Re: [Freesurfer] mri_surf2surf --projfrac error: cannot spec both --sval-xyz and --sval

[Douglas Greve]

Dont use --trgicoorder. Also, smooth the input, not the output (ie, use 
--fwhm not --fwhm-trg). Don't use projfrac there (which will fix the 
--sval-xyz error). Your 2nd command looks the same as the first


On 9/27/20 10:30 PM, 谢娆 wrote:


External Email - Use Caution

Hi,

To begin with, I want clarify my goal here: I want to resample my 
resting-state functional data infsaverage5 and then do some 
preprocessing before statistical analysis, and I get stuck in smooth now.


I tried the following command:

|mri_surf2surf --srcsubject sub-40 --srcsurfval 
/home/disk2/Data/HC/HCprep/derivatives/fmriprep/sub-40/ses-1/func/sub-40_ses-1_task-rest_run-1_space-fsnative_hemi-L_bold.func.gii 
--trgsubject fsaverage5 --trgicoorder 5 --trgsurfval 
/home/disk2/Data/HC/HCprep/sub-40_smooth6_proj.mgh --hemi lh 
--fwhm-trg 6 --projfrac white 0.5|


1.

--srcsubject: this is the freesurfer output folder from fmriprep
(in ...derivatives/freesurfer/...)

2.

--srcsurfval: I used fmriprep --output-space fsnative to resample
the resting data to subject native space.

3.

--trgsubject/--trgicoorder: I want to resample the data to a
fsaverage5 as I mentioned before

4.

--projfrac white 0.5: I followed your advice tosmooth
usemidthickness coordinates, but there is an error:
ERROR: cannot spec both --sval-xyz and --sval
then I tried to add these two parameters:
|mri_surf2surf --srcsubject sub-40 --srcsurfval

/home/disk2/Data/HC/HCprep/derivatives/fmriprep/sub-40/ses-1/func/sub-40_ses-1_task-rest_run-1_space-fsnative_hemi-L_bold.func.gii
--trgsubject fsaverage5 --trgicoorder 5 --trgsurfval
/home/disk2/Data/HC/HCprep/sub-40_smooth6_proj.mgh --hemi lh
--fwhm-trg 6 --projfrac white 0.5 --sval-xyz white --sval
/home/disk2/Data/HC/HCprep/derivatives/fmriprep/sub-40/ses-1/func/|
but the error still exist:
*ERROR: cannot spec both --sval-xyz and --sval*
I searched a lot but cannot found any useful help with it.

I also have another question about smooth: I can also smooth my data 
with following command:
|mri_surf2surf --srcsubject fsaverage5 --srcsurfval 
/home/disk2/Data/HC/HCprep/derivatives/fmriprep/sub-15/ses-1/func/sub-15_ses-1_task-rest_run-1_space-fsaverage5_hemi-L_bold.func.gii 
--trgsubject fsaverage5 --trgsurfval 
/home/disk2/Data/HC/HCprep/sub-40_smooth6_proj.mgh --hemi lh 
--fwhm-trg 6 --projfrac white 0.5| (--projfrac didn't work here too)


--srcsurfval: I used fmriprep --output-space fsaverage5 to resample 
the resting data to fsaverage5 in here


With |--srcsubject fsaverage5| specified here, will every subject use 
the same coordinate/distance info when performing smooth?Willthe 
command I used above performing smooth using every subjects' own 
coordinate/distance info?And which command is better?


Any help will be appreciated, Thanks a lot!
rao


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Re: [Freesurfer] mri_nu_correct.mni, mri_normalize extremely dark output

[Douglas Greve]

It's been a while since 5.3, but I vaguely remember something like this 
happening because there were one or two super bright voxels in the 
image. If this is the case, then you can find them and clip them.


On 9/18/20 10:32 AM, Fischl, Bruce wrote:


I don’t think adding 100 will work as once it scales everything down 
that far you only have a couple of bits of representation in the 
conformed ( 1 byte/voxel) images. Maybe someone else can comment on 
fixing nu_correct?


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Caspar M. 
Schwiedrzik

*Sent:* Friday, September 18, 2020 5:04 AM
*To:* Freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] mri_nu_correct.mni, mri_normalize extremely 
dark output


*External Email - Use Caution *

Hi!

I am having some issue at the interface between mri_nu_correct.mni and 
mri_normalize, using v5.3.


Specifically, the output when applying mri_nu_correct to a T1 is quite 
dark, with white matter in the range of 15. Contrast is ok. When I 
apply mri_normalize to nu, it does not scale the data to white matter 
110. This happens with and without a brain mask, and with various 
other parameter choices.


I am tempted to just add 100 to all voxels.

Any advice?

Thank you,

Caspar


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Re: [Freesurfer] Recon-all crooked volumes

[Douglas Greve]

I don't think there is anything wrong with it. The subject just has 
his/her head tilted a fair amount in the scanner. The final analysis 
looks ok from here


On 9/17/20 1:14 PM, Hasimoglu, Yasemin wrote:

Hello,

I recently ran recon-all on a group of subjects with FreeSurfer 7.1.0, 
and for one subject some of the resulting volumes look crooked. The 
001.mgz volume looks normal, but every other volume such as orig.mgz, 
T1.mgz, brainmask.mgz have a severe tilt to them. When we open 
surfaces on top of volumes, their orientations follow whichever volume 
is loaded first. I've attached 2 sample screenshots here.


We suspected that this could be related to a Talairach registration 
issue and inspected the volumes using the following command:

tkregister2 --mgz --s $sub --fstal --surf orig

However, everything seems to be aligned correctly on here, so we're 
not sure if there's anything we can do.


Is this something that needs additional correction, or can we use this 
data in analysis as is? I've also attached the recon-all.log in case 
it's helpful.


Best,
Yasemin


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Re: [Freesurfer] Prescan normalize and freesurfer

[Douglas Greve]

#2 is the safest. I think #1 is probably ok, but you'll want to check 
that the 12% does not correlate with some factor of interest (eg, all 
12% in the control group)


On 9/17/20 8:12 AM, Mikolas, Pavol wrote:


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Dear Freesurfer Developers,

I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) 
using Freesurfer. I found out, that most of the scans were performed 
with the ‘prescan normalize’ option. However, by approx..  12 % of 
participants, this option is missing. I also have complete data of all 
participants WITHOUT prescan normalize. In this analysis, we are 
interested in the correlation of GM volume in specific ROIs with 
clinical symptoms. Now we have two options:


1.Use the ‘prescan normalize’ dataset and account for the 12% without 
this option as a covariate


2.Use the complete dataset without ‘prescan normalize’

It would be very helpful, if you could share your arguments / 
experience with this, so that we proceed in the best manner.


Thank you, best regards

Pavol


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Re: [Freesurfer] peak MNI coordinates within a masked sig.mgh

[Douglas Greve]

If you know the vertex number, then you can get the RAS in "tkregister 
space", eg, in freeview (other ways too),  then use #2 on that page


On 9/17/20 4:18 AM, Fred Sampedro wrote:


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Thank you very much Prof Greve! I'm almost done! Now, using 
mri_volcluster I can identify the vertex number with highest 
significance within a ROI in a surface sig.mgh map (see attached txt). 
However I don't know how to compute the corresponding MNI coordinates 
of a specific vertex number (say 122288 in the file). I already 
checked the very helpful page 
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems, but I did 
not see the precise calculation "from a single vertex number to (MNIx, 
MNIy,MNIz)". Maybe I missed something but the mri_volcluster output 
only displayed the vertex number (i.e no RAS coords) to work with. I 
am always working on fsaverage space.


Thanks a lot in advance!

On Tue, Sep 15, 2020 at 5:27 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


Use mri_annotation2label to convert the, eg, ?h.aparc.annot to a
segmentation (--seg output), then use mri_binarize with 1031.

On 9/15/2020 10:41 AM, Fred Sampedro wrote:


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Thats precisely the point that I should be missing. To recap, I'm
interested in knowing the MNI coordinates of the vertex with
highest significance within a specific atlas-ROI (e.g.
ctx-lh-supramarginal) from a surface sig.mgh map (e.g. group
comparison in cortical thickness).

If I understood correctly, first I need a "surface binary mask"
of the atlas ROI, which I tried to get using mri_binarize but I
am not sure if I did it correctly. Then, I would fscalc mul the
sig.mgh map with the surface binary mask, and finally apply
mri_volcluster. I'm stuck in the first step of obtaining the
desired surface binary mask from the default FS atlas.



On Tue, Sep 15, 2020 at 4:10 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

What do you mean you are trying to overlay it on lh.inflated?
the output of mri_binarize will be a volume, so you'd have to
sample it onto the surface in some way

On 9/14/2020 9:28 AM, Fred Sampedro wrote:


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Just a follow-up, I got stuck at trying to obtain a mask
from binarizing a specific ROI from the aparc+aseg.mgz,
aiming to mask my sig.mgh with this ROI.If for instance, I'd
like to create a ROI from the left supramarginal gyrus, I
found that its label is 1031. Now, I tried:

mri_binarize --i aparc+aseg.mgz --o leftsupramarg.mgh
--match 1031

however when visualizing the output of this command in
freeview overlaying the mask on top of lh.inflated...it
seems that this approach was wrong.

Then looking at the mail archive I thought that this is
somehow more complex, involving mri_annot2label, and
mri_label2label with --outmask... however I tried for 2 days
and did not obtain a convincing binary ROI mgh file that I
could fscalc with the sig.mgh, I got lost with several
command params (srclabel/trglabel..).

Could you please help me with exact commands? I'm sure this
should be easy but I lost this battle!!
Thanks a lot in advance

On Tue, Aug 4, 2020 at 5:14 PM Fred Sampedro
mailto:fredsampe...@gmail.com>> wrote:

Thanks a lot!

I read the mri_volcluster doc, can you confirm that the
TalX TalY TalZ coordinates are those of the vertex with
maximum intensity within the cluster? (it could be those
of the cluster's center of gravity)

Finally, I would be very grateful if you could help me
with minor parameter tuning of the commands:

1) mri_binarize lh aparc --min
LABEL/NUMBER_OF_SUPRAMARG?(how do I get it?) --o roimask.mgh

2) fslcalc sig.mgh mult roimask.mgh -o maskedsig.mgh

3) mri_volcluster --in maskedsig.mgh --thmin 0.001 --sum
output.txt

Thanks a lot in advance!


On Mon, Aug 3, 2020 at 4:40 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>>
wrote:

Try mri_volcluster. Pass you masked sig as the input
and set --thmin 0.0001 and specify a summary file
with --sum. I think that should work

On 7/31/2020 9:38 AM, Fred Sampedro wrote:


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Dear FS experts,

I have a rather simple question:

I would like to obtain the MNI coordinates of the
most significant vertex in a sig.mgh map but within
a specific ROI (for instance the left supramarginal
region).

 

Re: [Freesurfer] Make BEM with corrected brainmask

[Douglas Greve]

Try mris_expand

On 9/16/20 10:24 PM, Kadwani, Manorama wrote:

Thank you, I got a brain surface using the mri_binarize function.
Is there a function for expanding the surface radially by a few 
millimeters? I want to create the inner skull surface as an expansion 
of the brain surface.


Thanks,
Manorama

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Wednesday, September 9, 2020 6:25 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] Make BEM with corrected brainmask
I'm not sure, but you might be able to just create a surface from the 
brain mask with

mri_binarize --i brainmask.mgz --min 0.5 --surf brainmask.surf
You can smooth it a bit if you add --surf-smooth 2
where 2 is the number of iterations (more for smoother)
Try that

On 9/9/2020 6:01 PM, Kadwani, Manorama wrote:

Hi,

Why does the "mri_watershed" function create a new brainmask? Is 
there a way to create BEM surfaces from an existing or already 
corrected brainmask?


I had manually edited the brainmask during recon-all process. After 
the recon-all process completed, the pial surfaces looked good.
But when I ran 'make_watershed_bem', the BEM surfaces came out 
incorrect. The function 'mri_watershed' re-created a brainmask with 
the same errors that I had corrected earlier.


I saw there was a question on this topic already, but couldn't find 
answers: 
https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+mri_watershed%22&o=newest&f=1


Thanks,
Manorama

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Re: [Freesurfer] Cohen's D calculation and interpretation

[Douglas Greve]

You have created a circularity that is classic in neuroimaging (see 
Vul's paper on "VooDoo Correlations"). By using only voxels inside a 
cluster, you have selected voxels that are sure to show hi D values

On 9/16/20 7:48 PM, Alejandro Meruelo wrote:
>  External Email - Use Caution
>
> Hi everyone,
>
> I reviewed some of the other answers on the mailing list to compute a
> Cohen's d value following the sequence of commands below for a Qdec
> Freesurfer analysis:
>
> 1) cd glmdir/contrast  fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh
>
> 2) mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0
> --sum test.output
>
> However, my test.output file looks like:
>
> # ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev
> Min Max Range
>
>1   1  2398 2398.0  Seg0001 4.9611 0.8313 3.6525
>  7.3172 3.6647
>
>2   2  5893 5893.0  Seg0002 5.1281 1.1535 3.6520
>  8.8040 5.1520
>
> Why are the mean Cohen's d values (4.9611, 5.1281) so large? Am I
> interpreting these incorrectly?
>
> Many thanks in advance for your help,
> Josh
>
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Re: [Freesurfer] Resting state fMRI preproc-sess registration error

[Douglas Greve]

Can you send the commands you used to check the registration ?

On 9/16/20 2:24 PM, Wenzhen Zhao wrote:
>  External Email - Use Caution
>
> Dear freesurfer developers,
>
> I am working on preprocessing resting state fMRI and used the following 
> command.
>
> $ preproc-sess -s sess01 -fsd rest -stc siemens -surface fsaverage lhrh 
> -surf-fwhm 5 -mni305-2mm -vol-fwhm 0 -per-session
>
> When I tried to visualize f.nii.gz with registration file applied and 
> overlaid with aparc+aseg.mgz from structural analysis, they do not overlap. 
> It seems like the orientation is not the same, and the f.nii.gz with 
> registration seems to be 90 degree rotated from apjarc+ aseg. mgz.  (I wish I 
> could attach a screenshot, but last time I tried, it says my email exceeded 
> the capacity and sent to the moderator)
>
> I also tried bbregister. I was suggested not to use —init-rr, so I tried all 
> the other registration methods, but same problem occurs.
>
> $bbregister --mov sess01/rest/001/template.nii.gz --t2 --s subject --lta 
> register.dof6.lta
>
> —init-rr does a good job when I checked visually by applying registration on 
> f.nii.gz and checked if it overlaps with structural scan. But, I thought the 
> registration file goes both ways, but when I checked structural scan 
> (orig.mgz or aparc+aseg.mgz) with registration file and overlapped with 
> functional scan (f.nii.gz), it does not overlap.
>
> Is there a specific way that I have to apply a registration file to visualize 
> the transformation in the opposite direction?
> If preprocess registration does not work, is there any other method that I 
> can try to make them aligned?
>
> Thank you  for your time and help !
>
> Best,
> Wenzhen
>
>
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Re: [Freesurfer] left-right flip?

[Douglas Greve]

I'm sorry to hear it, but at least you figured it out. You're best 
option is just to convert directly from the dicoms if you have them 
using mri_convert, dcmunpack, or just passing a dicom file directly to 
recon-all as input. If you don't have access to the dicoms, you can run

mri_convert inputfile.nii.gz --left-right-reverse-pix outputfile.nii.gz



On 9/16/20 12:03 PM, Fischl, Bruce wrote:


I think so, but I defer to Doug

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Ellen Ji

*Sent:* Wednesday, September 16, 2020 11:05 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] left-right flip?

*External Email - Use Caution *

Thanks for your reply Bruce. Could you confirm if I can run 
mri_convert on the incorrectly flipped niftis to appropriately correct 
them? (https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal)


Something like:

mri_convert --in_orientation LIA subject1.nii subject1_corrected.nii

best,

Ellen

On 9/16/2020 4:47 PM, Fischl, Bruce wrote:

Hi Ellen

Sorry to say it, but you really should start over. Not everything in the 
brain is bilaterally symmetric so processing and flipping won't be the same as 
flipping then processing.

Cheers

Bruce

-Original Message-

From:freesurfer-boun...@nmr.mgh.harvard.edu  
  
  
  On Behalf Of Ellen Ji

Sent: Wednesday, September 16, 2020 3:41 AM

To:freesurfer@nmr.mgh.harvard.edu  

Subject: Re: [Freesurfer] left-right flip?

     External Email - Use Caution

Hi Douglas,

I found the dicoms and confirm that the fiducial is on the opposite side 
relative to the nifti. Additionally, the PI just informed me that the fiducial 
was placed on the right side of the head and the nifti indicates left. I will 
enquire as to what method was used to convert from dicom as that appears to be 
the issue.

I already performed recon-all and aparcstats2table on the flipped nifti.

Could you please advise if there is there an efficient way to deal with 
this or if I should start from the beginning?

Many thanks,

Ellen

On 9/15/2020 7:19 PM, Douglas N. Greve wrote:

First we have to determine whether it is really LR flipped or not. Do

you still have the dicoms? If so, can you convert to mgz using

mri_convert one-dicom-file.dcm test.mgz Then look at test.mgz and see

if the fiducial has changed sides relative to the nifti.

That is a fiducial. And do you know what side the fiducial was placed

on? mri_info does not help. How did you convert from dicom?

ps. Please make sure to post to the list and not to us personally

On 9/15/2020 12:58 PM, Ellen Ji wrote:

   External Email - Use Caution

group cc'd - thanks for the reminder.

My input data was the niftis. Example: recon-all -i 1kl5011.nii

-subjid

1kl5011 -all

Is there an efficient way to handle the flipped L-R or should I

mri_convert the nifti and then do recon-all?

(Assuming that I can't just switch lh_ and rh_ in the

aparcstats2table)

Ellen

On 9/15/2020 6:51 PM, Fischl, Bruce wrote:

Hi Ellen

Can you cc the list so that others can respond? What was your 
input data? Did you not have dicoms?

Cheers

Bruce

-Original Message-

From: Ellen Ji  


Sent: Tuesday, September 15, 2020 12:38 PM

To: Fischl, Bruce  


Subject: Re: [Freesurfer] left-right flip?

    External Email - Use Caution

Hi Bruce,

Unfortunately I just found the fiducial and realised that the 
L-R is incorrect. Can I simply switch the lh_ and rh_ output from 
aparcstats2table or do I need to run mri_convert on the nifti and run recon-all 
from the beginning again?

Thanks,

Ellen

On 9/15/2020 5:44 PM, Fischl, Bruce wrote:

And what is your input to recon-all? If it is dicom you 
should be

pretty confident that we will get it correct

-Original Message-

From:freesurfer-boun...@nmr.mgh.harvard.edu  


  
  On Behalf Of Douglas N.

Greve

Sent: Tuesday, September 15, 2020 10:17 AM

To:freesurfer@nmr.mgh.harvard.edu  


Subject: Re: [Freesurfer] left-right

Re: [Freesurfer] papers that have reported results using FS5.2

[Douglas Greve]

I can't remember what the issues where, but I don't think they were all 
that bad, something with surface placement. Bruce might remember better 
than me


On 9/15/20 7:22 PM, Paul wrote:


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Dear Freesurfer Developers,
With Freesurfer 5.2 being listed as deprecated, are there any possible 
issues with papers that have reported results using FS5.2?

Thanks,
Paul

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Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

[Douglas Greve]

In both cases, the surfaces are placed on the high-resolution images. 
I'm not sure whether volume segmentation (ie, aseg) of highres images is 
better than at 1mm.


On 9/9/20 10:30 AM, Alexopoulos, Dimitrios wrote:


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Falk and Doug, thx for clarifying.  Before we begin processing a new 
cohort using 7.1, I want to make sure I have a good grasp of the 
options/output. We want good volumes and surfaces, for potential 
cortical surface expansion analysis, thickness, etc.


So, if you want better aseg segmentations/volumes use -hires, however, 
-conf2hires will give better surfaces (since they are placed on the hi 
res image) and thus more accurate cortical thickness and aparc measures.


Jim


Get Outlook for Android 


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Wednesday, September 9, 2020, 9:11 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

** External Email - Caution **

Hi Jim, and thanks for jumping in Falk. This description is almost all 
correct. The one inaccuracy is that the -hires option will downsample 
the surface to a number of vertices equal to the number that would 
have resulted if recon-all had been run at 1mm. The main difference is 
that you will get volume segmentations at the higher resolution with 
-hires where as you will get them at 1mm with -conf2hires.


