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.mgh 
--annot aparc --cwpvalthresh 0.05 --o 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.masked.mgh 
--no-fixmni --csd 
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/neg/th20/mc-z.csd
 
--csdpdf 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.pdf.dat --vwsig 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.voxel.mgh 
--vwsigmax 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.voxel.max.dat 
--oannot 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.annot 
--bonferroni 2 --surf white
Creating CDFs from CSD files
csd->threshsign = -1
thsign = neg, id = -1
version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $
hemi   = lh
srcid  = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = neg
thmin  = 2
thmax  = -1
fdr= -1
minarea= 0
Bonferroni  = 2
xfmfile= talairach.xfm
nth = -1
outid= 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.masked.mgh 
MGH
ocnid= 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.mgh MGH
sumfile  = 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.summary
subjectsdir= /home/cper2/BeneMin/Freesurfer
FixMNI = 0
Found 149955 vertices in mask
Found 149955 vertices in mask
Found 149955 points in clabel.
- XFM matrix (RAS2RAS) ---
/home/cper2/BeneMin/Freesurfer/fsaverage/mri/transforms/talairach.xfm
  1.0   0.0   0.0   0.0;
  0.0   1.0   0.0   0.0;
  0.0   0.0   1.0   0.0;
  0.0   0.0   0.0   1.0;
MRISread(?): could not open file
No such file or directory

Reading source surface 
/home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white
mri_surfcluster.bin: could not read surface 
/home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white
No such file or directory

However, the files 
/home/cper2/BeneMin/Freesurfer/fsaverage/mri/transforms/talairach.xfm 
and /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white both exist 
and I can read them looking at the permissions.

I was wondering if you might have any advice for this.

Many thanks,
Colleen

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[Freesurfer] How to automate recon-all command for multiple subjects

2018-11-19 Thread Vivek Sharma

External Email - Use Caution

Hi,
I'm using freesurfer to generate head surfaces using MRI file.
I want to execute recon-all command for number of subjects, but unable to
run it.
The script I'm using is:

for i in `cat *subs.txt*`
do
recon-all -s $i -all -qcache
done

subs.txt contains the name of folder that contains .nii file.
The scripts ends with the following error:

ERROR: no run data found in
/cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri. Make sure to
have a volume called 001.mgz in
/cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
Linux cblhost 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26 18:10:19
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

Please let me know how I can run recon-all for multiple subjects.
Thank you.

-- 
Vivek Sharma
Mobile: +919953582034
Skype: vivek.sharma1015
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[Freesurfer] Error tkmedit

2018-11-19 Thread Rosalia Dacosta Aguayo

External Email - Use Caution

Dear Free Surfer experts,

I am trying to load my brainmask and the T1 to make editions but I have a
problem I do not know how to solve.
I would much appreciate your helping here.
Best regards,
Rosalia

*Problem: *
ms_naroa@neuroimagen1:~/Escritorio/subjects_controls$ ls
001  006  013  021  027  031  035  039  047  fsaverage
002  008  014  023  028  032  036  040  betn_controlsNN
004  009  015  024  029  033  037  043  correct_errors
005  010  017  026  030  034  038  046  Errors_list.ods
ms_naroa@neuroimagen1:~/Escritorio/subjects_controls$ tkmedit 002
brainmask.mgz -aux T1.mgz
*ERROR: cannot find subject 002 in /home/ms_naroa/subjects or it is not
readable by you*
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