Re: [Freesurfer] mri_normalize, 110 is too dark

[Bruce Fischl]

Hi Tom

it's tough for us to tell without some images or the data. If you upload 
the entire subject dir of a subject that failed we will take a look. You 
can't just change which peak is the WM - lots of things downstream would 
fail

cheers
Bruce


On Fri, 29 Jul 2016, tvg[fs] wrote:

> Dear community and developers,
>
> I am experiencing issues during the normalization step, converting
> NU.mgz to T1.mgz. Gray matter is falsely recognized as white matter
> and high intensity WM is ignored. The resulting T1.mgz collapses the
> wrong voxels into the 110 bin.
>
> It seems that what mri_normalize assumes a peak in the WM intensity
> distribution that is too low.
> In NU.mgz WM seems centered around 140 not 110. Note that this is not
> due to RF-field inhomogeneities. It is likely of physiological origin
>
> - Is there a way to explicitly tell mri_normalize to use a different
> intensity peak?
>
> I realize that correction can be done with control points, however I
> understand that does not compute a new intensity distribution, but
> merely adds voxels around CPs. This is undesirable since I have >20
> scans to process. Also this will not correct the falsely tagged GM
> voxels.
>
> I've tried to trick mri_normalize by adjusting NU.mgz intensity by -30
> (140-30 = 110). This did not give me the wished-for effect.
> - Is it possible to bypass preprocessing steps of mri_normalize before
> collapsing?
>
> - In general it would help if there is some elaboration on the options:
> -no1d,
> -nosnr,
> -gentle,
> -f vs -fonly,
> -prune,
> -g,
> -monkey
> - is [-monkey] just shorthand for [-no1d -n 1]?
>
> Thanks,
> Tom
>
> System:
> Mac OS X 10.10.5
> freesurfer-Darwin-lion-stable-pub-v5.3.0
>> mri_normalize --version
> stable5
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>
>
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Re: [Freesurfer] brain mask and T1 are not the same size

[Douglas Greve]

So you're saying that the dimension changed after you ran freeview and 
saved the volume? Can you replicate it? ie, if you make a copy of the 
brainmask.mgz, then edit the copy, does it do the same thing every time 
you make a copy and edit it?



On 7/29/16 12:09 PM, Isabelle Deschamps wrote:

Dear FreeSurfer experts,

I am trying to fix the skull strip manually for a group of 
participants. For all participants except 4, I get an error when 
running recon-all -autorecon-pial -subjid S07_FS, after editing 
manually in Freeview the brainmask.


In freeview, I followed the instruction for Edits to the brainmask 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewEditingaRecon)


I open freeview using this command on my participant's data:

*freeview -v pial_edits_before/mri/brainmask.mgz \*
*-f pial_edits_before/surf/lh.white:edgecolor=yellow \*
*pial_edits_before/surf/lh.pial:edgecolor=red 
pial_edits_before/surf/rh.white:edgecolor=yellow \*

*pial_edits_before/surf/rh.pial:edgecolor=red *

Then, I follow these instructions, which are on the website.
*To fix this type of error you can simply edit away the offending 
voxels from the brainmask.mgz volume. To do this you will need to 
select the edit voxels tool and set the brush to a size and shape 
comfortable for you. A circle brush of radius 2 works well for this 
edit. Then you can simply use the shift key and your mouse button to 
erase the voxels in the brainmask.mgz, or you can set the brush value 
to 1 (so that the edits can be detected if you decide to run 
"recon-all -show-edits") and simple draw over the voxels you want to 
disappear.*

Then I save the brainmask volume using the save volume button.
When running *recon-all -autorecon-pial -subjid S07_FS* to correct the 
pial surface, I get the following error:

ERROR: dimension mismatch between source and mask
The source of the problem is the the brainmask, in which one of the 
dimensions is no longer 256. It is either 255 or 254. Prior the 
modifications, the brainmask and the T1 had the same dimensions 256^3. 
Following the brainmask edits, one dimension (it varies for the 4 
problematic participants) is no longer 256. I do not understand why 
for all participants except 4, the brainmask edits worked. I followed 
the exact same procedure for all participants.



Any ideas or suggestions?

Thank you in advance for the help,

Isabelle




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[Freesurfer] mri_normalize, 110 is too dark

[tvg[fs]]

Dear community and developers,

I am experiencing issues during the normalization step, converting
NU.mgz to T1.mgz. Gray matter is falsely recognized as white matter
and high intensity WM is ignored. The resulting T1.mgz collapses the
wrong voxels into the 110 bin.