On 9/9/2020 3:13 AM, falk.luesebr...@med.ovgu.de wrote:


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Hi Jim,

The -hires will conform the data to the highest resolution of your 
input data, instead of 1mm^3. In case it was an isotropic resolution, 
it will stay at native resolution. If it is anisotropic, e.g. 
0.3x0.3x0.7, it will be resampled to 0.3mm^3 – which is not really 
recommended. The segmentation and surface placement will take place 
at that resolution.


The -conf2hires flag will conform your input data to 1mm^3. 
Segmentation and initial surface placement will be handled at 
conformed (1mm) resolution. Then the initial surface placement is 
used at native resolution to refine the surface placement.


With -hires the number of vertices per hemisphere depends on your 
input resolution being roughly at 300k at 0.7mm and 500k at 0.5 mm. 
With -conf2hires the number of vertices will be around 140k per 
hemisphere and, therefore, processing (especially the topologic 
correction) will be much faster compared to -hires. The principle 
behind -conf2hires was used in the processing pipeline of the HCP 
(https://doi.org/10.1016/j.neuroimage.2013.04.127) and has been shown 
to improve the segmentation in highly myelinated areas, e.g. around 
the visual cortex or central sulcus.


Natalia Zaretskaya and Jon Polimeni 
(https://doi.org/10.1016/j.neuroimage.2017.09.060) and I 
(https://doi.org/10.1016/j.neuroimage.2012.12.016) could show that 
the principles behind the -hires flag yield different results than 
downsampling high resolution input data or using 1mm data to being 
with. It is hypothesized that using high resolution data with the 
-hires flag leads to better surface placement and, therefore, more 
accurate cortical thickness measures. However, missing ground truth 
always makes it complicated to proof.


To answer your question which is recommended: In the release notes of 
FreeSurfer it is written with regards to conf2hires “This was 
originally programmed for the HCP. The now-standard hi-res stream 
should work just as well, but we kept conf2hires for backwards 
compatibility.”


I don’t think someone published a comparison between -hires and 
-conf2hires, yet. However, I would use the -hires flag instead of 
-conf2hires. I assume the surface placement to be equally good, with 
potential benefits towards -hires due to the higher number of 
vertices. The drawbacks of -hires (e.g. longer processing time) 
should be compensated to some extent by the new denoising feature 
prior to the intial surface placement. Personally, I haven’t had much 
time to test v7 intensively, though.


Hope this helps.

Best,

Falk

*Von:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *Im Auftrag von 
*Alexopoulos, Dimitrios

*Gesendet:* Mittwoch, 9. September 2020 05:27
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* [Freesurfer] -hires vs -conf2hires in 7.1.1.

*External Email - Use Caution *

Does the hires flag still generate segs at the native hi resolution 
and place surfaces on the 1mm volumes, whereas conf2hires generates 
volumes at 1mm but places surfaces on the hires images?


Which option is recommended and why?

Jim

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Re: [Freesurfer] midline to cut the brain stem into Left and Right

[Douglas Greve]

Not that I know of, sorry

On 9/1/20 10:20 AM, 刘梦醒 wrote:


External Email - Use Caution

Hi Freesurfer group,

For some reason, I have to use the left and right brain stem separately.
I wonder if there is one way to have a midline, to cut the brain stem 
into Left and Right?


Many thanks,
Mengxing


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Re: [Freesurfer] recon-all error

[Douglas Greve]

Try running it with --no-surfs


On 8/29/20 12:34 PM, Jie Zhao wrote:


External Email - Use Caution

Hi, Douglas


I first heared the tkregisterfv, tryed the tkregisterfv --fstal --s 
mprage


the output error was this:

ERROR: cannot find /usr/local/freesurfer/subjects/mprage/surf/lh.white

Best,

Jie



-Original Messages-
*From:*"Douglas N. Greve" 
*Sent Time:*2020-08-29 23:31:44 (Saturday)
*To:* freesurfer@nmr.mgh.harvard.edu
*Cc:*
*Subject:* Re: [Freesurfer] recon-all error

What is the error? tkregister2 is an old program, and it might not
work on all systems. You can try using tkregisterfv instead,
available here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/tkregisterfv

On 8/29/2020 11:26 AM, Jie Zhao wrote:

 External Email - Use Caution

Hi All

I tryed the tkregister2 to change the postion for Talairach 
Registration,but some error occured in the tkregister, so some button were not  
functioning well.

I can not find useful info. on the internet, could you tell me how to 
correct it.Thanks.

Please check the error log file attached.

King regards,
Jie



-Original Messages-
From: "Douglas N. Greve"  Sent Time: 2020-08-28 
00:06:31 (Friday)
To:freesurfer@nmr.mgh.harvard.edu  Cc:
Subject: Re: [Freesurfer] recon-all error

This is the automatic failure detection raising a warning flag. Did you
notice that the output suggested that you take some action?

On 8/27/2020 11:39 AM, Fischl, Bruce wrote:

Hi Jie

I would start by looking at your input volume in freeview:

freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii

and make sure that the orientation it displays in is correct (that is, that 
what freeview thinks is anterior/superior/left are indeed those directions). 
Usually when we see this type of failure it is because the direction cosines in 
the input volume are incorrect (typically because the volume was at some point 
converted to analyze format). Not always, but usually.

Cheers
Bruce


-Original Message-
From:freesurfer-boun...@nmr.mgh.harvard.edu  
  On Behalf Of Jie Zhao
Sent: Thursday, August 27, 2020 11:21 AM
To: Freesurfer support list  Subject: Re: 
[Freesurfer] recon-all error

  External Email - Use Caution

Hi, Andrew

 Attached is the right recon-all.log file, please check it.
 I am new to the freesurfer, so really need you advice, Thanks

Kind Regards,
Jie



-Original Messages-
From: "Hoopes, Andrew"  Sent Time: 2020-08-26
10:17:00 (Wednesday)
To: "Freesurfer support list"  Cc:
Subject: Re: [Freesurfer] recon-all error

Hi Jie, this appears to be the log for your original issue, and not the 
talairach registration failure.
Andrew

On 8/25/20, 9:23 AM,"freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jie 
Zhao"wrote:

  External Email - Use Caution
  
  Hi Andrew
  
  Thanks fro your response.

  I have soruced the Freesurfer.
  Attached is the recon-all log.
  
  Best,

  Jie
  
  
  > -Original Messages-

  > From: "Hoopes, Andrew"  > Sent Time: 
2020-08-24 22:22:28 (Monday)
  > To: "Freesurfer support list"  > Cc:
  > Subject: Re: [Freesurfer] recon-all error
  >
  > Hi Jie,
  >
  > Can you send the subject's full recon-all.log file to provide some 
more context for this failure? Usually this error is due to a poor registration, 
but there might be something else going wrong here based on those p values. Have 
you sourced freesurfer in your environment? Adding the freesurfer bin dir to your 
PATH will provide access to binaries, but there are a few other PATH variables and 
settings that get configured by running `source 
$FREESURFER_HOME/SetUpFreeSurfer.sh`.
  >
  > best
  > Andrew
  >
  > On 8/24/20, 10:12 AM,"freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Jie Zhao"wrote:
  >
  > External Email - Use Caution
  >
  > Hi, Tim
  >
  > Thanks for your quick response.
  > I set the PATH environment varible to include Freesurfer binary 
directory.
  >
  > I have the new problem when using recon-all , the error is like 
this:
  > ERROR: talairach_afd: Talairach Transform: 
transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050
  >
  > How can solve this error?
  >
  > Regards,
  > Jie
  >
  > > -原始邮件-
  > > 发件人: "Tim Schäfer"  > > 发送时间: 2020-08-23 
16:24:28 (星期日)
  > > 收件人: "Freesurfer support list"  
> > 抄送:
  > > 主题: Re

Re: [Freesurfer] recon-all error (incorrect orientation)

[Douglas Greve]

You can use the Transform volume tool in FreeView, though it will be a 
pain if you have to do a bunch. Getting the original dicoms is a much 
better place to start.


On 9/1/20 9:13 AM, Ellen Ji wrote:

External Email - Use Caution
Dear Bruce (and Jie),

I believe I am encountering the same problem as Jie - see the attached 
screenshot from freeview. I was given niftis for a cohort of subjects 
and some of them are sideways. Thus, this resulted in Talairach 
failure when performing recon-all and cannot simply be readjusted 
using tkregister2 as far as I know.


What is the easiest way to fix the orientation?

Many thanks for your help,

Ellen

On 8/30/2020 4:14 AM, Fischl, Bruce wrote:

Hi Jie

The orientations are incorrect. What freeview thinks is 
anterior/posterior (labeled with "A" and "P") is actually 
inferior/superior. Do you have the dicoms from this dataset? If not, 
how was it converted? You need to orient it properly so it shows 
correctly in freeview before we will be able to process it.


Cheers
Bruce

-

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jie Zhao

Sent: Saturday, August 29, 2020 10:08 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all error

 External Email - Use Caution

Here is the snapshot of my freeview window attached.



-Original Messages-
From: "Fischl, Bruce"  Sent Time: 2020-08-30
02:07:50 (Sunday)
To: "Freesurfer support list" 
Cc:
Subject: Re: [Freesurfer] recon-all error

Why do you want to change it? Can you post a snapshot from freeview 
so we can make sure we are on the same page?


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
 On Behalf Of Jie Zhao
Sent: Saturday, August 29, 2020 12:25 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all error

 External Email - Use Caution

Hi Bruce

Thank you for quick answer。

I tryrd the freeview -v
/usr/local/freesurfer/subjecs/2018MPRAGE_p4iso.nii, my freeview
orienatation is RAS. could you tell me how to change it from RAS to
(ASL)anterior/superior/left. Thanks

Best,
Jie




-原始邮件-
发件人: "Fischl, Bruce" 
发送时间: 2020-08-27 23:39:20 (星期四)
收件人: "Freesurfer support list" 
抄送:
主题: Re: [Freesurfer] recon-all error

Hi Jie

I would start by looking at your input volume in freeview, my
orientation on freeview is RAS. Could you tell me

freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii

and make sure that the orientation it displays in is correct (that 
is, that what freeview thinks is anterior/superior/left are indeed 
those directions). Usually when we see this type of failure it is 
because the direction cosines in the input volume are incorrect 
(typically because the volume was at some point converted to 
analyze format). Not always, but usually.


Cheers
Bruce


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
 On Behalf Of Jie Zhao
Sent: Thursday, August 27, 2020 11:21 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all error

 External Email - Use Caution

Hi, Andrew

    Attached is the right recon-all.log file, please check it.
    I am new to the freesurfer, so really need you advice, Thanks

Kind Regards,
Jie



-Original Messages-
From: "Hoopes, Andrew"  Sent Time:
2020-08-26
10:17:00 (Wednesday)
To: "Freesurfer support list" 
Cc:
Subject: Re: [Freesurfer] recon-all error

Hi Jie, this appears to be the log for your original issue, and 
not the talairach registration failure.

Andrew

On 8/25/20, 9:23 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on 
behalf of Jie Zhao" behalf of zjuzhao...@zju.edu.cn> wrote:


 External Email - Use Caution
  Hi Andrew
  Thanks fro your response.
 I have soruced the Freesurfer.
 Attached is the recon-all log.
  Best,
 Jie
   > -Original Messages-
 > From: "Hoopes, Andrew" 
 > Sent Time: 2020-08-24 22:22:28 (Monday)
 > To: "Freesurfer support list" 
 > Cc:
 > Subject: Re: [Freesurfer] recon-all error
 >
 > Hi Jie,
 >
 > Can you send the subject's full recon-all.log file to 
provide some more context for this failure? Usually this error is 
due to a poor registration, but there might be something else 
going wrong here based on those p values. Have you sourced 
freesurfer in your environment? Adding the freesurfer bin dir to 
your PATH will provide access to binaries, but there are a few 
other PATH variables and settings that get configured by running 
`source $FREESURFER_HOME/SetUpFreeSurfer.sh`.

 >
 > best
 > Andrew
 >
 > On 8/24/20, 10:12 AM, 
"freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jie Zhao" 
zjuzhao...@zju.edu.cn> wrote:

 >
 > External Email - Use Caution
 >
 > Hi, Tim
 >
 > Thanks for your quick response.
 > I set the PATH environment varible to include 
Freesurfer binary directory.

 >
  

Re: [Freesurfer] tkregister2 deprecated for FS7.1?

[Douglas Greve]

In 7.1.1, you can use tkregisterfv instead of tkregister2 (same command 
line otherwise).  If you don't want to download 7.1.1, you can get just 
tkregisterfv from 
https://gate.nmr.mgh.harvard.edu/safelinks/greve/tkregisterfv


On 8/31/20 3:42 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


Hi FS devs,


I am following 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview​ 
as a tutorial to fix the bad talaiarch file I have. I know that 
tkmedit is deprecated, but I was wondering if tkregister2 is too. If 
so, I was wondering what software I would use (or commands, I assume 
using freeview) since that page still refers to tkregister2.



Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--



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Re: [Freesurfer] mri_preproc error with FS6.0

[Douglas Greve]

Why are you specifying the target as average instead of fsaverage?

On 8/31/20 12:13 PM, chelseach...@yahoo.com wrote:


External Email - Use Caution

Hello,
I am running into an error while running the LGI analyses using 
FreeSurfer 6.0 following Jove article recommendations ( 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369773/). The error is 
occuring when I try to run the following command:


mris_preproc --fsgd FSGD.txt --target average --hemi lh --meas 
pial_lgi --out lh.lgi.mgh



Here is the error message:

nsubjects = 57
tmpdir is ./tmp.mris_preproc.174575
/data/EDresearch/AdolAN_All/enigma/output
Log file is lh.lgi.mris_preproc.log
Mon Aug 31 08:25:13 PDT 2020
setenv SUBJECTS_DIR /data/EDresearch/AdolAN_All/enigma/output
cd /data/EDresearch/AdolAN_All/enigma/output
/usr/local/freesurfer/bin/mris_preproc --fsgd FSGD.txt --target 
average --hemi lh --meas pial_lgi --out lh.lgi.mgh


Linux induction3.sdsc.edu 
 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 
23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

$Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
tmpdir is ./tmp.mris_preproc.174575
Src lh average.sphere.reg
Trg lh sphere.reg




---
#@# 1/57 541202132011 Mon Aug 31 08:25:13 PDT 2020 --
---
mri_surf2surf --srcsubject 541202132011 --srchemi lh --srcsurfreg 
average.sphere.reg --trgsubject average --trghemi lh --trgsurfreg 
sphere.reg --tval ./tmp.mris_preproc.174575/541202132011.1.mgh --sval 
/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi 
--sfmt curv --noreshape --cortex
MRISread(/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg): 
could not open file

Source registration surface changed to average.sphere.reg
Target registration surface changed to sphere.reg

$Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $

setenv SUBJECTS_DIR /data/EDresearch/AdolAN_All/enigma/output
cd /data/EDresearch/AdolAN_All/enigma/output
mri_surf2surf --srcsubject 541202132011 --srchemi lh --srcsurfreg 
average.sphere.reg --trgsubject average --trghemi lh --trgsurfreg 
sphere.reg --tval ./tmp.mris_preproc.174575/541202132011.1.mgh --sval 
/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi 
--sfmt curv --noreshape --cortex


sysname  Linux
hostname induction3.sdsc.edu 
machine  x86_64
user     chays
srcsubject = 541202132011
srcval     = 
/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi

srctype    = curv
trgsubject = average
trgval     = ./tmp.mris_preproc.174575/541202132011.1.mgh
trgtype    =
srcsurfreg = average.sphere.reg
trgsurfreg = sphere.reg
srchemi    = lh
trghemi    = lh
frame      = 0
fwhm-in    = 0
fwhm-out   = 0
label-src  = lh.cortex.label
label-trg  = lh.cortex.label
OKToRevFaceOrder  = 1
UseDualHemi = 0
Reading source surface reg 
/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg

No such file or directory
mri_surf2surf: could not read surface 
/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg

No such file or directory
/
/


Of note, this command works fine when substituting the fsaverage 
rather than study average template, however this is an adolescent 
sample so we are not able to use the fsaverage. Any help would be 
greatly appreciated!


Best,
Chelsea



Chelsea C. Hays, Ph.D.
Neuropsychology Postdoctoral Fellow
Center of Excellence in Stress and Mental Health
UC San Diego|VA San Diego Healthcare System
ch...@ucsd.edu |chelsea.ha...@va.gov 






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Re: [Freesurfer] mris_anatomical_stats

[Douglas Greve]

Yes, that is the effect of including the cortex.label

On 8/31/20 8:28 AM, Palin, Tara wrote:


External Email - Use Caution

When using the following command line:


mris_anatomical_stats -th3 -mgz- cortex ../label/?h.cortex.label -f 
../stats/?h.aparc.pial.stats -b -a ../label/?h.aparc.annot -c 
../label/aparc.annot.ctab subject ?h pial



do we generate a pial surface area (for each hemisphere) that excludes 
the medial wall?



Thank you,

Tara


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Re: [Freesurfer] Schwartz atlas reference in recon-all 3T flag

[Douglas Greve]

No, not published. Probably won't be. It has a small effect on the 
output anyway


On 8/31/20 1:47 AM, Hye Min Shin wrote:


External Email - Use Caution

Hello,

I understand that from a previous FreeSurfer question the Schwartz 
atlas used in the 3T flag during recon-all is not published yet 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47175.html). 



Since this question was asked back in 2016 I wanted to double-check if 
the reference atlas for the Schwartz atlas is still not published yet.


Best,
Julia Shin

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Re: [Freesurfer] One hemisphere recon-all and aparc+aseg.mgz

[Douglas Greve]

There is a bug in recon-all when trying to only run with one hemi 
(actually there are several bugs). Currently, it is failing at 
mris_volmask, which needs to have --lh appended to the command line. You 
can do this with an expert options file. This is  simple text file that 
should have the contents

mris_volmask --lh
Also, when you run recon-all with -lh instead of -hemi lh
I think there will be more problems, but this might get an 
aparc+aseg.mgz with only one hemi


On 8/30/20 6:32 AM, Alina Rojas wrote:


External Email - Use Caution

Hello Freesurfer experts,

i’m attempting to run recon-all on only one hemisphere for further 
processing steps. For these I need wmparc.mgz, aparc.a2009s+aseg.mgz, 
aparc+aseg.mgz.


recon-all -sd ${TARGET_FOLDER}-subjid $SUBJECTID-i $T1-qcache -openmp 
${OMP_NUM_THREADS}-all -hemi lh -no-isrunning


It crashes before the files are made. How can I get these files? I 
attached the recon-all.log file.



Thank you,

Alina Rojas






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Re: [Freesurfer] recon-all exited with errors

[Douglas Greve]

Try looking at our wiki
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview


On 8/30/20 7:16 AM, Vinny K wrote:


External Email - Use Caution

Hi,

I've tried to process a scan but it gets hung up on a particular large 
defect and then exits with error.  I've had large defects with other 
scans before but recon-all was able to get past it.  How can I correct 
this?  I've attached the recon-all log.


Thanks,

Vinny

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Re: [Freesurfer] Petsurfer - negative values after RBV partial volume correction

[Douglas Greve]

Yes, this is not unusual. The GTM (which RBV is based on) is just a GLM 
where it uses a linear model to estimate the ROI intensities. There are 
no constraints on positivity. When the model is not exactly correct 
(which it never will be) it is possible to get negative values. Usually 
this only happens in small ROIs and/or low uptake regions. Why might the 
model not be perfect? It could be a number of things:

1. the MRI-PET registration is inaccurate
2. the MRI segmentation is inaccurate
3. the ideal segmentation is not reflected by the MRI segmentation (eg, 
one of the segmentations has a hot spot)


It could also be the case that the OSEM positivity constraint causes 
bias in low uptake regions (the GLM expects two-sided Gaussian noise)



On 8/28/20 7:27 PM, Albrecht, Daniel S. wrote:


Hello,

I’ve been running RBV partial volume correction on some amyloid PET 
data recently using mri_gtmpvc, and for ~90% of subjects the resulting 
rbv.nii.gz looks as expected with the exception of negative values in 
the bilateral accumbens (see attached image, thresholded from 0-4000 
in scanner units). Any ideas why this might be happening?


This is the command I’ve been using:

mri_gtmpvc --i $PETimg \
--reg $identity_mtrx  \
--seg $FSdir/${subject}/mri/gtmseg.mgz \
--psf 6 --default-seg-merge --auto-mask PSF .01 --rbv \
--no-rescale --threads 8 \
--o $outname

Thanks very much,

Dan


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Re: [Freesurfer] Covariates vs sample size

[Douglas Greve]

Yes, you will have enough DOF if that is what you are asking

On 8/28/20 4:31 AM, Sunil Khokhar wrote:


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Dear Experts,

With a sample size of 45, can I perform GLM analysis with one primary 
independent variable and 6 covariates?

Dependent variable is cortical thickness.


Thanks in advance!
Sunil.

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Re: [Freesurfer] Global surface area and global thickness values {Disarmed} {Disarmed}

[Douglas Greve]

Yes!

On 8/26/20 9:30 AM, Palin, Tara wrote:


External Email - Use Caution

Again, thank you for your explanation of how these variables are 
calculated. However, the the main question still left is, are these 
values the most representative of the whole cerebral surface area and 
the whole cerebral thickness for both the left and right hemispheres?



*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Monday, August 24, 2020 10:15:10 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Global surface area and global thickness 
values {Disarmed}
KKI SECURITY ALERT: This email is from an external source. Do not 
click on any links or open attachments unless you recognize the sender 
and know the content is safe.


The average thickness is the average over all the vertices in the 
cortex.label
The total surface area is the sum of all the triangles that have all 
three corners in the cortex.label


On 8/24/2020 9:35 AM, Palin, Tara wrote:


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I was asking if the Mean Thickness value and the Pial Surface Area 
values at the top of the aparc.stats file that is generated when 
running freesurfer are the global measures. And if they are, I got 
very close values on multiple different apar.stats files by using the 
Surface Area and AvgThick ROI values printed at the bottom of the 
file. Basically, how are those values stated in the first sentence 
being calculated.



Thank you.


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. 
Greve 

*Sent:* Friday, August 21, 2020 6:42:38 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Global surface area and global thickness 
values
KKI SECURITY ALERT: This email is from an external source. Do not 
click on any links or open attachments unless you recognize the 
sender and know the content is safe.


I'm not sure what your question is. You can't just average the ROI 
values to get the global value unless you weight by the ROI size.


On 8/21/2020 2:55 PM, Palin, Tara wrote:


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Hello freesurfer experts,


I am looking to extract the global surface and global thickness 
measurements and am curious if my understanding of the output on the 
aparc.stats (for lh and rh) are correct. When looking at these 
files, at the very top you will find the Pial Surface Total Area and 
a Mean Thickness value which I am assuming are the global measures. 
Below you have all of the ROIs listed (this was not changed by us or 
generated by us this is what comes out of freesurfer to my 
understanding) that includes everything EXCEPT the corpus callosum 
and the unknown. However, I summed all the surface areas and took 
and average of all the thickness measurements and they are very 
close to the values printed at the top of the sheet. Another 
observation I had made was that the total surface area measurement 
has a decimal and the surface area for the ROIs appears to be 
rounded and if they were not rounded the values would be the same. 
For the thickness values, the value I calculated and the one on the 
sheet are within the average of the standard deviation each other.



If my understanding is incorrect please let me know and provide 
insight into how we may calculate these global measurements correctly.



Thank you in advance for your time,

Tara Palin




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Re: [Freesurfer] Questions about speed up the longitudinal processing

[Douglas Greve]

Rather than -parrallel, use -threads to indicate the number of 
processors to use


On 8/5/20 10:47 AM, Yang Molly wrote:


External Email - Use Caution

Hi list,

I tried to run some longitudinal data with two time points with the 
latest version Freesurfer (7.1.0) on the Ubantu 16 system. "recon-all 
-base" with two time points need 5 hours to complete on my PC, and 
recon-all -long need 2 hours. I try to use the command "recon-all 
-long pre009 sub009base -parallel" and it went with errors.  I was 
wondering if I can use other flags to speed up the recon-all -base and 
recon-all -long for each terminal.


Thank you
Molly

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Re: [Freesurfer] PetSurfer Crashing

[Douglas Greve]

Did you really mean to pass subject/mri/gtmseg.lta ? The registration is 
supposed to be the registration of the input (PET.template.nii.gz) to 
the anatomical. subject/mri/gtmseg.lta is the registration of gtmseg.mgz 
to the anatomical.


On 7/20/20 11:21 AM, Crawford, Anna wrote:


External Email - Use Caution

Hello,


I am trying to run the PetSurfer process for the first time. I was 
able to run gtmseg and mri_coreg which seemed to go okay. When I tried 
running mri_gtmpvc, it is crashing, but I am not sure why. The command 
I am using and output are below. Do you have any guidance as to what 
is going wrong?



Thank you,

Anna



mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg 
subject/mri/gtmseg.lta --psf 6 --seg subject/mri/gtmseg.mgz  
--default-seg-merge --auto-mask PSF .01 --mgx .01 --o 
subject/gtmpvc.output

Loading input ../CTPET/PET.template.nii.gz
  done loading input 1 frames

$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $
setenv SUBJECTS_DIR /mnt/netRAID18/7T/study709/S2sdt/
cd /mnt/autofs/netRAID18/7T/study709/S2sdt
mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg 
subject/mri/gtmseg.lta --psf 6 --seg subject/mri/gtmseg.mgz 
--default-seg-merge --auto-mask PSF .01 --mgx .01 --o 
subject/gtmpvc.output

sysname  Linux
hostname fmri15
machine  x86_64
user crawforda
vgthresh   0.001000
nReplace   18
0. 0. 0. 0. 0. 0.
20 avail.processors, using 1
Creating output directory subject/gtmpvc.output
Loading seg for gtm subject/mri/gtmseg.mgz
Loading seg ctab subject/mri/gtmseg.ctab
Reading subject/mri/gtmseg.lta
Replacing 18
Pruning ctab
Checking tissue type
done with seg vol
maxFWHM = 2.95567 (voxels), PadThresh=0.0001, nPad=10
Computing auto mask
Automask, reducing FOV
region 256 256 109 reduced to 21 11 3  235 245 106
ERROR: LTAconcat(): LTAs 0 and 1 do not match
LTA 0 ---
type  = 0 # LINEAR_VOX_TO_VOX
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
9.97615814209e-01 0.000e+00 -8.381903171539307e-09 
-7.62939453125e-06
7.450580596923828e-09 9.98807907104e-01 0.000e+00 
0.000e+00
-7.450580596923828e-09 7.450580596923828e-09 9.98211860657e-01 
-1.52587890625e-05
0.000e+00 0.000e+00 0.000e+00 
9.99403953552e-01

src volume info
valid = 1  # volume info valid
filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00 
1.000e+00
xras   = -1.000e+00 0.000e+00 
0.000e+00
yras   = 0.000e+00 0.000e+00 
-1.000e+00

zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = 4.125e+00 3.554792785644531e+01 
-2.000e+01

dst volume info
valid = 1  # volume info valid
filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00 
1.000e+00
xras   = -1.000e+00 0.000e+00 
0.000e+00
yras   = 0.000e+00 0.000e+00 
-1.000e+00

zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = 4.125e+00 3.554792785644531e+01 
-2.000e+01

subject subject
fscale 0.15
LTA 1 ---
type  = 0 # LINEAR_VOX_TO_VOX
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
9.99403953552e-01 0.000e+00 0.000e+00 
-2.09237060547e+01
0.000e+00 9.99403953552e-01 0.000e+00 
-1.10762939453e+01
0.000e+00 0.000e+00 1.000e+00 
-3.000e+00
0.000e+00 0.000e+00 0.000e+00 
1.000e+00

src volume info
valid = 1  # volume info valid
filename = ../CTPET/PET.template.nii.gz
volume = 256 256 109
voxelsize = 2.121269941329956e+00 2.121269941329956e+00 
2.02971389771e+00
xras   = -1.000e+00 -0.000e+00 
0.000e+00
yras   = -0.000e+00 1.000e+00 
0.000e+00
zras   = -0.000e+00 -0.000e+00 
1.000e+00

cras   = 3.660461425781250e+00 1.723927307128906e+02 1.247645019531250e+03
dst volume info
valid = 1  # volume info valid
filename =
volume = 235 245 106
voxelsize = 2.121269941329956e+00 2.121269941329956e+00 
2.02971389771e+00
xras   = -1.000e+00 -0.000e+00 
0.000e+00
yras   = -0.000e+00 1.000e+00 
0.000e+00
zras   = -0.000e+00 -0.000e+00 
1.000e+00
cras   = -1.861288452148438e+01 1.840597229003906e+02 
1.250690063476562e+03

--
Data load time 10.9 sec
nmask = 3714389, nsegs = 100, excluding segi

Re: [Freesurfer] Fwd: One hemisphere recon-all ERROR

[Douglas Greve]

sorry, I thought I answered this a while back. Try using -hemi lh 
instead of -lh


On 7/18/20 1:22 PM, Alina Rojas wrote:


External Email - Use Caution

Hello Freesurfer community,

I was wondering if you could look at the e-mail below. Thank you!

Alina


Anfang der weitergeleiteten Nachricht:

*Von: *Alina Rojas mailto:alinacol...@gmail.com>>
*Betreff: **One hemisphere recon-all ERROR*
*Datum: *13. Juli 2020 um 15:25:18 MESZ
*An: *Freesurfer support list >


Hello Freesurfer community,

I'm attempting to compare the cortical thickness of one side of the 
brain between stroke subjects. I got "ERROR: you must include rh 
white and pial surfaces“. I used recon-all -sd 
${TARGET_FOLDER}-subjid $SUBJECTID-i $T1-T2 $T2-qcache-all -3T 
-T2pial -lh. I attached the recon-all.log file. Ist it a way to get 
the aparc?


Thank you for your help,

Alina Rojas





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Re: [Freesurfer] Right and left on MRI scan and on images

[Douglas Greve]

This information is extracted out of the dicom header, so as long as you 
are converting directly from dicom, the information will be correct. You 
can run

mri_info orig.mgz
and it will print out a lot of information, including the orientation 
string. Eg, RAS means that the fastest (column) dimension increases to 
the right. When you look at a volume in freeview, you will see 
coordinates in the control window. These will be RAS


On 7/17/20 7:45 PM, Cibele Bandeira wrote:


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Hello,
I have an MRI sample collected on a Siemens Magnetom Spectra 3T 
scanner. However, we do not place any pointing devices inside the 
scanner to indicate which side is the right and which is the left. I 
was wondering how the images were acquired -  from the front of the 
individuals, meaning that the left in the image is the right in the 
patient? Or otherwise?
When processing the T1-weighted images on Freesurfer, I also have a 
doubt...  the DICOM images are synchronized? Left in DICOM is left in 
the patient? And after freesurfer preprocessing? It flips the images 
or not?


Thank you very much!
--
*Cibele Edom Bandeira*
Doutoranda em Genética e Biologia Molecular (PPGBM)
Universidade Federal do Rio Grande do Sul (UFRGS)


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Re: [Freesurfer] mris_convert error

[Douglas Greve]

Do you mean that the inflated is not somehow in line with the pial? They 
are not supposed to be (and it is not clear what that would mean). The 
white and pial look aligned


On 7/6/20 7:16 AM, Mason Wells wrote:


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Hi Experts,

I am using mris_convert to convert native FreeSurfer surf files 
(inflated, pial and white) to GIFTI files. However, when I view them 
in Freeview, there seems to be a misalignment/error (attached). The 
commands I ran followed this structure:


Mris_convert lh.inflated lh.inflated.surf.gii

Any help would be great.

Mason

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk 

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage 





*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk 

*/Ffôn/*: 02920 879628


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Re: [Freesurfer] Destrieux atlas volume based in matlab

[Douglas Greve]

you can run recon-all on the MNI152 itself, though it will not reflect 
the average of the subjects that went into it


On 7/3/20 4:42 AM, Gian Marco Duma wrote:


External Email - Use Caution

Dear Freesurfers experts,
I need to obtain in the volume and not in the surface, in MNI space 
with voxels of 2mm. At this moment I do not need to obtain a 
parcellation of a single subject, even a parcellation in the volume 
from the MNI template would be great. Do you have any suggestions?

thanks

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Re: [Freesurfer] Recon-all 5.3.0 failing and I can't see the error message

[Douglas Greve]

Do all subjects have this problem or just this one? Have you looked at 
orig.mgz to rule out any major problems?


On 6/30/20 8:13 AM, Ian wrote:


External Email - Use Caution

Here you go Doug, thanks.

docker@7d97b79d7546:/execute/freesurfer2016/mri$ mri_nu_correct.mni 
--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o 
orig_nu.mgz

/execute/freesurfer2016/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o 
orig_nu.mgz

nIters 1
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
Linux 7d97b79d7546 5.3.0-59-generic #53~18.04.1-Ubuntu SMP Thu Jun 4 
14:58:26 UTC 2020 x86_64 GNU/Linux

Tue Jun 30 12:13:22 UTC 2020
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva 
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37

tmpdir is ./tmp.mri_nu_correct.mni.835
/execute/freesurfer2016/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.835/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.835/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=7.92, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.835/nu0.mnc...


Iteration 1 Tue Jun 30 12:13:23 UTC 2020
nu_correct -clobber ./tmp.mri_nu_correct.mni.835/nu0.mnc 
./tmp.mri_nu_correct.mni.835/nu1.mnc -tmpdir 
./tmp.mri_nu_correct.mni.835/0/ -iterations 1000 -distance 50
Can't use 'defined(@array)' (Maybe you should just omit the 
defined()?) at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em 
line 165.
nu_correct: crashed while running nu_estimate_np_and_em (termination 
status=65280)

ERROR: nu_correct

On 29/06/2020 15:50, Douglas N. Greve wrote:

Not sure. Can you run this

cd /execute/freesurfer2016/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 
--no-rescale --i orig.mgz --o orig_nu.mgz


and send the terminal output?


On 6/29/2020 7:01 AM, Ian wrote:


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I have attached the log - is there any chance you could tell me what 
the problem is?


Thanks,

Ian

--


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*Ian Hardingham*

Chief Technology Officer

signature_873986710

ian.harding...@oxfordbraindiagnostics.com 



+44 (0)7789 770555

Oxford Centre for Innovation | New Road | Oxford | OX1 1BY

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Wales | Company No. 11703979 | VAT No. 321 3026 62



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Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}

[Douglas Greve]

If you want to save it on label format, then mri_cor2label is the right 
way to go. Make sure to use the --surf option. If you want them in 
separate mgz files, then use mri_binarize with --match



On 6/12/20 7:35 PM, Mason Wells wrote:


External Email - Use Caution

Hi Doug,

Yes, I mean a surface overlay, it is the mgz format. It essentially 
has 25 visual areas, shown in the attached. I wanted to split them up, 
so that each ROI is its own label. I saw I could use mri_cor2label, 
but is there a better way?


Cheers,
Mason

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk 

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage 





*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk 

*/Ffôn/*: 02920 879628

*From: * on behalf of "Douglas 
N. Greve" 

*Reply to: *Freesurfer support list 
*Date: *Friday, 12 June 2020 at 15:44
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] Splitting surface overlay into separate files

When you say "surface" do you mean a surface overlay or a surface with 
xyz and neighbor relations? Assuming you mean an overlay (eg, 
something in an mgh or mgz file), you can try fscalc. Or do you have 
25 frames  in a single file and you want to split them into separate 
files? You might be able to convert the mgh/mgz file to nii and use 
FSL tools and then convert them back (sometimes works, sometimes not)


On 6/12/2020 10:24 AM, Mason Wells wrote:

*External Email - Use Caution *

Hi Experts,

Apologies if this is a rather simple question. Is there a
FreeSurfer equivalent of fslmaths? I have an atlas overlay that
has 25 visual areas in a single .mgz file. I want to separate each
atlas region into a different file, so that I end up with 25
surface atlas regions. Is there a command that could achieve this?

My next question is whether or not there is a Freesurface command
that can be used to complete surface based correlations. For
example, if I want to check for the overlap between two ROIs. I
have been using fslcc to do this in the volume, but perhaps
freesurfer has something similar to do this on the surface?

Cheers,

Mason

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk 

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage




*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

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Re: [Freesurfer] Longitudinal edits on norm.mgz instead of brainmask

[Douglas Greve]

Which edits did you make? Control points are not linked to a volume and 
will be applied appropriately. Or did you make edits meant to fix the mask?

On 5/17/20 4:29 AM, Elena Pozzi wrote:
>  External Email - Use Caution
>
> Dear experts,
>
> I have a longitudinal study with 2 time points and I created the base 
> template following the longitudinal tutorial. I open the images to inspect 
> the result and I made some edits to the base. However, I made the edits on 
> the norm.mgz image instead of the brainmask.mgz. I suspect this is not right. 
> Is there any way to transfer the edits when I re-run recon-all before 
> creating the longitudinal runs? Or do I have to do all the edits again? Thank 
> you very much in advance.
>
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Re: [Freesurfer] Group Analysis Covariates

[Douglas Greve]

And what is your new question?

On 5/17/20 12:10 PM, Hua, Jessica wrote:


External Email - Use Caution

Sure, attached are the files again and here is our previous 
correspondence:


Original question:

After running the permutation and finding significant clusters, I am 
trying to calculate the value for each participant for these 
significant clusters.


The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to 
get the adjusted values accounting for age, sex, and ICV (this is a 
three group design).  What would be the best way of calculating that?


Your response:

There is not an easy way to do it, but you can do it in matlab
cd glmdir
X = load('Xg.dat');
y = load('perm.th30.abs.y.ocn.dat');
beta = inv(X'*X)*X'*y;
yhat = X(:,[i j k ...]*beta([i j k ...])

where i j k ... indicate the factors you want keep in your data. Each
factor gets a column in the design matrix (and a beta). If you need help
figuring this out, send the fsgd file.


---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri

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Re: [Freesurfer] Apply transformation

[Douglas Greve]

Yes, mri_vol2vol

On 2/15/20 11:07 AM, Adam Rytina wrote:


External Email - Use Caution

Hello all,

I want to apply the saved transformation (a transformation matrix 4x4 
acquired by registration of an anatomical and a diffusion image) on my 
input anatomical mask and change a final FOV by specifying a diffusion 
reference image (its voxels size). It means to apply the same command 
as the command ApplyXFM in FSL FLIRT. Does this option exist also in 
Freesurfer?


Thanks a lot
Regards
Adam



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Re: [Freesurfer] About statistical analysis of volumetric results

[Douglas Greve]

It is valid to compare just the absolute volumes, but it might improve 
the results to divide by the ETIV. I would compute the average ETIV and 
divide by that. Alternatively, you can compute a relative change 
(vol2-vol1)/((vol1+vol2)/2)



On 2/15/20 10:23 AM, Halil Aziz VELİOĞLU wrote:


External Email - Use Caution



Hi Mr/Mrs

We treated a group of patients. We performed volumetric analysis in 
freesurfer before and after treatment.

Is it correct to take volumetric values directly into a paired test?

Or should we perform statistical analysis after dividing all values 
before and after treatment by "Estimated Total Intra Cranial Vol"?

Is normalization by doing this way?

Best regards
Halil Aziz
--
Öğr. Gör. Dr. Halil Aziz Velioğlu
Kognitif Sinirbilim Anabilim Dalı



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Re: [Freesurfer] Overlay electric field distribution on pial surface

[Douglas Greve]

Did you look at the results of the registration to make sure that they 
are ok? But you probably don't need to run the registration anyway since 
the surfaces are in the T1.mgz space anyway. How are you verifying that 
the efield is properly aligned to the T1.mgz? Is it also 1mm^3 and 
256^3? Does it have the same vox2ras matrix as the T1.mgz? use mri_info 
--vox2ras T1.mgz Dep48_DLPFC_normE_CORRECTED.nii


On 9/17/18 8:42 AM, Meusen - Klooster, D.C.W. wrote:
>  External Email - Use Caution
>
> Dear Prof. Fischl,
>
> Sorry for the lack of clarity. I used bbregister to generate a 
> registration.dat file. I used simnibs to calculate the Efield distribution 
> and this has the option to convert the Efield mesh files to .nii files. So I 
> registered the high resolution T1 (from simnibs, that aligns with the Efield) 
> to the original T1 data. Consecutively, I used  tksurfer to visualize.
>
> bbregister --s Dep48_T1_origANAT --mov 
> /home/debby/Desktop/FigModPap_Depr48/fs_HeadmeshDep48_origT1/mri/T1.mgz --reg 
> /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat --t1
>
> tksurfer FigModPap_Depr48 lh pial -sdir /home/debby/Desktop -overlay 
> /home/debby/Desktop/FigModPap_Depr48/Dep48_DLPFC_normE_CORRECTED.nii 
> -overlay-reg 
> /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat -fthresh 
> -2 -fmid 150
>
> Best,
> Debby
> 
> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Verzonden: zaterdag 15 september 2018 17:21
> Aan: Freesurfer support list
> Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial 
> surface
>
> Hi Debby
>
> you need to give us a lot more information. What commands did you use to
> sample the field onto the surface? What was the output of those commands?
> Note that tksurfer is deprecated, so I wouldn't worry about how it looks
>
> cheers
> Bruce
>
>
> On Sat, 15 Sep 2018, Meusen -  Klooster, D.C.W. wrote:
>
>>  External Email - Use Caution
>>
>> Dear all,
>> I am studying transcranial magnetic stimulation (TMS) and would like to 
>> nicely visualize my TMS
>> induced electric fields over a pial surface, preferably using Freesurfer to 
>> stay in line with my
>> other images. I have a .nii file of the electric field distribution, 
>> registered to T1, representing
>> field strengths in every voxel. Visualization in freeview looks okay, but 
>> visualization using
>> tksurfer does not really give the right results (most of the brain is 
>> yellow... no field
>> distribution visible). I guess something goes wrong in the setting of the 
>> colorbar. Preferably I
>> would like to see the field strengths (min:max) in a blue-red colorscheme. 
>> Can anybody tell me how
>> to accomplish this?
>> Thank you very much in advance.
>> Best,
>> Debby
>>
>>
>
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Re: [Freesurfer] Seeing the Results in the Original Space

[Douglas Greve]

check out this page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat


On 9/9/18 11:18 AM, Maedeh Khalilian wrote:


External Email - Use Caution

Dear FreeSurfer Experts,
How can i have the results of FreeSurfer in its original space?
The results have rotation and also the axial and the coronal images 
are replaced with each other.