It seems that what mri_normalize assumes a peak in the WM intensity
distribution that is too low.
In NU.mgz WM seems centered around 140 not 110. Note that this is not
due to RF-field inhomogeneities. It is likely of physiological origin

- Is there a way to explicitly tell mri_normalize to use a different
intensity peak?

I realize that correction can be done with control points, however I
understand that does not compute a new intensity distribution, but
merely adds voxels around CPs. This is undesirable since I have >20
scans to process. Also this will not correct the falsely tagged GM
voxels.

I've tried to trick mri_normalize by adjusting NU.mgz intensity by -30
(140-30 = 110). This did not give me the wished-for effect.
- Is it possible to bypass preprocessing steps of mri_normalize before
collapsing?

- In general it would help if there is some elaboration on the options:
-no1d,
-nosnr,
-gentle,
-f vs -fonly,
-prune,
-g,
-monkey
- is [-monkey] just shorthand for [-no1d -n 1]?

Thanks,
Tom

System:
Mac OS X 10.10.5
freesurfer-Darwin-lion-stable-pub-v5.3.0
> mri_normalize --version
stable5
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[Freesurfer] Running Retinotopy in FSFAST, Design Matrix has Empty Regressors

[Taylor, Johnmark]

Hello,

I am trying to run a retinotopy analysis in fsfast, using only polar angle.
However, when I try to run it, I am getting the error "Input to SVD must
not contain NaN or Inf." I have traced this error and it looks like the
design matrix X has 12 regressors (the first 12) that consist solely of
zeros. I am using the following commands:

mkanalysis-sess -analysis retinotopy -fsd bold -runlistfile runlist.txt

-native -funcstem fmc -nuisreg mcextreg 3

-retinotopy 36.4 -per-session -paradigm retino.par -inorm

-spmhrf 0 -TR .650 -polyfit 2 -nskip 19


selxavg3-sess -analysis retinotopy -sf sublist.txt -df sessdir

Any idea what the first 12 regressors in the design matrix might correspond
to in retinotopy analyses and why they'd be empty? I have looked at the
documentation and there doesn't seem to be a clear labeling of the
retinotopy design matrix anywhere, although perhaps I'm missing something.

Thank you very much,

JohnMark
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[Freesurfer] MNI coordinates of all the vertices of fsaverage

[Sabin Khadka]

Hi Doug, I tried to pick up from the thread below to get MNI coordinates of
each destrieux parcellation region.


https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html

I created label files from
mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation
aparc.a2009s --outdir label_destrieux   # which works fine

And I tried to get the coordinates of each labels using

mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel
 --sum  --centroid --thmin 0
--hemi lh --subject fsaverage

But, all left labels would produce the same coordinates and so does right
labels. (I've attached few example files here with). Also, it says TalX,
TalY, TalZ are these coordinates in MNI or Talairach?

Thanks for help.


rh_G_S_Ant
Description: Binary data


rh_S_suborbital
Description: Binary data


lh_S_suborbital
Description: Binary data


lh_G_S_Ant
Description: Binary data
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Re: [Freesurfer] error during longitudinal -long stream

[Martin Reuter]

Hi Jinsong,

can you give an example of what exactly does not work.

Thanks, Martin

On 07/29/2016 12:26 PM, Jinsong Tang wrote:

Hi Martin,

I checked all data are completed except the link to fsaverage, 
lh.EC_average and rh.EC_average.   I run one analysis from the 
terminal. it works. if I run multiple analysis at the same time, it 
failed.
When I manually linked the 3 files, then run multiple analysis at the 
same time, it works good.


Best,

Jinsong

On Wed, Jul 27, 2016 at 8:11 AM, Martin Reuter 
> wrote:



Hi Jinsong,

maybe not everything was copied? The link to fsaverage should be
automatically created if it is missing. I often process cross in a
different directory from base and long (and create symlinks to the
cross subject dirs). It automatically creates fsaverage then.
Try to replicate your problem with a single subject that failed.
First try to do everything on the same computer, then try to do
what you did before (copying parts of it).

Best, Martin



On 07/20/2016 12:56 PM, Jinsong Tang wrote:

Hi Martin,

We run all cross, base and long with 5.3. I guess the problem
maybe we run cross on  a computer and then copy the results to
another computer to run the cross and long. the "/fsaverage" is
not copied. Does this matter？/

Best，

Jinsong

On Wed, Jul 20, 2016 at 12:21 AM, Martin Reuter
> wrote:

Hi Jinsong,

I have never seen this. Stable 5.3 is very stable and I doubt
it is a bug. How did you process base and cross sectionals?
Also with 5.3 ?