Thanks in advance
Best regards,
Maedeh


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Re: [Freesurfer] recon-all error

[Douglas Greve]

The terminal output is evrything that gets printed to the screen. The 
analysis in the recon-all.log file looks  like it did not finish right 
away (and there is no error msg in it)


On 9/7/18 11:51 AM, Song, Da-Yea wrote:


External Email - Use Caution

I have attached the recon-all.log on this email. I’m not so sure what 
you mean by the terminal output file?


Thanks,

Da-Yea

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas 
Greve

*Sent:* Friday, September 07, 2018 11:36 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] recon-all error

can you send the terminal output and recon-all.log?
thanks

On 9/7/18 9:58 AM, Song, Da-Yea wrote:

*External Email - Use Caution *

Hello,

I’m running some subjects through recon-all but have noticed that
some error out (terminate the job) within seconds of starting. Any
suggestions would be really appreciated. Here is the recon-all.cmd
error message:

#-

# New invocation of recon-all Fri Sep  7 09:34:58 EDT 2018

mri_convert /g5/dcn/freesurfer/MPRAGE/PS070/001
/g5/dcn/freesurfer/subjects/PS070/mri/orig/001.mgz

#

#@# MotionCor Fri Sep  7 09:35:30 EDT 2018

cp /g5/dcn/freesurfer/subjects/PS070/mri/orig/001.mgz
/g5/dcn/freesurfer /subjects/PS070/mri/rawavg.mgz

mri_convert /g5/dcn/freesurfer/subjects/PS070/mri/rawavg.mgz
/g5/dcn/freesurfer /subjects/PS070/mri/orig.mgz --conform

mri_add_xform_to_header -c /g5/dcn/freesurfer
/subjects/PS070/mri/transforms/talairach.xfm /g5/dcn/freesurfer
/subjects/PS070/mri/orig.mgz /g5/dcn/freesurfer
/subjects/PS070/mri/orig.mgz

#

#@# Talairach Fri Sep  7 09:35:44 EDT 2018

mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1
--proto-iters 1000 --distance 50

#-

# New invocation of recon-all Fri Sep  7 09:36:58 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:37:03 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:39:43 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:39:47 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:42:58 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:43:02 EDT 2018

Best,

Da-yea



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Re: [Freesurfer] FsPalm patch

[Douglas Greve]

Actually, I figured it out. Everything is there now, just follow the 
instructions in the README.

On 9/7/18 11:48 AM, Douglas Greve wrote:
> I have recreated the patch. The only problem is that I don't quite
> remember what should be in it. The wiki says that there are 3 files to
> install, but I can only remember two. Tom, can you install those two
> files and run it and see what fails? That will tell me what the 3rd file is.
> thanks
> doug
>
>
> On 9/7/18 11:30 AM, ts...@rcmd.org wrote:
>>   External Email - Use Caution
>>
>> Hi Tom and Zahra,
>>
>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>>  on behalf of Tom Parker
>>>> I am attempting to download the FsPalm patch 
>>>> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm)
>>> On September 7, 2018 at 4:10 PM "Nasiriavanaki, Zahra" 
>>>  wrote:
>>> I downloaded it from this link.
>>> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide
>> I think you are talking about 2 different things: PALM and FsPalm.
>>
>> @Tom: On the problem with the FsPalm download: the FreeSurfer FTP server is 
>> currently unavailable due to a hard disk failure, see this recent message on 
>> this list:
>>
>> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg59312.html
>>
>> Just wait a bit.
>>
>>
>> Best,
>>
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Re: [Freesurfer] FsPalm patch

[Douglas Greve]

I have recreated the patch. The only problem is that I don't quite 
remember what should be in it. The wiki says that there are 3 files to 
install, but I can only remember two. Tom, can you install those two 
files and run it and see what fails? That will tell me what the 3rd file is.
thanks
doug


On 9/7/18 11:30 AM, ts...@rcmd.org wrote:
>  External Email - Use Caution
>
> Hi Tom and Zahra,
>
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Tom Parker
>>> I am attempting to download the FsPalm patch 
>>> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm)
>> On September 7, 2018 at 4:10 PM "Nasiriavanaki, Zahra" 
>>  wrote:
>> I downloaded it from this link.
>> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide
> I think you are talking about 2 different things: PALM and FsPalm.
>
> @Tom: On the problem with the FsPalm download: the FreeSurfer FTP server is 
> currently unavailable due to a hard disk failure, see this recent message on 
> this list:
>
>https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg59312.html
>
> Just wait a bit.
>
>
> Best,
>

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Re: [Freesurfer] recon-all error

[Douglas Greve]

can you send the terminal output and recon-all.log?
thanks

On 9/7/18 9:58 AM, Song, Da-Yea wrote:


External Email - Use Caution

Hello,

I’m running some subjects through recon-all but have noticed that some 
error out (terminate the job) within seconds of starting. Any 
suggestions would be really appreciated. Here is the recon-all.cmd 
error message:


#-

# New invocation of recon-all Fri Sep  7 09:34:58 EDT 2018

mri_convert /g5/dcn/freesurfer/MPRAGE/PS070/001 
/g5/dcn/freesurfer/subjects/PS070/mri/orig/001.mgz


#

#@# MotionCor Fri Sep  7 09:35:30 EDT 2018

cp /g5/dcn/freesurfer/subjects/PS070/mri/orig/001.mgz 
/g5/dcn/freesurfer /subjects/PS070/mri/rawavg.mgz


mri_convert /g5/dcn/freesurfer/subjects/PS070/mri/rawavg.mgz 
/g5/dcn/freesurfer /subjects/PS070/mri/orig.mgz --conform


mri_add_xform_to_header -c /g5/dcn/freesurfer 
/subjects/PS070/mri/transforms/talairach.xfm /g5/dcn/freesurfer 
/subjects/PS070/mri/orig.mgz /g5/dcn/freesurfer 
/subjects/PS070/mri/orig.mgz


#

#@# Talairach Fri Sep  7 09:35:44 EDT 2018

mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 
--proto-iters 1000 --distance 50


#-

# New invocation of recon-all Fri Sep  7 09:36:58 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:37:03 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:39:43 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:39:47 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:42:58 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:43:02 EDT 2018

Best,

Da-yea


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Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal

[Douglas Greve]

I'm not sure what this is referring to, but you should be very careful 
flipping images. If you want to compare left and right, then use the 
xhemi tool https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi


On 9/4/18 10:41 AM, Martin Reuter wrote:

Hi Xiaoyu,

please keep the previous conversation as inline citation below so I 
know what we discussed before.


What I mean is to process every subject only once and not twice (with 
flipped images, if that is what you did?).


Then run xhemi analysis on the subject-level. Invert the sign of the 
left-right difference depending on which is the diseased hemi. Then do 
a regular analysis on that. Nothing paired.


Best, Martin



On 30. Aug 2018, at 18:29, Wang, Xiaoyu 
> wrote:




Thanks Martin,
Yes, I did mean to have the right hemisphere added to the left 
hemisphere as a new time point.

Can you explain on what you mean by run every subject only once?
Do you mean to run xhemi for all of the subjects and then run a 
paired analysis?

Xiaoyu
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Re: [Freesurfer] NIFTI to pial.vtk space

[Douglas Greve]

what is your mris_convert command line?

On 9/3/18 4:10 PM, M. Jordan wrote:


External Email - Use Caution

Hello,

I have a CT NIFTI coregistered to the MRI NIFTI used for reconAll. 
When I export the .pial files to .vtk using mris_convert, they are 
shifted with respect to the MRI. Is there a way to process the CT 
NIFTI in such a way that it will match the .vtk pial files?


Thank you!



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Re: [Freesurfer] error using -taskreg

[Douglas Greve]

are you using matlab or octave? If matlab, which version? The problem 
appears to be with the "basename" function, which I wrote in fsfast. It 
may be that a function of that name already exists in your path and 
selxavg is not calling my function. You can try putting 
$FREESURFER_HOME/fsfast/toolbox as the first directory in the matlab 
path and see if it fixes it.


On 9/1/18 3:45 PM, Addison Wu wrote:


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Dear List,

I'm trying to use an external regressor to analyze fs-fast tutorial 
data. I understand a paradigm file would be the sane way to do it, but 
I'm just trying to understand how external regressors work.
I first created a Extreg.dat file for each run of sess01, which 
contains a 142*5 matrix, saved it in the "00x" run folder. Then I ran 
mkanalysis-sess command:


mkanalysis-sess \

-fsd bold -stc up  -surface fsaverage rh \

-fwhm 5 -notask -TR 2 -taskreg Extreg.dat  1  \

-nskip 4 -analysis test.rh -force -per-run


And a selxavg3-sess command:

selxavg3-sess -s sess01 -analysis test.rh


But I got an error report of this:

Extension format = nii.gz

INFO: key nSliceGroups unrecognized, line 11, skipping

Error using basename

Too many input arguments.


Error in fast_ldanaflac (line 437)

  taskregevname = basename(taskreg,'dat'); % remove .dat


Error in fast_selxavg3b (line 107)

flac0 = fast_ldanaflac(analysis);

437     taskregevname = basename(taskreg,'dat'); % remove .dat

K>> --

ERROR: fast_selxavg3() failed\n


I've tried a bunch of things, including removing the ".dat" manually 
for the file, or in the command lines, or changing the "taskreg" to -1 
or 5, but none of them worked.



Is there anyway I can solve the problem and use external regressors 
for the tutorial data?



Thank you!

Addison



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Re: [Freesurfer] Seeing the Parcels as Volumes

[Douglas Greve]

Have you looked at aparc+aseg.mgz? You can change it to nii with 
mri_convert aparc+aseg.mgz aparc+aseg.nii



On 8/27/18 5:54 AM, Maedeh Khalilian wrote:


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Dear FreeSurfer experts,
I have used "mri_annnotation2label" and "mri_label2vol" to change the 
parcellation output of FreeSurfer e.g the lh.aparc.annot into an 
".nii" so i can see the parcels in Mricro.

Now I can see the parcels just on the cortex not on the whole graymatter.
The first question I have is that, is the parcellation done on the 
whole graymatter?
And if yes, is there a way that I can see the volumes on the whole 
graymatter, not just on the cortex?

I would be grateful if you could help me.
best regards,
Maedeh,


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Re: [Freesurfer] Using a cluster as an ROI for further analysis

[Douglas Greve]

First, run mris_preproc and mri_surf2surf commands as before to create a 
stack of P2 and P3. If you ran mri_glmfit-sim on P1,  then you will have 
an "ocn" output file. You can run
mri_segstats --i P2P3.stack.mgh --seg ocn.mgh --id N --avgwf 
P2P3.means-in-clusterN.dat

where N is the number of your cluster
P2P3.means-in-clusterN.dat will have a row for each subject in the 
stack, the value will be the mean in cluster N



On 8/13/18 11:48 PM, Martin Juneja wrote:


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For instance, if there is any way to extract spatial location of 
cluster X1 and use this location to extract thickness values of all 
the subjects from P2 and P3, that way I can perform two-sample t-test. 
I am not sure if that's feasible and if so, then how can we do that?


On Mon, Aug 13, 2018 at 7:04 PM, Martin Juneja > wrote:


Hi experts,

I found a cluster X1, which showed significant difference in
cortical thickness between two groups C1 and P1, determined
using mris_preproc, mri_surf2surf and mri_glmfit commands.

I am interested in determining if the same cluster X1 has
significantly different cortical thickness group between two other
groups P2 and P3.

I would really appreciate if you could please give me the
step-by-step guidance how this can be done.

Thanks.




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Re: [Freesurfer] ERROR: matrix is ill-conditioned or badly scaled, condno = 18696.1

[Douglas Greve]

The main problem is the 4th group where you only have two subjects and 
they are almost exactly the same age. This makes it hard to estimate the 
age slope and is causing the ill-conditioned error. You can try 
normalizing the ages (ie subtract the mean and divide by the stddev), 
you can remove age as a covariate,  you can eliminate this group. 
Alternatively, you can elimate the age slope just for this group (this 
requires that you create your own design matrix).


On 8/14/18 6:00 AM, Nabin Koirala wrote:


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Hi freesurfer community,

I am trying to do QDEC with a data for 2 groups but stuck in this 
error for many hours now. Tried and checked everything I could think 
of. Also went through the old threads and checked those recommneded 
but still could not solve it. Your hint will be very helpful.


/ERROR: matrix is ill-conditioned or badly scaled, condno = 18696.1/
//
/Possible problem with experimental design:/
/Check for duplicate entries and/or lack of range of/
/continuous variables within a class./
/If you seek help with this problem, make sure to send:/
/  1. Your command line:/
/    mri_glmfit --y 
/gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd 
/gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/qdec.fsgd 
dods --glmdir 
/gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled --surf 
fsaverage lh --label 
/gpfs/fs1/home/mmuthura/freesurfer/subjects/fsaverage/label/lh.aparc.label 
--C 
/gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat 
--C 
/gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-f-m-Intercept-thickness.mat 
--C 
/gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-Epi-Chr-Intercept-thickness.mat 
--C 
/gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/contrasts/lh-X-gender-Group-Intercept-thickness.mat/

/
/
/2. The FSGD file (attached)/
/
/
/3. Design Matrix/

Design matrix --
 1.000   0.000   0.000   0.000  31.300   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000  22.760   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000  29.390   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000  49.160   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000  23.810   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000  45.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000  0.000   21.830   0.000   0.000;
 1.000   0.000   0.000   0.000  49.540   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000  40.550   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000  0.000   22.660   0.000   0.000;
 1.000   0.000   0.000   0.000  26.080   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000  0.000   32.570   0.000   0.000;
 0.000   1.000   0.000   0.000  0.000   47.190   0.000   0.000;
 1.000   0.000   0.000   0.000  27.710   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000  25.860   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000  25.180   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000  0.000   0.000   27.630   0.000;
 0.000   0.000   1.000   0.000  0.000   0.000   51.930   0.000;
 0.000   0.000   1.000   0.000  0.000   0.000   25.060   0.000;
 0.000   0.000   0.000   1.000  0.000   0.000   0.000   60.650;
 0.000   0.000   1.000   0.000  0.000   0.000   59.360   0.000;
 0.000   0.000   0.000   1.000  0.000   0.000   0.000   62.450;
 0.000   0.000   1.000   0.000  0.000   0.000   20.480   0.000;
 0.000   0.000   1.000   0.000  0.000   0.000   36.550   0.000;
 0.000   0.000   1.000   0.000  0.000   0.000   37.000   0.000;



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Re: [Freesurfer] T1 mapping

[Douglas Greve]

On 8/10/18 3:26 PM, Fotiadis, Panagiotis wrote:


Hi Doug,


Thanks for your response! I had a couple follow-up questions:


1) If I used mri_fit_parms to calculate the T1 maps, then created a 
surface mid-cortex (with mris_expand) with that T1 map as a reference, 
and uploaded that file into MATLAB through MRIread, would the 
resulting values represent absolute "pure" T1 values?



If by "pure" you mean quantitative (ie, values in milisec), then yes.



2) Even though we are scanning on a Siemens scanner we have been 
acquiring a tfl_mgh_multiecho_4E_P2_1MM_ISO sequence. Do you think I 
could do T1 mapping based on that sequence (with the same method as 
the one described in the previous question)?


Multiecho does not help for measuring T1. But if you have multiple flip 
angles or multiple inversions with you rmultiecho, then you can use the 
multiecho data to compute T1



Thanks again, and I apologize for the potential triviality of the 
questions!



Best,

Panos


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 


*Sent:* Friday, August 10, 2018 1:59:47 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] T1 mapping
mri_fit_parms should do it. BTW, if you are using a siemens scanner, 
you should just collect an MP2RAGE. That automatically outputs a 
quantitative T1 map using the two inversion technique. The results are 
much more accurate than using multiple flip angles


On 8/8/18 5:00 PM, Fotiadis, Panagiotis wrote:


Hello,


I am interested in doing some T1-mapping analyses on some ex vivo 
brains. We have collected flash sequences under multiple flip angles 
(5, 10, 15, 20, 25 and 30). How would you suggest that I proceed? 
Should I use the mri_ms_fitparms to come up with the T1 maps for each 
subject and then maybe calculate the signal intensity 1mm into the 
cortex, or is there another way that you would recommend?



Thanks in advance for any advice!


Best,

Panos


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869


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Re: [Freesurfer] Plotting QDEC results

[Douglas Greve]

On 8/11/18 12:02 PM, Avi Gharehgazlou wrote:


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Thank you for your reply. I chose the 1.3 threshold based on LGI 
papers in the ASD literature, but I will use 2.0.

2 is still too low. You'd need at least 3.


1. By permutation do you mean FDR correction?

no, permutation and FDR are different


2. If I use monte carlo at 2.0 (0.01 p-value) would this be okay for 
LGI, or do you still recommend FDR correction?
No, 2 is too low. At least 3, and that may be too low. Permutation will 
be better.


Many thanks,

Avi


On Fri, Aug 10, 2018 at 1:53 PM, Douglas Greve <mailto:dgr...@mgh.harvard.edu>> wrote:


Each row is a subject and each column is a cluster. BTW, a
threshold of 1.3 is way too low for lGI. If you want to use a
threshold that low, you should use permutation instead of monte
carlo (in general, permutation is better, but certainly for lGI).

On 8/9/18 1:39 PM, Avi Gharehgazlou wrote:


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Hi experts,

I looked at association between LGI and a behavioural scale on
QDEC. after the analysis, to plot the significant clusters/
blobs, I wanted to export LGI values for each subject from each
significant blob and based on instructions in previous archives I
ran the following command line:

mri_glmfit-sim –glmdir (qdec output directory) --cache 1.3 abs

which generated a "cache.th13.abs.y.ocn.dat" file. This file
contains 3 columns and 36 rows. I'm assuming the values in the
three columns correspond to LGI values for each significant blob
for each subject? (I had 3 significant blobs and 36 participants)

Will you please confirm I am doing (and interpreting) this correctly?

Thanks so much,

Avi


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Re: [Freesurfer] coregistering with bbregister

[Douglas Greve]

On 8/10/18 6:48 PM, Ben M wrote:


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Hi Doug,

Thank you for your suggestions, I'll try them.
Could you please let me know if my code is actually doing what I 
intend it to do? Specifically, the idea is to perform 
functional-to-structural registration.


so first I did
$ bbregister --t2 --reg /data/bbregister/reg.dat --mov 
/data/mean_func.nii.gz --s 001
That is right. The only thing I would change is to use reg.lta instead 
of reg.dat. The lta file has more info in it and we're trying to get 
people to move to it.


I'm not sure if the --mov image should be the motion-corrected mean 
functional image or the skull-stripped anatomical image. I think if I 
want to do functional-to-structural registration it should actually be 
the anatomical image as --mov right? Or it doesn't matter which one I 
choose?

Yes, it matters. The mov should be the functional.


I then did
$ mri_vol2vol --mov /data/bet_structural.nii.gz --targ 
/data/brain.nii.gz --o /data/coregistered_structural.nii.gz --reg  
/data/bbregister/reg.dat --inv –-nearest
 which I thinks applies the transformation matrix to the structural 
image, am I correct? In this case it would be a 
structural-to-functional registration I think.