I would recommend to process cross and base with 5.3, then
re-run the long and see if you can replicate this problem.
Let me know what happens.

Best, Martin


> On Jul 20, 2016, at 12:48 AM, Jinsong Tang
> wrote:
>
> Hi all,
>
> I found an error during the longitudinal -long stream:
>
> recon-all -long P1001-2 P1001 -all
> ..
>
> FREESURFER_HOME /space/raid/fmri/freesurfer
> Actual FREESURFER_HOME /space/raid/fmri/freesurfer
> build-stamp.txt:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7
17:32:21 UTC 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux
> ..
>
> mris_spherical_average -erode 1 -orig white -t 0.4 -o
P1001-2.long.P1001 label lh.entorhinal lh sphere.reg
lh.EC_average lh.entorhinal_exvivo.label
>
> painting output onto subject P1001-2.long.P1001.
> processing subject lh.EC_average...
>

MRISread(/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg):
could not open file
> eroding label 1 times before writing
> thresholding label stat at 0.400 before writing
> Not a directory
> mris_spherical_average: could not read surface file

/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg
> Not a directory
> Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7
17:32:21 UTC 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s P1001-2.long.P1001 exited with ERRORS at Fri
Jul  8 21:33:02 PDT 2016
>
>
> Please help me fix this error!
>
> Thanks and best regards,
>
> Jinsong
>
>
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Re: [Freesurfer] error during longitudinal -long stream

[Jinsong Tang]

Hi Martin,

I checked all data are completed except the link to  fsaverage,
lh.EC_average and rh.EC_average.   I run one analysis from the terminal. it
works. if I run multiple analysis at the same time, it failed.
When I manually linked the 3 files, then run multiple analysis at the same
time, it works good.

Best,

Jinsong

On Wed, Jul 27, 2016 at 8:11 AM, Martin Reuter 
wrote:

>
> Hi Jinsong,
>
> maybe not everything was copied? The link to fsaverage should be
> automatically created if it is missing. I often process cross in a
> different directory from base and long (and create symlinks to the cross
> subject dirs). It automatically creates fsaverage then.
> Try to replicate your problem with a single subject that failed. First try
> to do everything on the same computer, then try to do what you did before
> (copying parts of it).
>
> Best, Martin
>
>
>
> On 07/20/2016 12:56 PM, Jinsong Tang wrote:
>
> Hi Martin,
>
> We run all cross, base and long with 5.3. I guess the problem maybe we run
> cross on  a computer and then copy the results to another computer to run
> the cross and long. the "*fsaverage" is not copied. Does this matter？*
>
> Best，
>
> Jinsong
>
> On Wed, Jul 20, 2016 at 12:21 AM, Martin Reuter <
> mreu...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Jinsong,
>>
>> I have never seen this. Stable 5.3 is very stable and I doubt it is a
>> bug. How did you process base and cross sectionals? Also with 5.3 ?
>>
>> I would recommend to process cross and base with 5.3, then re-run the
>> long and see if you can replicate this problem. Let me know what happens.
>>
>> Best, Martin
>>
>>
>> > On Jul 20, 2016, at 12:48 AM, Jinsong Tang < 
>> tangjinson...@gmail.com> wrote:
>> >
>> > Hi all,
>> >
>> > I found an error during the longitudinal -long stream:
>> >
>> > recon-all -long P1001-2 P1001 -all
>> > ..
>> >
>> > FREESURFER_HOME /space/raid/fmri/freesurfer
>> > Actual FREESURFER_HOME /space/raid/fmri/freesurfer
>> > build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>> > Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21 UTC
>> 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux
>> > ..
>> >
>> > mris_spherical_average -erode 1 -orig white -t 0.4 -o
>> P1001-2.long.P1001 label lh.entorhinal lh sphere.reg lh.EC_average
>> lh.entorhinal_exvivo.label
>> >
>> > painting output onto subject P1001-2.long.P1001.
>> > processing subject lh.EC_average...
>> >
>> MRISread(/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg):
>> could not open file
>> > eroding label 1 times before writing
>> > thresholding label stat at 0.400 before writing
>> > Not a directory
>> > mris_spherical_average: could not read surface file
>> /space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg
>> > Not a directory
>> > Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21 UTC
>> 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux
>> >
>> > recon-all -s P1001-2.long.P1001 exited with ERRORS at Fri Jul  8
>> 21:33:02 PDT 2016
>> >
>> >
>> > Please help me fix this error!
>> >
>> > Thanks and best regards,
>> >
>> > Jinsong
>> >
>> >
>> > ___
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>>
>>
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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.
>>
>>
>
>
>
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>
>
> --
> Martin Reuter, PhD
> Assistant Professor of Radiology, Harvard Medical School
> Assistant Professor of Neurology, Harvard Medical School
> A.A.Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Research Affiliate, CSAIL, MIT
> Phone: +1-617-724-5652
> Web  : http://reuter.mit.edu
>
>
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[Freesurfer] brain mask and T1 are not the same size

[Isabelle Deschamps]

Dear FreeSurfer experts,


I am trying to fix the skull strip manually for a group of participants. For all participants except 4, I get an error when running recon-all -autorecon-pial -subjid S07_FS, after editing manually in Freeview the brainmask. 


In freeview, I followed the instruction for Edits to the brainmask (https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewEditingaRecon)


I open freeview using this command on my participant's data:


freeview -v pial_edits_before/mri/brainmask.mgz \
-f pial_edits_before/surf/lh.white:edgecolor=yellow \
pial_edits_before/surf/lh.pial:edgecolor=red pial_edits_before/surf/rh.white:edgecolor=yellow \
pial_edits_before/surf/rh.pial:edgecolor=red 


Then, I follow these instructions, which are on the website.
To fix this type of error you can simply edit away the offending voxels  from the brainmask.mgz volume.  To do this you will need to select the edit voxels tool and set the brush to a size and shape comfortable for you.  A circle brush of radius 2 works well for this edit. Then you can simply use the shift key and your mouse button to erase the voxels in the brainmask.mgz, or you can set the brush value to 1 (so that the edits can be detected if you decide to run "recon-all -show-edits") and simple draw over the voxels you want to disappear.

Then I save the brainmask volume using the save volume button.
When running recon-all -autorecon-pial -subjid S07_FS to correct the pial surface, I get the following error:
ERROR: dimension mismatch between source and mask
The source of the problem is the the brainmask, in which one of the dimensions is no longer 256. It is either 255 or 254. Prior the modifications, the brainmask and the T1 had the same dimensions 256^3. Following the brainmask edits, one dimension (it
 varies for the 4 problematic participants) is no longer 256. I do not understand why for all participants except 4, the brainmask edits worked. I followed the exact same procedure for all participants.





Any ideas or suggestions?


Thank you in advance for the help,


Isabelle






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Re: [Freesurfer] How does Optseq2 arrange order of conditions?

[Douglas Greve]

On 7/29/16 3:17 AM, 連 志浩 wrote:


Hello all,


I'm a new user of Optseq2, and I have 2 questions about optseq2 after 
I got some sequences and read Dale (1999).



I'll be grateful to anyone can provide help.


1.  I'm curious about why optseq2 arranged the order of conditions, 
does anyone can provided some references to me?



Dale (1999) just discussed about mean ISI and fixed/randomizes ISI 
design, I wonder what's the difference if I just keep the duration 
order of null condition (jitter) and randomly present different 
conditions.


It tries a bunch of random orders until it finds one that is optimum in 
terms of efficiency (you can also specifically optimize with respect to 
counter balancing, use the --focb switch; I usually choose 100 for n). 
With jittering (instead of a fixed ISI), you get more temporal 
randomization (ie, differential overlap between adjacent events).



2. This question is about the total duration of experiments. I'm used 
to execute experiments by E-Prime 2.0, and the presentation may delay 
in E-Prime (I know this situation can be deal with "Pre-release"). If 
there's a fixation period (15s) after my trials is over (but 
participants are still scanned), and the delay just affect the 
duration of the fixation period. Should I reduce the duration of 
delayed stimulus in terms of the delayed time? Or I don't need to care 
about the delay, because the key point is the order of conditions and 
null/jitter?


I'm not sure what you mean. How can it be a delay if it is after the 
trial is over?



Thanks for your reading.


Best regards,

Chih-Hao




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Re: [Freesurfer] significance overlay in freeview

[Ruopeng Wang]

Hi Caroline,

Are you running FS 5.3? The command on the webpage is based on the upcoming 
6.0, I believe. So some of the command line options are not available in 5.3.