Did you see the examples (run mri_vol2vol --help)
So, if I intend to perform functional-to-structural registration I 
should actually rather do


$ bbregister --t2 --reg /data/bbregister/reg.dat --mov 
/data/bet_structural.nii.gz --s 001
$ mri_vol2vol --mov /data/mean_func.nii.gz --targ /data/brain.nii.gz 
--o /data/coregistered_functional.nii.gz --reg  
/data/bbregister/reg.dat --inv –-nearest


Could you please confirm if this is correct?

Thank you very much,
Ben




Sometimes the FSL initialization will fail. If you are using FS version
6, then run it without specifying --init-fsl and it will use mri_coreg,
which is more robust. If your anatomical and functional were acquired at
the same time, you might be able to get away with --init-header instead.

On 8/9/18 2:12 PM, Ben M wrote:
>//>/External Email - Use Caution />//>/Hi, />/I'm trying to coregister the strucural image to the mean functional />/image using bbregister, so after reconall I did: />//>/bbregister --t2 --init-fsl --reg /data/bbregister/reg.dat --mov />//data/mean_func.nii.gz --s 001 />//>/bet /data/structural.nii.gz /data/bet_structural.nii.gz />//>/#brain.nii.gz is the brain.mgz from reconall output (in freesurfer 
space) />/mri_vol2vol --mov /data/bet_structural.nii.gz --targ />//data/brain.nii.gz --o /data/coregistered_structural.nii.gz --reg />//data/bbregister/reg.dat --inv –-nearest />//>/But when I load the coregistered_structural.nii.gz and the />/mean_func.nii.gz they are not aligned. I'm sure I'm doing something />/wrong, could someone help me figure it out please? />//>/Thanks in advance, />/Ben/




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Re: [Freesurfer] Cortical surface

[Douglas Greve]

You can break up the aparc annotation into labels 
(mri_annotation2label), then create a new annotation with just the 
insula (mris_label2annot)



On 8/12/18 5:17 AM, 郑凤莲 wrote:


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Dear experts,
  I an using FS 6.0 for cortical reconstructions.  I can show whole 
brain regions (tksurfer...), as shown in the picture. However,  I just 
want to show insular region. Is there any way to complete it? I am 
looking forward to your reply. Thanks very much.

Sincerely,
Zheng




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Re: [Freesurfer] Surface Area in Toddlers/Children

[Douglas Greve]

Yes. -qcache actually calls mris_preproc. At one point, FS did not 
preserve total area when  mapping to fsaverage. I fixed it a while ago, 
but maybe something was still off in 5.1


On 8/10/18 2:06 PM, Derek Sayre Andrews wrote:


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Hi Douglas,

Thank you for the response.

I did not use mris_preproc to prepared the data.

The data was mapped to fsaverage using recon-all with -qcache. I then 
loaded the l/rh.area.pial.fwhm15.fsaverage.mgh files into MATLAB using 
SurfStatReadData <http://www.math.mcgill.ca/keith/surfstat/> and 
summed them across each vertex.


Would the terminal output of recon-all -qcache be helpful?

Best, Derek

*Derek Sayre Andrews, PhD*

Postdoctoral Scholar

Department of Psychiatry and Behavioral Sciences

The M.I.N.D Institute

University of California Davis


Telephone: +1 916 703 0360
Email: dandr...@ucdavis.edu <mailto:dandr...@ucdavis.edu>

*From: * on behalf of Douglas 
Greve 

*Reply-To: *Freesurfer support list 
*Date: *Friday, August 10, 2018 at 10:25 AM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] Surface Area in Toddlers/Children

It should be preserving total surface area. Can you send your 
mris_preproc command line and the terminal output? It might be 
something with 5.1 as well.


On 8/9/18 3:49 PM, Derek Sayre Andrews wrote:

*External Email - Use Caution *

Dear Freesurfer Developers and Experts,

I have been exploring various vertex wise (mass univariate)
effects using freesurfer measures of cortical thickness and
surface area in a cohort of toddlers/children aged 25-70 months.

When looking at the effect of age on surface area using
individuals’ measures mapped to fsaverage and smoothed at 15mm
fwhm (area.pial. fwhm15.fsaverage.mgh) I observed a widespread
negative effect of age (i.e. decreased surface area with age).
Given the age group of the cohort this seems implausible. Plotting
the sum of each individuals lh+rh.area.pialfsaverage.fwhm15.mgh
against age shows the relationship:

cid:image001.png@01D42FCE.C197B360

However, plotting the lh+rh total surface area returned by
mris_anatomical_stats reveals a much more plausible relationship
between surface area and age:

cid:image002.png@01D42FCE.C197B360

My working hypothesis is that the significantly smaller brain
sizes of our cohort compared to fsaverage, and the fact(?) that
-qcache does not preserve global surface area, is causing an “over
adjustment” in our cohorts smallest brains when mapped to fsaverage.

Thus, my questions are three fold

 1. Is the mapping of our significantly smaller brains to
fsaverage a potential explanation for the results we are
seeing in our mass univariate analyses of surface area?

 2. If this is the case, would this effect be limited to surface
area or also extend to other freesurfer measures including
cortical thickness, lGI, sulcal depth etc.

 3. How would you recommend approaching vertex wise analyses in a
cohort of this age? Create a study specific average subject
using make_average_subject to map onto?

Thank you for your insight and guidance!

Best, Derek

PS: All processing was performed using freesurfer v5.1

cid:image003.png@01D42FCE.C197B360

*Derek Sayre Andrews, PhD*

Postdoctoral Scholar

Department of Psychiatry and Behavioral Sciences

The M.I.N.D Institute

University of California Davis


Telephone: +1 916 703 0360
Email: dandr...@ucdavis.edu <mailto:dandr...@ucdavis.edu>




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Re: [Freesurfer] Confusion about MRI_GLMFIT

[Douglas Greve]

On 8/8/18 2:17 PM, Funk, Quentin wrote:


External Email - Use Caution

Freesurfer experts,


I'm trying to figure out what values I get from mri_glmfit as in the 
tutorial. 
In 
particular, I'm interested in how I can compare these values to what I 
get from QDEC.


QDEC runs mri_glmfit, so they will be the same assuming you give it the 
same input, design, and contrast.



In that tutorial, the software does a linear regression for each 
gender and then computes a F_ratio for the two two fits. (How does 
this relate to the average in the contrast listed?)


If the average were 0, then you would have no result whereas the F test 
will test for any combination of  the two



The F_ratio then gives a way to get P-values (under certain 
assumptions)--so then from the F_ratio, pvals are computed--this leads 
to sig.mgh.



But what are the other files? The descriptions are a bit too vague for 
me to understand, unfortunately. The ones I'm interested in primarily are:



pcc.mgh -- partial (pearson) correlation coefficient (surface overlay)

Do you know what a pearson correlation is? The pearson can only be 
computed between two sets of numbers. When you have multiple regression, 
you use a partial pearson.


z.mgh -- z-stat that corresponds to the significance (surface overlay)


This is the p-value converted into a z.



The z-stat should be some sort of standard score--so a standard score 
of significance (so p-value?) compared to what distribution?



Second, what if I were interested in a different categorical 
variable--say I had a group of Alzheimer's patients and a group of 
Healthy patients. In QDEC, I click "diagnosis" as the variable to do 
the analysis on. What contrast does this correspond to? What type of 
linear fit is being compared--the slope of the regression with respect 
to age? If I leave out nuisance variables (like age), I should 
conceivably get an F-test between the two constant models, which 
should be more or less similar to a voxelwise t-test?


The contrast will be [-1 +1]. The sig.mgh will be the sig of the t-test 
(ie, a signed test).




Any help here is appreciated!


Quentin Funk, PhD
Houston Methodist Research Institute
713-363-9003 

Houston Methodist. Leading Medicine.

Houston Methodist is ranked by /U.S. News & World Report/ as the No. 1 
hospital in Texas for patient care. Houston Methodist is nationally 
ranked in 8 specialties and is designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org 
. Follow us at twitter.com/MethodistHosp 
 and facebook.com/HoustonMethodist.


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Re: [Freesurfer] Correlations on QDEC

[Douglas Greve]

did you see the text where it says "If you seek help with this problem, 
make sure to send:" and then it gives a list of things to send? There 
will be a file called y.fsgd in the output, make sure to send that


On 8/8/18 4:40 PM, Avi Gharehgazlou wrote:


External Email - Use Caution

Hi experts,

I have examined the relation between LGI and a behavioural continuous 
scale (SCQ) on QDEC while controlling for sex, age and surface area in 
my model. When I want to do another analysis, doing exactly this but 
also controlling for diagnosis as well, QDEC gives the following error:


ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08



Possible problem with experimental design:

Check for duplicate entries and/or lack of range of

continuous variables within a class.

If you seek help with this problem, make sure to send:

1. Your command line:

mri_glmfit.bin --y 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/y.mgh 
--fsgd 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/qdec.fsgddods 
--glmdir 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0 
--surf fsaverage lh --label 
/d/mjt/9/users/avideh/data/recon/fsaverage/label/lh.aparc.label --C 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Avg-Intercept-pial_lgi.mat 
--C 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Avg-pial_lgi-RBS-Cor.mat 
--C 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Diff-ADHD-ASD-Intercept-pial_lgi.mat 
--C 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Diff-ADHD-ASD-Cor-pial_lgi-RBS.mat 
--C 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Diff-M-F-Intercept-pial_lgi.mat 
--C 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Diff-M-F-Cor-pial_lgi-RBS.mat--C 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-X-Dx-Sex-Intercept-pial_lgi.mat 
--C 
/d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-X-Dx-Sex-Cor-pial_lgi-RBS.mat


2. The FSGD file (if using one)

3. And the design matrix above

Attempting to diagnose further

SumSq: Min=0.488835 (col 11), Max=3.834060 (col 6)

... could not determine the cause of the problem


My understanding is that QDEC allows for controlling for 2 discrete 
variables, thus I don't know what I am doing wrong if I also control 
for diagnosis (in addition to sex)?


I would really appreciate your help,

Thanks so much,

Avi



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Re: [Freesurfer] T1 mapping

[Douglas Greve]

mri_fit_parms should do it. BTW, if you are using a siemens scanner, you 
should just collect an MP2RAGE. That automatically outputs a 
quantitative T1 map using the two inversion technique. The results are 
much more accurate than using multiple flip angles


On 8/8/18 5:00 PM, Fotiadis, Panagiotis wrote:


Hello,


I am interested in doing some T1-mapping analyses on some ex vivo 
brains. We have collected flash sequences under multiple flip angles 
(5, 10, 15, 20, 25 and 30). How would you suggest that I proceed? 
Should I use the mri_ms_fitparms to come up with the T1 maps for each 
subject and then maybe calculate the signal intensity 1mm into the 
cortex, or is there another way that you would recommend?



Thanks in advance for any advice!


Best,

Panos


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869


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Re: [Freesurfer] mri_volcluster not recognize --mindistance

[Douglas Greve]

Try --mindist not --mindistance

On 8/9/18 9:08 AM, Yagmur Ozdemir 19 wrote:


External Email - Use Caution

Hello FreeSurfer experts,

I am trying to run mri_volcluster with the following command to later 
create masks of clustered regions from functional data. I get an error 
saying that the option --mindistance is not recognized, even though 
this option is shown in mri_volcluster --help and the FS wiki page. 
Any idea what might be causing this?


mri_volcluster --in thresh_highres.nii.gz --sum volcluster.txt --ocn 
clustered_thresh_highres.nii.gz --thmin 1.5 --sign pos --regheader 
 --mindistance 10 --minsizevox 800 --fwhm 3

ERROR: Option --mindistance unknown

Best
Idil


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Re: [Freesurfer] Plotting QDEC results

[Douglas Greve]

Each row is a subject and each column is a cluster. BTW, a threshold of 
1.3 is way too low for lGI. If you want to use a threshold that low, you 
should use permutation instead of monte carlo (in general, permutation 
is better, but certainly for lGI).


On 8/9/18 1:39 PM, Avi Gharehgazlou wrote:


External Email - Use Caution

Hi experts,

I looked at association between LGI and a behavioural scale on QDEC. 
after the analysis, to plot the significant clusters/ blobs, I wanted 
to export LGI values for each subject from each significant blob and 
based on instructions in previous archives I ran the following command 
line:


mri_glmfit-sim –glmdir (qdec output directory) --cache 1.3 abs

which generated a "cache.th13.abs.y.ocn.dat" file. This file contains 
3 columns and 36 rows. I'm assuming the values in the three columns 
correspond to LGI values for each significant blob for each subject? 
(I had 3 significant blobs and 36 participants)


Will you please confirm I am doing (and interpreting) this correctly?

Thanks so much,

Avi


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Re: [Freesurfer] coregistering with bbregister

[Douglas Greve]

Sometimes the FSL initialization will fail. If you are using FS version 
6, then run it without specifying --init-fsl and it will use mri_coreg, 
which is more robust. If your anatomical and functional were acquired at 
the same time, you might be able to get away with --init-header instead.


On 8/9/18 2:12 PM, Ben M wrote:


External Email - Use Caution

Hi,
I'm trying to coregister the strucural image to the mean functional 
image using bbregister, so after reconall I did:


bbregister --t2 --init-fsl --reg /data/bbregister/reg.dat --mov 
/data/mean_func.nii.gz --s 001


bet /data/structural.nii.gz /data/bet_structural.nii.gz

#brain.nii.gz is the brain.mgz from reconall output (in freesurfer space)
mri_vol2vol --mov /data/bet_structural.nii.gz --targ 
/data/brain.nii.gz --o /data/coregistered_structural.nii.gz --reg 
/data/bbregister/reg.dat --inv –-nearest


But when I load the coregistered_structural.nii.gz and the 
mean_func.nii.gz they are not aligned. I'm sure I'm doing something 
wrong, could someone help me figure it out please?


Thanks in advance,
Ben


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Re: [Freesurfer] Viewing the output of mris_preproc in Freeview + export to Matlab

[Douglas Greve]

It is showing you the map of the first frame (subject in this case). You 
can adjust the frame with a slider on the left. Also, there is a time 
plot icon on the top. If you click on that it will show you a graph of 
the subjects at the chosen vertex.


On 8/10/18 8:16 AM, Alon Baram wrote:


External Email - Use Caution

Hello,

I want to overlay the .mgh file which is the output of mris_preproc in 
freeview on the fsaverage surface. This file has (according to 
mri_info) the dimensions Nverteces x 1 x 1 x Nsubjects: my data in 
fsaverage space for each of my subjects. But when I load it in 
freeview I can only see one value in each vertex.


Is there a way to view "4D" (it's actually 2D: Nverteces x Nsubjects) 
data in Freeview? If not, what is the single value (per vertex) that 
freeview chooses to show me? is it just the data from the first 
subject? I tried to look in the documentation for any clues about 
viewing time-series data in Freeview, but failed.


I would also be very happy to understand what is the best way to save 
this 4D .mgh file in a format that I can then import it into Matlab.


Thanks for the help!



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Re: [Freesurfer] Surface Area in Toddlers/Children

[Douglas Greve]

It should be preserving total surface area. Can you send your 
mris_preproc command line and the terminal output? It might be something 
with 5.1 as well.



On 8/9/18 3:49 PM, Derek Sayre Andrews wrote:


External Email - Use Caution

Dear Freesurfer Developers and Experts,

I have been exploring various vertex wise (mass univariate) effects 
using freesurfer measures of cortical thickness and surface area in a 
cohort of toddlers/children aged 25-70 months.


When looking at the effect of age on surface area using individuals’ 
measures mapped to fsaverage and smoothed at 15mm fwhm (area.pial. 
fwhm15.fsaverage.mgh) I observed a widespread negative effect of age 
(i.e. decreased surface area with age). Given the age group of the 
cohort this seems implausible. Plotting the sum of each individuals 
lh+rh.area.pialfsaverage.fwhm15.mgh against age shows the relationship:


cid:image001.png@01D42FCE.C197B360

However, plotting the lh+rh total surface area returned by 
mris_anatomical_stats reveals a much more plausible relationship 
between surface area and age:


cid:image002.png@01D42FCE.C197B360

My working hypothesis is that the significantly smaller brain sizes of 
our cohort compared to fsaverage, and the fact(?) that -qcache does 
not preserve global surface area, is causing an “over adjustment” in 
our cohorts smallest brains when mapped to fsaverage.


Thus, my questions are three fold

 1. Is the mapping of our significantly smaller brains to fsaverage a
potential explanation for the results we are seeing in our mass
univariate analyses of surface area?

 2. If this is the case, would this effect be limited to surface area
or also extend to other freesurfer measures including cortical
thickness, lGI, sulcal depth etc.

 3. How would you recommend approaching vertex wise analyses in a
cohort of this age? Create a study specific average subject using
make_average_subject to map onto?

Thank you for your insight and guidance!

Best, Derek

PS: All processing was performed using freesurfer v5.1

cid:image003.png@01D42FCE.C197B360

*Derek Sayre Andrews, PhD*

Postdoctoral Scholar

Department of Psychiatry and Behavioral Sciences

The M.I.N.D Institute

University of California Davis


Telephone: +1 916 703 0360
Email: dandr...@ucdavis.edu 



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Re: [Freesurfer] surface arithmetic?

[Douglas Greve]

Yea, just run mris_preproc on both subjects. There are even some options 
there for computing paired differences (simple differences or 
differences relative to the mean, etc)


On 8/7/18 6:10 PM, Rockers, Elijah D. wrote:


External Email - Use Caution

Hello,


I have a subject with two MRIs and surface reconstructions, several 
years apart. I would like to directly compare these surfaces if 
possible, for instance, to subtract (new - old) to see a "difference 
surface" or something similar. Is there a way to A) Get the surfaces 
into the same space so they can be combined mathematically, and B) 
performs operations with the surfaces, a la fslmaths?



Many thanks,

- Eli

Houston Methodist. Leading Medicine.

Houston Methodist is ranked by /U.S. News & World Report/ as the No. 1 
hospital in Texas for patient care. Houston Methodist is nationally 
ranked in 8 specialties and is designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org 
. Follow us at twitter.com/MethodistHosp 
 and facebook.com/HoustonMethodist.


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Re: [Freesurfer] Origin of freesusrfer output

[Douglas Greve]

On 8/7/18 1:45 AM, Ritesh Mahajan wrote:
>  External Email - Use Caution
>
> Hi Doug,
>
> I checked the link you suggested. What i understood from this is the origin 
> shift(physical co-ordinate of first voxel) is happening due to the rotation 
> of axis to RAS co-ordinate system. To counter rotation origin shift is done, 
> is that correct?
Yes, it rotates it and shifts the center.
>
> My concern is does free-surfer changes the origin, because it has to 
> re-sample the input image(eg: 512*512*166) to output image (256*256*256)? I 
> think free-surfer might be performing some interpolation to do this 
> re-sampling. Is this origin change is done due to re-sampling or due to 
> rotation or because of both ?
yes, it does perform an interpolation (trilinear by default)
>
> I am more interested in knowing whether the origin shift is done because of 
> re-sampling (input image(eg: 512*512*166) to output image (256*256*256))? If 
> yes, how this is encountered ?
The history of FS is that 20 years ago, it was not practical to deal 
with hires images, so everything was sampled to 1mm3 8bit. It has been 
hard to get a way from this.
>
> Thanks,
> Ritesh Mahajan
>
> Thanks,
> Ritesh Mahajan
>
> - Original Message -
> From: "Douglas N. Greve" 
> To: "freesurfer" 
> Sent: Monday, August 6, 2018 9:22:29 PM
> Subject: Re: [Freesurfer] Origin of freesusrfer output
>
> also, check out this web page
> http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
>
>
> On 08/05/2018 11:23 AM, Bruce Fischl wrote:
>> Hi Ritesh
>>
>> you can use the vox2ras matrix to compute the RAS coordinates of any
>> voxel. Just give it column,row,slice,1 indices as the input vector.
>>
>> cheers
>> Bruce
>> On Sun, 5 Aug 2018, Ritesh Mahajan wrote:
>>
>>>     External Email - Use Caution
>>>
>>> Thanks Bruce.
>>>
>>> Thanks Doug for clearing this. Can you please tell, how can i get
>>> back the first voxel of  input ?
>>> Also, can you tell what mathematical formula or equation is used
>>> convert this origin ?
>>>
>>> Thanks,
>>> Ritesh Mahajan
>>>
>>> - Original Message -
>>> From: "Douglas Greve" 
>>> To: "freesurfer" 
>>> Sent: Friday, August 3, 2018 9:51:30 PM
>>> Subject: Re: [Freesurfer] Origin of freesusrfer output
>>>
>>> To add on, the origin is changed in that the "first voxel" is not the
>>> same in the 256^3 volume as it is in the original dicom. Having said
>>> that, all our files (eg, mgz and nifti) have a  matrix that converts a
>>> col, row, slice into the scanner RAS, so you can always find your way
>>> back to the dicom coordinates.
>>>
>>> On 8/3/18 10:41 AM, Bruce Fischl wrote:
>>>> Hi Ritesh
>>>>
>>>> Doug can correct any inaccuracies, but
>>>>
>>>> 1. Yes, unless you tell recon-all not to.
>>>> 2. I'm not sure what you mean by the origin, but we do keep track of
>>>> the ras coordinates of the center of the volume after resampling
>>>> (the so-called "cras").
>>>> 3. We do keep track of the original dicom coordinates.
>>>> 4. mri_info will spit out various matrices, among them the voxel to ras
>>>> transform that should take you back to scanner ras coordinates.
>>>>
>>>> cheers
>>>> Bruce
>>>>
>>>> On Fri, 3 Aug 2018, Ritesh
>>>> Mahajan wrote:
>>>>
>>>>>      External Email - Use Caution
>>>>>
>>>>> Hi Bruce,
>>>>>
>>>>> 1) Free-surfer output is always 256*256*256, regardless of any
>>>>> input dimensions.
>>>>> 2) I have a doubt, while doing this re-sampling from input
>>>>> dimension to 256*256*256. Does free-surfer change the origin of image?
>>>>> 3) My input is an MRI dicom image, for dicom tag value (0020,0032)
>>>>> which gives me the image position(origin).
>>>>> 4) How can i know the origin of free-surfer output in nii format?
>>>>> Do free-surfer change this value during processing?
>>>>>
>>>>> Can you please provide your valuable comments on this.
>>>>>
>>>>> Thanks,
>>>>> Ritesh Mahajan
>>>>>
>>>>>
>>>>>
>>>> __

Re: [Freesurfer] SNR covariate in cortical thickness & volumetrics between groups analyses

[Douglas Greve]

I thought I answered this question last week. See my rsponse below

I don't think it is correct conceptually.  By including SNR as a 
covariate, you are saying that you expect the thickness to increase with 
higher SNR and decrease with lower SNR. This does not make sense to me. 
It sounds like you are trying to do a mixed effects analysis where you 
weight by the SNR. Still, mathematically, this is not a true mixed 
effect analysis (which requires estimates of the within and between 
subject noise). `


On 8/3/18 10:57 AM, John Anderson wrote:

External Email - Use Caution

Daer FS experts,
I would like to inquire about including SNR as a covariate for the 
between groups cpmparison in cortical thickness. Is this procedure 
correct mathematically? Do I need to demean the SNA values before 
including it covariates? Finally, do you recommend any quality 
parameters other than SNR to be included covariate?


I look forward to learn from your expertise,
Thanks,
John


On 8/5/18 1:04 PM, John Anderson wrote:


External Email - Use Caution



Dear FS experts,
I would like to inquire about including SNR as a covariate for the 
between groups comparison in cortical thickness. Is this procedure 
valid? I have some T1 images of low quality and the majority are high 
in quality. I reviewed the segmentation and the cortical surfaces and 
fixed manually as possible. I don't want to exclude images from the 
data sets, so I am thinking of regressing out SNR.
It seems that the command "mri_segstats" can report SNR for every ROI 
in the brain. Is it correct to include whole brain SNR covariate for 
between group comparisons (cortical thickness and volumetric analyses).
If yes, do I need to include actual SNR values in the FSGD file or 
the demeaned values ?


We appreciate your guidance!
John




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Re: [Freesurfer] SNA covariate in cortical thickness between groups analysis

[Douglas Greve]

I don't think it is correct conceptually.  By including SNR as a 
covariate, you are saying that you expect the thickness to increase with 
higher SNR and decrease with lower SNR. This does not make sense to me. 
It sounds like you are trying to do a mixed effects analysis where you 
weight by the SNR. Still, mathematically, this is not a true mixed 
effect analysis (which requires estimates of the within and between 
subject noise). `


On 8/3/18 10:57 AM, John Anderson wrote:


External Email - Use Caution

Daer FS experts,
I would like to inquire about including SNR as a covariate for the 
between groups cpmparison in cortical thickness. Is this procedure 
correct mathematically? Do I need to demean the SNA values before 
including it covariates? Finally, do you recommend any quality 
parameters other than SNR to be included covariate?


I look forward to learn from your expertise,
Thanks,
John


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Re: [Freesurfer] Origin of freesusrfer output

[Douglas Greve]

To add on, the origin is changed in that the "first voxel" is not the 
same in the 256^3 volume as it is in the original dicom. Having said 
that, all our files (eg, mgz and nifti) have a  matrix that converts a 
col, row, slice into the scanner RAS, so you can always find your way 
back to the dicom coordinates.

On 8/3/18 10:41 AM, Bruce Fischl wrote:
> Hi Ritesh
>
> Doug can correct any inaccuracies, but
>
> 1. Yes, unless you tell recon-all not to.
> 2. I'm not sure what you mean by the origin, but we do keep track of
> the ras coordinates of the center of the volume after resampling (the 
> so-called "cras").
> 3. We do keep track of the original dicom coordinates.
> 4. mri_info will spit out various matrices, among them the voxel to ras
> transform that should take you back to scanner ras coordinates.
>
> cheers
> Bruce
>
> On Fri, 3 Aug 2018, Ritesh
> Mahajan wrote:
>
>> External Email - Use Caution
>>
>> Hi Bruce,
>>
>> 1) Free-surfer output is always 256*256*256, regardless of any input 
>> dimensions.
>> 2) I have a doubt, while doing this re-sampling from input dimension to 
>> 256*256*256. Does free-surfer change the origin of image?
>> 3) My input is an MRI dicom image, for dicom tag value (0020,0032) which 
>> gives me the image position(origin).
>> 4) How can i know the origin of free-surfer output in nii format? Do 
>> free-surfer change this value during processing?
>>
>> Can you please provide your valuable comments on this.
>>
>> Thanks,
>> Ritesh Mahajan
>>
>>
>>
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Re: [Freesurfer] no register.dat file for mri_label2vol

[Douglas Greve]

since you are mapping back into the conformed anatomical space, you 
should be able to use --identity instead of specifing a registration matrix


On 7/26/18 8:25 PM, Ayzenberg, Vladislav wrote:


External Email - Use Caution

Greetings,

I am trying to convert a surface label (e.g., 
lh.V1_exvivo.thresh.label) into a volume to use as an ROI mask.


I have played around with the mri_label2vol command, but I can’t seem 
to get it to work. Here is the command I am using:


mri_label2vol --label lh.V1_exvivo.thresh.label --temp T1.mgz --reg 
register.dat --fillthresh .3 --proj frac 0 1 .1 --subject sub1 --hemi 
lh --o V1Test.nii.gz


The issue I believe is that I don’t have seem to have a register.dat 
file. However, I’m not sure how to generate the relevant registration 
file since the surface label I’m using is already in subject space. 
The label that I need was created when I used recon-all to generate 
surfaces from my anatomical image. If it is relevant, my original 
anatomical image is a skull stripped T1 generated using FSL which I 
then converted to .mgz.



Does anyone have any insight? Thank you!

Vlad




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Re: [Freesurfer] register mask to fsaverage

[Douglas Greve]

If the roi.nii does not include your areas of interest, then they will 
be masked out. The mask you create with mri_vol2surf may not be very 
accurate since it uses volume-based operation.


On 7/26/18 5:19 PM, John Anderson wrote:


External Email - Use Caution

Dear Dr Greve, thank you so much. kindly have one additional question 
and I appreciate your response.


I would like to move a mask from MNI152 to fsaverage so I can use it 
as a mask in flag --mask in the command "mri_glmfit". Does this 
procedure reduces the power of the analysis, meaning instead of 
correcting the the between group analyses to the whole cortex. I would 
like to do it in the ROI? In my analyses I see results when I correct 
for whole brain cortex. I mean when I use the command:
mri_glmfit --y data.nii.gz --fsgd fsgd.dat --C c.mtx --surf fsaverage 
lh --cortex --glmdir dir


I really lose these results when I use an ROI as a mask in the command 
mri_glmfit as follows:
mri_glmfit --y data.nii.gz --fsgd fsgd.dat --C c.mtx --surf fsaverage 
lh --mask roi.nii --glmdir dir

Thank you gain for any clarification,
John


Don't use --regheader, use --reg 
$FREESURFER_HOME/average/mni152.register.dat


On 7/26/18 4:40 PM, John Anderson wrote:



‐‐‐ Original Message ‐‐‐
On July 26, 2018 4:40 PM, John Anderson  
wrote:



Dear Freesurfer experts,
I have mask in MNI152 space. I would like to register this mask to 
fsaverage. How can I do this registration. I am thinking of 
"mri_vol2surf" as follows:


mri_vol2surf --mov mask.nii --mni152reg --regheader fsaverage --o 
mask_fsaverage.nii

Is this command correct?
Thank you for your valuable guidnace
John




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Re: [Freesurfer] register mask to fsaverage

[Douglas Greve]

Don't use --regheader, use --reg 
$FREESURFER_HOME/average/mni152.register.dat


On 7/26/18 4:40 PM, John Anderson wrote:


External Email - Use Caution

Dear Freesurfer experts,
I have mask in MNI152 space. I would like to register this mask to 
fsaverage. How can I do this registration. I am thinking of 
"mri_vol2surf" as follows:


mri_vol2surf --mov mask.nii --mni152reg --regheader fsaverage --o 
mask_fsaverage.nii

Is this command correct?
Thank you for your valuable guidnace
John


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Re: [Freesurfer] mri_glmfit

[Douglas Greve]

Use the mri.2mm aseg.mgz, eg,
 mri_binarize --i aseg.mgz --match 7 8 46 47 --dilate 1 --o cblummask.mgz
This will make a mask of cerebellum GM and WM and dilate it by 1 voxel.

On 7/26/18 4:49 PM, Piero Chiacchiaretta wrote:


External Email - Use Caution

Dear FS group,
I would like to restrict mri_glmfit analysis, on FS-FAST outputs, to 
the cerebellum.

Thus, I’m using —mask, adding the mask of cerebellum.
To this aim I can obtain it using mri_binarize. Do you agree?
mri_binarize --i ... --match 8 --o Left_Cerebellum.nii.gz
mri_binarize --i ... --match 45 --o Right_Cerebellum.nii.gz
Which is the correct input? aparc+aseg in fsaverage? In which 
dimension? mri.2mm? mri?

Thanks

Piero


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Re: [Freesurfer] brain parenchymal fraction

[Douglas Greve]

you'll have to be more specific about what "brain surface contour" means.

On 7/26/18 3:46 PM, Barletta, Valeria wrote:
> Dear Freesurfers,
> I need to extract the brain parenchymal fraction to check brain atrophy in my 
> patients.
> The BPF is defined as "the ratio of brain parenchymal tissue volume to the 
> total volume contained within the brain surface contour".
> In the text file aseg.stats, I found this info:
> # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1052408.00, 
> mm^3
> # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume 
> Without Ventricles, 1032104.00, mm^3
> # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation 
> Volume Without Ventricles from Surf, 1030608.836503, mm^3
>
> Can I extract the BPF from those, or is any of them the BPF?
>
> Thank you,
> Valeria
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Re: [Freesurfer] converting a mask made in MNI space to subject space

[Douglas Greve]

Definitly do not use --rot 180.
I think the registration matrix goes in the other direction, so try 
adding --inv to the command line and changing --targ and --mov


On 7/25/18 8:24 PM, Sims, Sara A wrote:


External Email - Use Caution

Hello,

I am trying to put a mask that I made on the MNI brain (that had been 
run through recon) into individual subject space. I have already 
created a registration matrix using the following command:


mni152reg --s $patient --o 
$registration/$patient/registermni_$patient.dat --1 --save-vol


Now I want to apply this matrix but from MNI -> subject. So I tried 
doing this:


mri_vol2vol --targ $patient/mri/orig.nii --mov 
$mnimask/net4splitmask_bin.nii --reg 
$registration/$patient/registermni_$patient.dat --o 
$outp/$patient/net4splitmask_bin.nii --nearest --rot 180 0 0


But it just spits back out the MNI mask 
($mnimask/net4splitmask_bin.nii) in MNI space. I tried using -inv but 
realized that was wrong because then it just gave me the subject’s 
orig. How can I get it to actually put the MNI-space mask onto the 
subject’s brain?


Sara



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Re: [Freesurfer] ICV as covariate for controls vs. patients

[Douglas Greve]

They give different results because they are supposed to. It may be that 
the effect you are seeing without regressing out ICV is due to ICV, and 
when you control for ICV the effect goes away. It could also be that the 
ICV causes the variance to increase. This is why I asked you to check 
the rstd (residual standard deviation). You said that did not change, so 
I would expect that the ICV must be removing your desired effect as seen 
the in gamma. Sorry, I don't know what else to tell you.




On 7/26/18 1:24 PM, Martin Juneja wrote:


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Dear Dr. Greve,

I am so sorry for annoying you with multiple emails.
I clearly got the difference between gamma.mgh files depending on 
whether I use ICV or not as a covariate. Next, I checked the ratio of 
gamma/rstd (Cohen's d) with and without ICV as covariate. Again, its 
totally different with and without ICV. Here I am attaching screen 
shot for that: left one is after I include ICV as covariate (minimum 
effect size) and the right one is without ICV as covariate (maximum 
effect size).


I really did not understand the idea behind comparing gamma.mgh and 
rstd.mgh (and may be their ratio), especially, if it's always the case 
that for surface area and volume, we need ICV as covariate.


On Thu, Jul 26, 2018 at 10:13 AM, Douglas Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


If you are using surface area or volume, then you need ICV


On 7/25/18 1:51 PM, Martin Juneja wrote:


External Email - Use Caution

Dr. Greve,

I am sorry if my questions were not clear in previous email.

Basically, I do not know what to conclude from this gamma
comparison i.e. with and without ICV as covariate.
Clearly, adding ICV as covariate here, is reducing effect size
all over the brain and without ICV effect size is higher at
specific locations.

So should I go ahead with or without ICV as covariate?

Thanks.

On Wed, Jul 25, 2018 at 7:33 AM, Douglas Greve
mailto:dgr...@mgh.harvard.edu>> wrote:


The gammas do look different, but it is hard to tell whether
they are, eg, changing sign. Not sure what you want me to
comment on.



On 7/24/18 2:17 PM, Martin Juneja wrote:


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Just to add some more info here:
The peak location of regions, X1 and X2, which I found
without including ICV as covariate are very close with the
peak locations I found in Gamma_Without_ICV (~5.15), whereas
Gamma_With_ICV is almost all over the brain (range -0.6 to
+0.6).
I am not sure if this additional info adds anything to
interpret gamma.mgh with and without ICV as covariate.

On Tue, Jul 24, 2018 at 10:10 AM, Martin Juneja
mailto:mj70...@gmail.com>> wrote:

Hi Dr. Greve,

So I checked both. The rstd.mgh files are very similar
in both cases (with and without ICV as covariate), but
gamma.mgh files are very different for both cases. Here
I am attaching screen shot for both cases:
Gamma_With_ICV as covariate and Gamma_Without_ICV as
covariate.

Could you please have a look at the attached screen
shots and provide your thoughts/interpretation of this
comparison?

Thanks.

On Tue, Jul 24, 2018 at 9:35 AM, Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>>
wrote:

For noise compare the values in the rstd.mgh file,
for effect size look
in the gamma.mgh file

On 07/24/2018 12:27 PM, Martin Juneja wrote:
>
> External Email - Use Caution
>
> Hi Dr. Greve,
>
> Thanks for your quick reply. Could you please give
me more details how
> can I check this whether its because of noise or
its because of less
> CV difference?
> I am not sure what method/way is the best and
commonly used to confirm
> these factors.
>
> Thanks.
    >
> On Tue, Jul 24, 2018 at 7:06 AM, Douglas Greve
mailto:dgr...@mgh.harvard.edu>
> <mailto:dgr...@mgh.harvard.edu
<mailto:dgr...@mgh.harvard.edu>>> wrote:
>
>     your results could have vanished after ICV
correction for one of
>     two reasons: the CV difference became less or
the values became
>     noisier (or a combination). So check in your
data which one of
>  

Re: [Freesurfer] ICV as covariate for controls vs. patients

[Douglas Greve]

If you are using surface area or volume, then you need ICV

On 7/25/18 1:51 PM, Martin Juneja wrote:


External Email - Use Caution

Dr. Greve,

I am sorry if my questions were not clear in previous email.

Basically, I do not know what to conclude from this gamma comparison 
i.e. with and without ICV as covariate.
Clearly, adding ICV as covariate here, is reducing effect size all 
over the brain and without ICV effect size is higher at specific 
locations.


So should I go ahead with or without ICV as covariate?

Thanks.

On Wed, Jul 25, 2018 at 7:33 AM, Douglas Greve <mailto:dgr...@mgh.harvard.edu>> wrote:



The gammas do look different, but it is hard to tell whether they
are, eg, changing sign. Not sure what you want me to comment on.



On 7/24/18 2:17 PM, Martin Juneja wrote:


External Email - Use Caution

Just to add some more info here:
The peak location of regions, X1 and X2, which I found without
including ICV as covariate are very close with the peak locations
I found in Gamma_Without_ICV (~5.15), whereas Gamma_With_ICV is
almost all over the brain (range -0.6 to +0.6).
I am not sure if this additional info adds anything to interpret
gamma.mgh with and without ICV as covariate.

On Tue, Jul 24, 2018 at 10:10 AM, Martin Juneja
mailto:mj70...@gmail.com>> wrote:

Hi Dr. Greve,

So I checked both. The rstd.mgh files are very similar in
both cases (with and without ICV as covariate), but gamma.mgh
files are very different for both cases. Here I am attaching
screen shot for both cases:
Gamma_With_ICV as covariate and Gamma_Without_ICV as covariate.

Could you please have a look at the attached screen shots and
provide your thoughts/interpretation of this comparison?

Thanks.

On Tue, Jul 24, 2018 at 9:35 AM, Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

For noise compare the values in the rstd.mgh file, for
effect size look
in the gamma.mgh file

On 07/24/2018 12:27 PM, Martin Juneja wrote:
>
> External Email - Use Caution
>
> Hi Dr. Greve,
>
> Thanks for your quick reply. Could you please give me
more details how
> can I check this whether its because of noise or its
because of less
> CV difference?
> I am not sure what method/way is the best and commonly
used to confirm
> these factors.
>
> Thanks.
    >
> On Tue, Jul 24, 2018 at 7:06 AM, Douglas Greve
mailto:dgr...@mgh.harvard.edu>
> <mailto:dgr...@mgh.harvard.edu
<mailto:dgr...@mgh.harvard.edu>>> wrote:
>
>     your results could have vanished after ICV
correction for one of
>     two reasons: the CV difference became less or the
values became
>     noisier (or a combination). So check in your data
which one of
>     those things happened.
>
>
>     On 7/23/18 8:30 PM, Martin Juneja wrote:
>>
>>     External Email - Use Caution
>>
>>     Hello experts,
>>
>>     I am interested in identifying regions of interest
by comparing
>>     cortical volume (CV) between controls and patients.
>>
>>     After including age and sex as my covariates, I
identified
>>     regions X1 and X2, which showed significantly
lower CV for
>>     patients (as compared to controls).
>>
>>     But after I include ICV as another covariate, my
results show
>>     that for none of the areas there is any
significant difference in
>>     CV, i.e. my results vanish.
>>
>>     When I checked subjectwise ICV for each group, I
found that there
>>     is almost significant difference (two-sampled
t-test, p = 0.067)
>>     in ICV between two groups, but interestingly mean
group ICV for
>>     patients group was larger compared than mean ICV
for controls.
>>     But as I said earlier, regions X1 and X2 had
significantly lower
>>     CV for patients (as compared to controls), when I
didn't include
>>     ICV as covariate.
>>
   

Re: [Freesurfer] ICV as covariate for controls vs. patients

[Douglas Greve]

The gammas do look different, but it is hard to tell whether they are, 
eg, changing sign. Not sure what you want me to comment on.



On 7/24/18 2:17 PM, Martin Juneja wrote:


External Email - Use Caution

Just to add some more info here:
The peak location of regions, X1 and X2, which I found without 
including ICV as covariate are very close with the peak locations I 
found in Gamma_Without_ICV (~5.15), whereas Gamma_With_ICV is almost 
all over the brain (range -0.6 to +0.6).
I am not sure if this additional info adds anything to interpret 
gamma.mgh with and without ICV as covariate.