Best,
Ruopeng

> On Jul 29, 2016, at 9:11 AM, Caroline Beelen  
> wrote:
> 
> Dear FS team,
>  
> Apologies in advance for perhaps again a rather basic question. I attempted 
> to load the aparc overlay in freeview by using the written command from the 
> group analysis page, however it failed to load correctly.  
>  
> I used the following command: 
> freeview -f 
> fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=roi.lh.area.dyslect_basic.glmdir/dyslect/sig.mgh:overlay_threshold=4,5
>  -viewport 3d
> è roi.lh.area.dyslect_basic.glmdir is the file obtained from the GLM-analysis 
> and dyslect is the contrast folder within this file (main effect of 
> dyslexia), containing a sig.mgh file (all seems fine)
>  
> Unfortunately, I got an error that it does not recognize 
> “overlay_treshold=4,5”. I used freeview –h and tried certain commands alike, 
> but they didn’t work. When leaving out this part, I got another error that it 
> failed to recognize “annot_outline=1”. Again, leaving this out too, freeview 
> loads itself and the DK-regions become visible. However, nothing else seems 
> to get activated, and even not when putting “configure overlay” (which is set 
> to sig.mgh) to 1.3 as minimum and 3 as maximum. So basically nothing happens. 
> When looking at the command line it says that it implemented the colortable 
> of DK-atlas (even twice), but it tells me nothing else. Also, after closing 
> and reloading Freeview by using the similar command and then clicking on 
> “configure overlay” the screen sometimes gets stuck, giving me the impression 
> that something must be wrong with the command.
>  
> Could you please help me out and provide me the right command-line for 
> loading the overlay of the significance map of 
> “roi.lh.area.dyslect_basic.glmdir/dyslect”?
>  
> Thanks in advance!
>  
> Kind regards, Caroline
>  
>  
>  
>  
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> 
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[Freesurfer] significance overlay in freeview

[Caroline Beelen]

Dear FS team,

Apologies in advance for perhaps again a rather basic question. I attempted to 
load the aparc overlay in freeview by using the written command from the group 
analysis page, however it failed to load correctly.

I used the following command:
freeview -f 
fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=roi.lh.area.dyslect_basic.glmdir/dyslect/sig.mgh:overlay_threshold=4,5
 -viewport 3d

? roi.lh.area.dyslect_basic.glmdir is the file obtained from the GLM-analysis 
and dyslect is the contrast folder within this file (main effect of dyslexia), 
containing a sig.mgh file (all seems fine)


Unfortunately, I got an error that it does not recognize 
"overlay_treshold=4,5". I used freeview -h and tried certain commands alike, 
but they didn't work. When leaving out this part, I got another error that it 
failed to recognize "annot_outline=1". Again, leaving this out too, freeview 
loads itself and the DK-regions become visible. However, nothing else seems to 
get activated, and even not when putting "configure overlay" (which is set to 
sig.mgh) to 1.3 as minimum and 3 as maximum. So basically nothing happens.
When looking at the command line it says that it implemented the colortable of 
DK-atlas (even twice), but it tells me nothing else. Also, after closing and 
reloading Freeview by using the similar command and then clicking on "configure 
overlay" the screen sometimes gets stuck, giving me the impression that 
something must be wrong with the command.

Could you please help me out and provide me the right command-line for loading 
the overlay of the significance map of 
"roi.lh.area.dyslect_basic.glmdir/dyslect"?

Thanks in advance!

Kind regards, Caroline




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[Freesurfer] How does Optseq2 arrange order of conditions?

[連 志浩]

Hello all,


I'm a new user of Optseq2, and I have 2 questions about optseq2 after I got 
some sequences and read Dale (1999).


I'll be grateful to anyone can provide help.


1.  I'm curious about why optseq2 arranged the order of conditions, does anyone 
can provided some references to me?


Dale (1999) just discussed about mean ISI and fixed/randomizes ISI design, I 
wonder what's the difference if I just keep the duration order of null 
condition (jitter) and randomly present different conditions.


2. This question is about the total duration of experiments. I'm used to 
execute experiments by E-Prime 2.0, and the presentation may delay in E-Prime 
(I know this situation can be deal with "Pre-release"). If there's a fixation 
period (15s) after my trials is over (but participants are still scanned), and 
the delay just affect the duration of the fixation period. Should I reduce the 
duration of delayed stimulus in terms of the delayed time? Or I don't need to 
care about the delay, because the key point is the order of conditions and 
null/jitter?


Thanks for your reading.


Best regards,

Chih-Hao

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