On Tue, Jul 24, 2018 at 10:10 AM, Martin Juneja <mailto:mj70...@gmail.com>> wrote:


Hi Dr. Greve,

So I checked both. The rstd.mgh files are very similar in both
cases (with and without ICV as covariate), but gamma.mgh files are
very different for both cases. Here I am attaching screen shot for
both cases:
Gamma_With_ICV as covariate and Gamma_Without_ICV as covariate.

Could you please have a look at the attached screen shots and
provide your thoughts/interpretation of this comparison?

Thanks.

On Tue, Jul 24, 2018 at 9:35 AM, Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

For noise compare the values in the rstd.mgh file, for effect
size look
in the gamma.mgh file

On 07/24/2018 12:27 PM, Martin Juneja wrote:
>
> External Email - Use Caution
>
> Hi Dr. Greve,
>
> Thanks for your quick reply. Could you please give me more
details how
> can I check this whether its because of noise or its because
of less
> CV difference?
> I am not sure what method/way is the best and commonly used
to confirm
> these factors.
>
> Thanks.
    >
    > On Tue, Jul 24, 2018 at 7:06 AM, Douglas Greve
mailto:dgr...@mgh.harvard.edu>
> <mailto:dgr...@mgh.harvard.edu
<mailto:dgr...@mgh.harvard.edu>>> wrote:
>
>     your results could have vanished after ICV correction
for one of
>     two reasons: the CV difference became less or the values
became
>     noisier (or a combination). So check in your data which
one of
>     those things happened.
>
>
>     On 7/23/18 8:30 PM, Martin Juneja wrote:
>>
>>     External Email - Use Caution
>>
>>     Hello experts,
>>
>>     I am interested in identifying regions of interest by
comparing
>>     cortical volume (CV) between controls and patients.
>>
>>     After including age and sex as my covariates, I identified
>>     regions X1 and X2, which showed significantly lower CV for
>>     patients (as compared to controls).
>>
>>     But after I include ICV as another covariate, my
results show
>>     that for none of the areas there is any significant
difference in
>>     CV, i.e. my results vanish.
>>
>>     When I checked subjectwise ICV for each group, I found
that there
>>     is almost significant difference (two-sampled t-test, p
= 0.067)
>>     in ICV between two groups, but interestingly mean group
ICV for
>>     patients group was larger compared than mean ICV for
controls.
>>     But as I said earlier, regions X1 and X2 had
significantly lower
>>     CV for patients (as compared to controls), when I
didn't include
>>     ICV as covariate.
>>
>>     Could you please help me in interpreting these results?
Is there
>>     any advice regarding inclusion of ICV as covariate? Or
my results
>>     are purely because of differences in ICV between
groups, and
>>     there is no real findings regarding the regions
identified (X1
>>     and X2)?
>>
>>     Thanks a lot !
>>
>>
>>     ___
>>     Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
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>>     <

Re: [Freesurfer] Matched analysis with 2 controls 1 case weighting

[Douglas Greve]

On 7/24/18 1:56 PM, Dowling, Kevin Francis wrote:

Hi Doug,
Thank you very much for your reply and my apologies for this belated response. 
The two approaches you mentioned were the only ones we could think that might 
work for a DV like cortical thickness.
That being said, we were originally thinking of a repeated measures anova. 
However, (and I may be mistaken here) I believe that such an approach would 
need to be implemented in the Freesurfer longitudinal stream.
No, not at all. See 
https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova

However, I recently saw a thread in the archives that suggested this approach 
is not recommended if the T1 images are from matched subjects (as opposed to 
multiple scans from the same subject over time). Is that correct?

Correct, you should not run the longitudinal stream on different subjects.

As an aside, as we're hoping to separately look at matched subjects in three 
groups a bit later using a 1:1:1 match. If we should avoid the longitudinal 
stream, is there any other way to implement an RM anova in Freesurfer?

See above
Otherwise, I think we're hoping to move forward by averaging the 2 
controls together with make_average_subject and then implement a 
paired analysis -- which was probably the more sound choice to begin 
with.


Thank you again!
Kind regards,
Kevin
> Douglas N. Greve 
Mon, 
16 Jul 2018 10:49:28 -0700 


>
>There is nothing to plug and play. I'm not even sure about the theory, 
>but I'd guess you'd use something like a repeated measures anova or 
>simply average the two controls together and do a simple paired test. Do 
>you know what the theory would be behind your statitical test?

>On 07/09/2018 01:27 PM, Dowling, Kevin Francis wrote:
>>
>> Hello Freesurfer Experts,
>>
>>
>> I'm writing with a quick question about matched analysis.
>>
>>
>> We have a cohort of MRI data collected such that there are two 
>> controls for each case, and these 2 controls are each matched to a 
>> specific case using a propensity score algorithm (~400 subjects 
>> total). For our analysis, we would like to try to implement a matched 
>> (or paired difference) analysis of cortical thickness (across the 
>> whole surface, not .aparcs) in Freesurfer. However, based all the 
>> documentation I have been able to find it seems that FS permits only 
>> paired difference analyses using matched pairs. Is this correct? Might 
>> there any way to implement such an analysis in Freesurfer using 
>> matched trios instead?

>>
>>
>> We are open to using any Freesurfer version for this analysis, 
>> including dev, though the scans are currently reconned with FS 5.3.

>>
>>
>> Thank you so much for your consideration!
>>
>>
>> With kind regards,
>>
>> Kevin
>>
>>
>> *Kevin F. Dowling *
>> Clinical Research Coordinator
>> Brain Genomics Laboratory
>> Division of Psychiatric Neuroimaging
>> Martinos Center for Biomedical Imaging
>> Massachusetts General Hospital
>> 149 13th Street
>> Charlestown, MA, 02129
>> (p) 617.643.3215
>> Pronouns: He / Him / His
>>
>>
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*Kevin F. Dowling *
Clinical Research Coordinator
Brain Genomics Laboratory
Division of Psychiatric Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA, 02129
(p) 617.643.3215
Pronouns: He / Him / His


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Re: [Freesurfer] petsurfer

[Douglas Greve]

On 7/25/18 8:31 AM, John Anderson wrote:


External Email - Use Caution

Dear Petsurfer experts,
I used partsurfer in FS6 and had applied partial volume correction 
(PVC) on PET data. I followed the same steps as in wiki which was very 
well explained! Thank you!.
The analyses went fine... I would like to inquire about some issues, 
and I highly appreciate any clarification:
1. The flag --psf in "mri_gtmpvc": Is the value of "psf" means the 
amount of smoothing (fwhm in mm) that will be applied on the corrected 
maps? If I give "psf" a value of "zero", does this means that the 
corrected maps are no longer going to be smoothed? The motivation of 
the question is that I would like to smooth the images at the end of 
the analysis, so I can apply the amount of smoothing on the PVC images 
vs analysis involve non-pvc images.
It has nothing to do with applied smoothing but rather the amount of 
blurring incurred during the PET acquisition and reconstruction process. 
It models the blurring function as an isotropic Gaussian filter of the 
given FWHM. Any smoothing you apply will be applied later. Note that 
applying volume smoothing to PV-corrected data is invalid. Surface 
smoothing is the only valid way to smooth PVCed data.


2. For some of my group analyses, I don't see any difference between 
the groups. When I apply PVC using "mri_gtmpvc", I see difference in 
pathologically relevant regions, and vice versa for some other 
analyses where I see difference between the groups without PVC then 
the difference disappear following PVC. I highly appreciate if you 
please clarify why PVC can find results or eliminate findings. What is 
the idea of partial volume effect PVE in this case?
This is a big topic. See https://www.ncbi.nlm.nih.gov/pubmed/26915497. 
That paper shows that atrophy can make the apparent effect of age on FDG 
be bigger than it really is. This is because PVEs reduce the FDG signal 
in GM which tends to be the same direction as the actual effect (ie, the 
PVEs reinforce what is already there making it too big and too 
significant). For another tracer where one expects the uptake to go down 
with age or disease (eg, PiB), then PVEs can make effects go away.


3. Group analysis: following PVC, I used "mri_concat" to combine the 
images "?.mgx.gm.nii.gz", then I smoothed the final combined images 
using the flag "fwhm" in "mri_surf2surf". I used fwhm=3mm and then 
fwhm=6mm. For all analyses I can see clusters of difference between 
the groups at fwhm=3mm. For some analyses the difference disappears 
when I use fwhm=6mm . Is this till a partial volume effect even after 
applying  pvc or this is relevant to an extra smoothing effect which 
obscure the PET signal? is there any recommended fwhm value for PET 
images?
The FWHM you chose to smooth by for analysis purposes is somewhat 
arbitrary. The ideal FWHM depends on the size of the activation you are 
expecting, which you don't know until you do the analysis, which you 
can't do until you set the FWHM. If you have some idea about the size of 
the effect you expect, then you can set the FWHM to that level. 
Otherwise, people just fall back to typical values between 5-10.




Thank you for your guidance,
John



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Re: [Freesurfer] tkregister2 scripting- help with saving reg.dat

[Douglas Greve]

no idea how to help with the vol2vol problem without a command line and 
more description of the problem


On 7/24/18 6:52 AM, Yagmur Ozdemir 19 wrote:


External Email - Use Caution

By copying the matrix that comes up in the terminal, then readjusting 
it, if needed, in a different .dat file, I can fix the issue. But I 
would still appreciate any suggestions on how to use mri_vol2vol with 
a binarized mask, or what might be causing the system to fill the 
whole volume.


Best
Idil

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yagmur Ozdemir 
19 [yozdemi...@amherst.edu]

*Sent:* Tuesday, July 24, 2018 1:23 PM
*To:* Freesurfer support list ‎[freesurfer@nmr.mgh.harvard.edu]‎
*Subject:* [Freesurfer] tkregister2 scripting- help with saving reg.dat

External Email - Use Caution

Hello freesurfer experts,

I am editing the registration matrix between two volumes (fsaverage's 
T1 to fit MNI152 from fsl) using tkregister2, and I cannot save the 
registration because I do not have permission to change the .dat file 
I originally opened with tkregister2. I cannot change the permissions. 
I do not want to lose all the editing I have done so far, so would 
really appreciate if someone could give me advice on how to save the 
registration as a seperate file either in GUI or from terminal.


FYI, I know ideally I shouldn't need to edit the registration but for 
some reason I had weird flipping issues when using mri_vol2vol and 
mni152.register.dat with --inv option. Also the system for some reason 
does not recognize a binary volume with the --interp nearest option, 
so fills in the whole volume. I would appreciate any suggestions.


Best
Idil





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Re: [Freesurfer] ICV as covariate for controls vs. patients

[Douglas Greve]

your results could have vanished after ICV correction for one of two 
reasons: the CV difference became less or the values became noisier (or 
a combination). So check in your data which one of those things happened.



On 7/23/18 8:30 PM, Martin Juneja wrote:


External Email - Use Caution

Hello experts,

I am interested in identifying regions of interest by comparing 
cortical volume (CV) between controls and patients.


After including age and sex as my covariates, I identified regions X1 
and X2, which showed significantly lower CV for patients (as compared 
to controls).


But after I include ICV as another covariate, my results show that for 
none of the areas there is any significant difference in CV, i.e. my 
results vanish.


When I checked subjectwise ICV for each group, I found that there is 
almost significant difference (two-sampled t-test, p = 0.067) in ICV 
between two groups, but interestingly mean group ICV for patients 
group was larger compared than mean ICV for controls. But as I said 
earlier, regions X1 and X2 had significantly lower CV for patients (as 
compared to controls), when I didn't include ICV as covariate.


Could you please help me in interpreting these results? Is there any 
advice regarding inclusion of ICV as covariate? Or my results are 
purely because of differences in ICV between groups, and there is no 
real findings regarding the regions identified (X1 and X2)?


Thanks a lot !


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Re: [Freesurfer] Aparc.stats based on fsaverage?

[Douglas Greve]

The parcellation starts off in fsaverage space. It is mapped through the 
surface-based registration into the native subjects surface space. 
There, the boundaries are refined to better fit the individual. The 
transformation is based on folding patterns which are pretty consistent 
across the age span.


On 7/24/18 6:50 AM, Martin Steppan wrote:


External Email - Use Caution

Dear Freesurfer/s,
Sorry, it might be a stupid question, since I am a newbie in this field.
Is the ?.aparc.stats file somehow based on transformation to fsaverage 
space? I am aware that this is the case for -qcache, but is this also 
true for the predefined ROI results?
I am asking, because we also have juvenile brains, and transformation 
to the average adult brain could be a problem.

Does anyone have useful information for me?

Best wishes,
Martin


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Re: [Freesurfer] fcseedcor -- pca output for vcsf.dat and wm.dat

[Douglas Greve]

you would do it in fcseed-config by using -mean instead of -pca

On 7/20/18 4:06 PM, Eryilmaz, H. Hamdi wrote:


Thanks Doug!


One last question: If I wanted to regress out the average signal from 
the ventricles and the white matter (instead of using the PCA output), 
could I directly incorporate that into fcseedcor?



Best,

Hamdi



*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 


*Sent:* Friday, July 20, 2018 9:23:58 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] fcseedcor -- pca output for vcsf.dat and 
wm.dat

Hi Hamdi, sorry for the delay. Answers below.

On 6/26/18 2:50 PM, Eryilmaz, H. Hamdi wrote:

Hi Doug and Freesurfers,

I am using fcseedcor to compute the correlation between two time 
courses for each subject in my group. The command that I run is as 
follows:


fcseedcor -s $subject -fsd resting -seed seed1.dat -seed seed2.dat 
-xreg global.waveform.dat 1 -xreg vcsf.dat 5 -xreg wm.dat 5 -xreg 
mcprextreg 6 -hpf .01 -lpf .08 -nskip 4 -o cor_s1s2.dat


My first question is about the size of the vcsf.dat and wm.dat files. 
They seem to be (N+1)xN matrices, where N is the number of timepoints 
in the signal. Does this mean there are N+1 components for each time 
point (i.e., N+1 potential regressors to add)? What do they exactly 
correspond to and how do they relate to the average signal from the 
ventricles, CSF, and white matter?
Each ROI consists of a matrix of size Ntp-by-Nvoxels. A PCA is 
computed from this matrix. The the number of temporal components of 
the PCA will be either Ntp or Nvoxels, which ever is less. In this 
case, Nvoxels>Ntp, so you see the Ntp components (each Ntp long). The 
components are whatever the PCA finds. The mean is removed, so it no 
component represents the mean.


My other question is about the number of components to include for 
vcsf.dat and wm.dat. I have seen 5 recommended in examples, however, 
five components seem to explain very different amount of variance in 
different subjects and if I change this number for a given subject, I 
see substantial changes in the resulting correlation value. I would 
appreciate any suggestion on how to select an unbiased value for 
the number of components to include. Could including up to the 
component at which fixed percentage of cumulative variance is 
explained be a solution?
When I was doing experiments with this years ago, i did not find much 
of a difference with different numbers of components, but I did the 
experiments on whole brain resting state, so the ROI-wise correlation 
may be different. It seemed like 5 components explained the bulk of 
the variance within the ROI (WM or CSF). You could vary the number of 
components for each subject. Sorry, I don't have any better guidance 
on how to go about selecting the number.

doug


Many thanks for your help!

Best,
Hamdi













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Re: [Freesurfer] mri_binarize

[Douglas Greve]

It was just an oversight on my part when I wrote the program. I've just 
updated the file in our repository and put a copy here:

https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize
You can also specify all the structures you want by using the --match flag

On 7/20/18 10:00 AM, John Anderson wrote:


External Email - Use Caution

Dear Freesurfer experts,
I would like to inquire about the flag --subcort-gm in mri_binarize. 
It seems that the final product of this flag create a mask include the 
brain stem which is largely white matter. Why it was included in the 
subcortical gray matter structures?


Thanks for any clarification,
john


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Re: [Freesurfer] Exporting results from QDEC

[Douglas Greve]

which results?

On 7/20/18 9:11 AM, Avi Gharehgazlou wrote:


External Email - Use Caution

Hi experts,

I want to make plots of my results that I have from QDEC, however, I'm 
having difficulty exporting values from QDEC. I examined LGI 
differences between groups, and I want to export my results, so the 
LGI values of significant between-group differences. Will you please 
tell me how I can do this?


Thanks,

Avi


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Re: [Freesurfer] Bug in make_average_subject

[Douglas Greve]

where did you get the make_average_subject script? It is not the one 
that is released with version 6.


On 7/20/18 3:46 AM, Raffington, Laurel wrote:


External Email - Use Caution


Dear Freesurfer Developers,


My goal is to build a study-specific pediatric template brain to rerun 
the recon-all-all. I am encountering the same error while running 
make_average_subject Freesurfer version 6.0.0 on MacOS High Sierra 
10.13.6 as described here and implemented the suggested changes 
replacing mri_glmfit-sim, make_average_subject, make_average_surface, 
and mri_aparc2aseg: 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-November/054933.html 



Yet, another error persists.


Any help would be appreciated.


Thanks,


Laurel



Laurel Raffington

Postdoctoral Researcher

Center for Lifespan Psychology

Max Planck Institute for Human Development

Lentzeallee 94, 14195 Berlin, Germany

https://www.mpib-berlin.mpg.de/en/staff/laurel-raffington






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Re: [Freesurfer] fcseedcor -- pca output for vcsf.dat and wm.dat

[Douglas Greve]

Hi Hamdi, sorry for the delay. Answers below.

On 6/26/18 2:50 PM, Eryilmaz, H. Hamdi wrote:

Hi Doug and Freesurfers,

I am using fcseedcor to compute the correlation between two time 
courses for each subject in my group. The command that I run is as 
follows:


fcseedcor -s $subject -fsd resting -seed seed1.dat -seed seed2.dat 
-xreg global.waveform.dat 1 -xreg vcsf.dat 5 -xreg wm.dat 5 -xreg 
mcprextreg 6 -hpf .01 -lpf .08 -nskip 4 -o cor_s1s2.dat


My first question is about the size of the vcsf.dat and wm.dat files. 
They seem to be (N+1)xN matrices, where N is the number of timepoints 
in the signal. Does this mean there are N+1 components for each time 
point (i.e., N+1 potential regressors to add)? What do they exactly 
correspond to and how do they relate to the average signal from the 
ventricles, CSF, and white matter?
Each ROI consists of a matrix of size Ntp-by-Nvoxels. A PCA is computed 
from this matrix. The the number of temporal components of the PCA will 
be either Ntp or Nvoxels, which ever is less. In this case, Nvoxels>Ntp, 
so you see the Ntp components (each Ntp long). The components are 
whatever the PCA finds. The mean is removed, so it no component 
represents the mean.


My other question is about the number of components to include for 
vcsf.dat and wm.dat. I have seen 5 recommended in examples, however, 
five components seem to explain very different amount of variance in 
different subjects and if I change this number for a given subject, I 
see substantial changes in the resulting correlation value. I would 
appreciate any suggestion on how to select an unbiased value for 
the number of components to include. Could including up to the 
component at which fixed percentage of cumulative variance is 
explained be a solution?
When I was doing experiments with this years ago, i did not find much of 
a difference with different numbers of components, but I did the 
experiments on whole brain resting state, so the ROI-wise correlation 
may be different. It seemed like 5 components explained the bulk of the 
variance within the ROI (WM or CSF). You could vary the number of 
components for each subject. Sorry, I don't have any better guidance on 
how to go about selecting the number.

doug


Many thanks for your help!

Best,
Hamdi













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Re: [Freesurfer] glmfit-sim FWHM 34?

[Douglas Greve]

can you send more info? command line, terminal output, what you are 
analuyzing, etc. If the fwhm is still 34, then something may be wrong.


On 7/12/18 11:48 AM, Ting Li wrote:


External Email - Use Caution

Hi Douglas,

I try to use permutation but it takes forever. I never see the end. Do 
I have to update the freesurfer to use the permutation? As it was 
recommended in this year?


Best,
Ting
On Jul 3, 2018, at 11:07 AM, Douglas N. Greve > wrote:


Also, I'm encouraging people to use permutation rather than
monte-carlo-based correction.




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Re: [Freesurfer] Volumetric Group Analysis

[Douglas Greve]

The slicing (axial or otherwise) should not matter. But if the 
resolution (voxel size) is not good enough (~1mm), then you might get 
some blurry results.



On 7/2/18 10:23 AM, Mr. Tass wrote:



Good morning
I hope everyone had a gr8 weekend.

im new here so i hope someone can help me understand a little about 
the right way to use freesurfer in order to calculate the gray matter 
volume for different areas of the brain and compare the volume between 
left and right hemisphere.


so far i have freesurfer installed and recon-all
a couple of test subjects. and everything seems to be working fine.

i have several subjects with the axial cut MRI. is the axial cut 
enough to output accurate results? im little concerned as the T1 
representation Outputted in FREEVIEW seems a bit fuzzy




im following the below link for my group analysis.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/VolumetricGroupAnalysis

please if possible to sheld some light on this kind of analysis and if 
i am on the right track.



thanks alot to you all
best regards


Sarah

Get Outlook for Android 



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Re: [Freesurfer] degrees of freedom

[Douglas Greve]

There are several questions here. First, the "optimal" design is to have 
an equal number in both groups. But this assumes that you have a fixed 
total number that you need to divide between the two groups. It is 
always better to have more subjects, even if the groups are not balanced 
in numbers. Second, it is not "either-or" in terms of matching your 
groups and using the GLM. Matching is generally good experimental design 
because you don't know that the GLM will always account for differences. 
That said, many, many studies use unmatched designs. Third, even if you 
have matched subjects, it can be a good idea to include nuisance 
variables if they can explain extra variance.


On 7/1/18 11:16 AM, John Absher wrote:


External Email - Use Caution

In group analysis, is it better to have matched controls (1:1) or to 
use age, education and other characteristics as confounds in the glm? 
In the latter situation, we would control for these demographic 
variables in the glm and the control group n could be smaller, the 
same or larger than the test group. We are looking at TBI+ and TBI- 
subjects across a broad age range to look at patterns of cortical 
thinning. Thanks.


*John R. Absher, MD, FAAN*

*GHS Neurosciences*

jabs...@ghs.org 

864-350-6655 (mobile)



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Re: [Freesurfer] TIV should be considered as a covariant for thickness, volume and area analyses

[Douglas Greve]

Yes, for area and volume, no for thickness

On 6/29/18 3:06 PM, Ting Li wrote:
>  External Email - Use Caution
>
> Hi FreeSurfer Experts,
>
> I would like to do the surface analysis among two groups, like the thickness, 
> volume and area. When I run the GLM, do I have to consider the eTIV as a 
> covariant or not? Thanks a lot!
>
> Best wishes,
> Ting
>
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Re: [Freesurfer] mri_glmfit question

[Douglas Greve]

You can create a surface overlay in matlab and display it using 
freeview.  See 
https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m

To read it into matlab, you can run
pcc = MRIread('pcc.mgh');

You can convert it to text with mri_convert --ascii pcc.mgh outputtextfile

On 6/28/18 4:42 PM, Nillo, Ryan Michael R wrote:


External Email - Use Caution

Hello FreeSurfer Users,


I want to run an ROI-based analysis on mri_glmfit as opposed to 
vertex-based. I know that if I run mri_glmfit with the --table flag 
and give it the output of asegstats2table or aparcstats2table, it will 
run the analysis on the ROIs and output tables showing significance. 
In each contrast directory that was created from mri_glmfit, I see 
there is a pcc.mgh. Is there any way to display this on the surface or 
put it into a table format?



Mahalo,


Ryan M Nillo

Staff Research Associate I

UCSF Department of Radiology and Biomedical Imaging



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Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

[Douglas Greve]

you can try
tkmeditfv subject orig.mgz -surfs -ov clustermap.nii.gz -fminmax .01 3
you may have to adjust the thresholds (fminmax)

On 6/26/18 10:43 PM, srishti goel wrote:


External Email - Use Caution

Hello Bruce,

You had mentioned about loading the volumetric maps with the surface 
to check that all my clusters are contained within the surfaces. Since 
I am very new to freesurfer, could you please guide to where I can 
find an appropriate command to do that.


Thank you so much for all the help!

Best,
Srishti

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu>
skype: srishti.goel12


On Mon, Jun 25, 2018 at 11:50 AM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:


Hi Srishti

you should be able to load the volumetric maps with the surfaces
and make sure that your clusters are contained within the surface.

cheers
Bruce

On Mon, 25 Jun 2018, srishti goel wrote:


External Email - Use Caution

They are separate clusters not the same clusters but we both
of those don't show up when we
project the volume maps on surface. Every other cluster comes
up and this has happened in
about 2-3 files. Are you absolutely sure that the surface in
freesurfer includes dACC and
insula?

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu>
skype: srishti.goel12


On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

      It should be included. But dACC and insula are not close
to each other. How can
      there be a cluster that spans both?


      On 6/23/18 7:54 PM, srishti goel wrote:

      External Email - Use Caution

      Hello,
I am using mri_vol2surf to project my volume maps on to the
surface. There is a
dACC/insula cluster visible in my volume maps that doesn't
show up when I project
it on the surface.

Is that because dACC/insula is not included in surfaces on
Freesurfer?

Thanks!

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu>
skype: srishti.goel12



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Re: [Freesurfer] Question about GLM results in Freesurfer

[Douglas Greve]

Each contrast is a test, so you have 8 tests. Like I said, the ultimate 
right thing to do is to correct for all your tests, but this might not 
leave you with anything if you do. This is often a judgement call. I 
rarely, if ever, see people correct over multiple tests. However, if you 
try to publish with a bunch of tests and only one is sig, that might 
raise some flags with the reviews. Often people have a  priori tests and 
then other tests that they are vaguely interested in.



On 6/26/18 5:15 AM, jahanvi patel wrote:


External Email - Use Caution

Hello Doug,

We are doing one test I supposed. Because we inputted all covariates 
into glm_fit.


This is our command line.

We entered all behavioral scores as covariates and obtained each 
folder named as covariate's name with sig.mgh in each folder.



Does it mean we only have just one test, or several tests if we did 
the below way?



Best regards,
Jahanvi

mri_glmfit \
  --glmdir GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2 \
  --y lh.testretest_only_TP2.thickness-pc1.stack.fwhm15.mgh \
  --label lh.testretest.fsaverage.cortex.label \
  --fsgd 
GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/TP1_TP2.fsgd \
  --C 
GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/main.mtx \
  --C 
GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_age.mtx 
\
  --C 
GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_CesD_score.mtx 
\
  --C 
GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_STATI_state.mtx 
\
  --C 
GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_STATI_trait.mtx 
\
  --C 
GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_total_medi_min.mtx 
\
  --C 
GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_FFMQ_f1.mtx 
\
  --C 
GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_FFMQ_f2.mtx 
\

  --surf fsaverage lh

Message: 4
Date: Mon, 25 Jun 2018 10:45:42 -0400
From: Douglas Greve mailto:dgr...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] Question about GLM results in Freesurfer
To: mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: <10e16d65-9ac1-c85c-875d-405e852ce...@mgh.harvard.edu
<mailto:10e16d65-9ac1-c85c-875d-405e852ce...@mgh.harvard.edu>>
Content-Type: text/plain; charset="utf-8"
Are you doing 5 different tests or just one test? It is a tricky
question as to whether you should correct across? 5 tests or not.
Ideally, one should, but I don't think I've ever seen it done in
practice. As a reviewer, I might not demand it for only 5 tests.




On 6/20/18 9:17 AM, jahanvi patel wrote:
>
>
> Hello,
>
> We have a question about using glm_fit in freesurfer.
>
> When we model several covariates (behavioral scores) in glm, and we
> wanted to know the correlation between cortical thickness changes with
> the changes of behavioral scores.? We obtained the correlation results
> nicely after using freesurfer's monte carlo correction (eg. increase
> of behavioral scores is correlated with the increase of cortical
> thickness changes).
>
> Should we still perform the bonefferi corrections on the results we got ?
> (because we have entered?5 covariates into the glm?model, so we are
> wondering if it is still needed to divide the?alpha-value by 5
> to?determine the final significant findings)?
>
>
> Thank you so much for helping us,
>
> Jahanvi
>
>
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Re: [Freesurfer] Using T2 or Flair data to improve pial surfaces

[Douglas Greve]

You have to have a separate command line for each one, but you can 
always write a script to do that, eg



foreach subject (subjeta subjectb )

  recon-all -s $subject -qcache

end


On 6/19/18 10:53 AM, Heidi Lindroth wrote:



I did not. Can I re-run a batch of scans with the -qcache command or 
do I need to do it one by one?



Heidi Lindroth BSN RN
 PhD Candidate| School of Nursing
 Program Assistant | School of Medicine and Public Health, Department 
of Anesthesiology

 Predoctoral Fellow | Veterans Administration (Madison WI)

University of Wisconsin-Madison
 701 Highland Avenue, Madison WI 53705
 608-219-4294 | hlindr...@wisc.edu


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 


*Sent:* Tuesday, June 19, 2018 9:38:25 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Using T2 or Flair data to improve pial 
surfaces


Did you run recon-all with -qcache ?


On 6/19/18 9:30 AM, Heidi Lindroth wrote:


External Email - Use Caution

Hi there,


I have used T2/Flair images to improve the pial surface 
reconstruction, however, when I tried to analyze these data in QDEC, 
I was unable to load the files because the T1/T2 processed scans do 
not have the following file type: lh.thickness.fwhm10.fsaverage.mgz 
or .mgh file. .  Instead, they have this file 
type: lh.smoothwm.FI.crv. Is there a way to convert the crv file to a 
mgz/mgh file? Is there an alternate way to analyze the T1/T2 data 
using QDEC?



Thank you,


Heidi Lindroth BSN RN
 PhD Candidate| School of Nursing
 Program Assistant | School of Medicine and Public Health, Department 
of Anesthesiology

 Predoctoral Fellow | Veterans Administration (Madison WI)

University of Wisconsin-Madison
 701 Highland Avenue, Madison WI 53705
 608-219-4294  | hlindr...@wisc.edu <mailto:hlindr...@wisc.edu>



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Re: [Freesurfer] Question about GLM results in Freesurfer

[Douglas Greve]

Are you doing 5 different tests or just one test? It is a tricky 
question as to whether you should correct across  5 tests or not. 
Ideally, one should, but I don't think I've ever seen it done in 
practice. As a reviewer, I might not demand it for only 5 tests.




On 6/20/18 9:17 AM, jahanvi patel wrote:



Hello,

We have a question about using glm_fit in freesurfer.

When we model several covariates (behavioral scores) in glm, and we 
wanted to know the correlation between cortical thickness changes with 
the changes of behavioral scores.  We obtained the correlation results 
nicely after using freesurfer's monte carlo correction (eg. increase 
of behavioral scores is correlated with the increase of cortical 
thickness changes).


Should we still perform the bonefferi corrections on the results we got ?
(because we have entered 5 covariates into the glm model, so we are 
wondering if it is still needed to divide the alpha-value by 5 
to determine the final significant findings)?



Thank you so much for helping us,

Jahanvi


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Re: [Freesurfer] Group Analysis Covariates

[Douglas Greve]

sorry for the delay. There is not a super easy way to do this, but it is 
possible in matlab. cd into the glmdir folder and start matlab, then


X = load('Xg.dat');

beta = MRIread('beta.mgh');

betamat = fast_vol2mat(beta);

yhatmat = X(:,[i j k m n])*betamat([i j k m n],:);

yhat = beta;

yhat.vol = fast_mat2vol(yhat,yhat.volsize);

MRIwrite(yhat,'yhat.ijkmn.mgh');


The key here is that you need to select the covariates (i j k m n) that 
you want to include. Each one will form a column in the design matrix 
and will have an element in the beta. By selecting the components you 
want, you exclude the ones you don't want. this simple formulation won't 
work if a given component spans both a factor of interest and a nuisance 
factor (eg, Male-AD when you want remove the effects of gender). But 
there is a way around this too. let me know.





On 6/24/18 9:58 AM, Hua, Jessica wrote:



Hi FreeSurfer experts,


Just bringing this question back up to the top: I analyzed my data 
following the guidelines on the FreeSurfer Tutorial/Group Analysis 
page . I am trying to plot the adjusted values (covariates: age, sex, 
and ICV) for the significant clusters for each of my participants.


Is there a way to extract or calculate the adjusted values for each 
participant in each cluster after accounting for covariates (age, sex, 
and ICV)?



Best,


Jessica





*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 
freesurfer-requ...@nmr.mgh.harvard.edu 


*Sent:* Saturday, June 23, 2018 11:00 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Freesurfer Digest, Vol 172, Issue 36
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Today's Topics:

   1. FreeSurfer Manual Edit Sequence (David S Lee)
   2. Using grad_unwarp (James Gullickson)


--

Message: 1
Date: Fri, 22 Jun 2018 11:37:44 -0500
From: David S Lee 
Subject: [Freesurfer] FreeSurfer Manual Edit Sequence
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:

Content-Type: text/plain; charset="utf-8"

    External Email - Use Caution

Hello Experts,

When performing manual edits on brain masks, white matter, and gray 
matter,

do I have to strictly follow the sequences(process stages) listed here
?

For instance, the link suggests that "autorecon2-pial is used after 
editing

brain volume *after running -autorecon2".

In other words, is it okay to perform "autorecon2-pial" before
"autorecon2-wm"?

Thank you for your time,
--
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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Message: 2
Date: Fri, 22 Jun 2018 13:55:53 -0500
From: James Gullickson 
Subject: [Freesurfer] Using grad_unwarp
To: Freesurfer support list 
Message-ID:

Content-Type: text/plain; charset="utf-8"

    External Email - Use Caution

All,

I am interested in using grad_unwarp. I have been reading up on the
documentation a bit and from what I understand not all the necessary files
are distributed with the public version of Freesurfer, due to proprietary
information in the tables. However, there is a script called 
grad_unwarp in

 my $FREESURFER_HOME/bin directory. I have access to the .grad files
necessary for my project, so I was planning to just piece together the
environment manually. Based on: https://surfer.nmr.mgh 
.

harvard.edu/fswiki/GradUnwarp there are a few pieces I'm missing:

   - create_displacement_tables script
   - grad_unwarp_converter.pl script
   -  matlab files

Is there somewhere I can locate these missing scripts/files?

Thanks,

James
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The information in this e-mail is intended only for the person to whom 
it is
addressed. If you believ

Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

[Douglas Greve]

It should be included. But dACC and insula are not close to each other. 
How can there be a cluster that spans both?



On 6/23/18 7:54 PM, srishti goel wrote:


External Email - Use Caution

Hello,

I am using mri_vol2surf to project my volume maps on to the surface. 
There is a dACC/insula cluster visible in my volume maps that doesn't 
show up when I project it on the surface.


Is that because dACC/insula is not included in surfaces on Freesurfer?

Thanks!

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu 
skype: srishti.goel12



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Re: [Freesurfer] Using T2 or Flair data to improve pial surfaces

[Douglas Greve]

Did you run recon-all with -qcache ?


On 6/19/18 9:30 AM, Heidi Lindroth wrote:


External Email - Use Caution

Hi there,


I have used T2/Flair images to improve the pial surface 
reconstruction, however, when I tried to analyze these data in QDEC, I 
was unable to load the files because the T1/T2 processed scans do not 
have the following file type: lh.thickness.fwhm10.fsaverage.mgz or 
.mgh file. .  Instead, they have this file type: lh.smoothwm.FI.crv. 
Is there a way to convert the crv file to a mgz/mgh file? Is there an 
alternate way to analyze the T1/T2 data using QDEC?



Thank you,


Heidi Lindroth BSN RN
 PhD Candidate| School of Nursing
 Program Assistant | School of Medicine and Public Health, Department 
of Anesthesiology

 Predoctoral Fellow | Veterans Administration (Madison WI)

University of Wisconsin-Madison
 701 Highland Avenue, Madison WI 53705
 608-219-4294 | hlindr...@wisc.edu



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Re: [Freesurfer] mri_gtmpvc

[Douglas Greve]

Yes, if you  set  --psf 0 then it will only apply correction for the 
tissue fraction effect (TFE).



On 6/15/18 10:53 AM, Alshikho, Mohamad J. wrote:


Dear Dr Greve,

Kindly, I’d like t to inquire about the command “mri_gtmpvc” in PET 
surfer. Can I use this command to apply partial volume correction on 
non-PET data (e.g. DTI or ASL)?


Thanks!

Mohamad



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Re: [Freesurfer] TotalGrayVol and SubCortGrayVol for multiple subjects

[Douglas Greve]

It should auotmatically be included in the output asegstats2table. is it 
not?



On 6/15/18 10:23 AM, Fernanda Hansen P. de Moraes wrote:


External Email - Use Caution

Good morning all,

I want to get the TotalGrayVol and SubCortGrayVol for multiple 
subjects. Is there any flag that I can use with asegstats2table? Or 
how should I use mri_segstas to creata a new aseg.stats file for my 
subjects?
If that's the case, how should I define the output file from 
mri_segstats so asegstats2table can read it?


Thank you very much in advance,
Fernanda Hansen P. de Moraes
--
Fernanda Hansen P. de Moraes
Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz


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Re: [Freesurfer] Cortical Thickness Using N30R83 Atlas

[Douglas Greve]

There are files called lh.area and lh.volume that you can use instead of 
lh.thickness. Make sure to use the --jac flag when applying 
mri_surf2surf to area or volume (but not thickness). This applies 
jacobian correction to preserve the total area or volume. When you run 
mri_segstats, include the --accumulate flag so that it reports the total 
area or volume.



On 6/14/18 6:42 PM, Ryan Flores wrote:

 External Email - Use Caution

Hi again Doug,

Sorry for not realizing this earlier, but I actually found a workflow that you 
created, which outlines the steps really well. 
(https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness)

However, instead of 'fsaverage' I used the the MNI brain I had previously 
recon-ed to map the ROI to the surface. By using mri_surf2surf I mapped my 
subject's thickness data to the mni brain and optained the cortical thickness. 
My questions are the following: how do I obtain the surface area and volume for 
this ROI? Is there a way to also obtain non-segmented stats? Also, the reason I 
didn't map the ROI to fsaverage was because I didn’t have access...is there a 
way to change that?

Thank you for your time.

Best,

Ryan



-- Ryan Flores Clinical Research Coordinator On 6/14/18, 11:32 AM, 
"freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve" 
dgr...@mgh.harvard.edu> wrote: You can create an annotation with 
mris_seg2annot and then view it in freeview. Run it with --help to get 
docs On 06/14/2018 02:18 PM, Ryan Flores wrote: > External Email - Use 
Caution > > Great. That seemed to have worked. Is there a way to inspect 
that the ROIs have been correctly placed? Perhaps by using freeview? > > 
Best, > > Ryan > - Ryan Flores Clinical Research Coordinator On 6/14/18, 
11:02 AM,"freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. 
Greve" dgr...@mgh.harvard.edu> wrote: The --trgsurfval is just the output (ie, 
lh.atlas.nii.gz sampled onto the surface of the subject). Use nii.gz or 
mgz for the output (not img). On 06/14/2018 01:46 PM, Ryan Flores wrote: 
> External Email - Use Caution > > Thank you for your response. Just to 
clarify, the first command should be mri_vol2surf, correct? It appears 
to have worked; however, I'm not sure what my --trgsurfval should be? 
I'm trying the following commands, where mni is the subject directory 
for the mni brain I recon-ed and sub01 is the subject I want to transfer 
the atlas to so that I can obtain the cortical thickness. > > 1. 
mri_vol2surf --mov atlas.nii.gz --regheader mni --hemi lh --projfrac-max 
0 1 .1 --o lh.atlas.nii.gz > 2. mri_surf2surf --srcsubject mni 
--srcsurfval lh.atlas.nii.gz --trgsubject sub01 --trgsurfval 
hammers-01-lh.img --mapmethod nnf > > I tried running mri_surf2surf 
--help, but unfortunately the examples didn’t really apply to my case. I 
apologize for the potential trivial question in advance. Thanks again 
for your help. > > Best, > > Ryan > -- Ryan Flores Clinical Research 
Coordinator On 6/14/18, 8:33 AM, "freesurfer-boun...@nmr.mgh.harvard.edu 
on behalf of Douglas N. Greve" on behalf of dgr...@mgh.harvard.edu> wrote: You can always get info by 
running the command with --help. mri_vol2vol --mov atlas.nii.gz 
--regheader subject --hemi lh --projfrac-max 0 1 .1 --o lh.atlas.nii.gz 
This assumes that the atlas is in registration with the mni152 (you can 
test with tkregister --mov atlas.nii.gz --s subject --regheader --reg 
deleteme.dat, the two volumes should be in registration) You can take 
lh.atlas.nii.gz and use it as input to mri_surf2surf to transfer to an 
individual. Make sure to use --mapmethod nnf On 06/13/2018 06:59 PM, 
Ryan Flores wrote: > > External Email - Use Caution > > Hello all, > > I 
am hoping to obtain structural information (e.g., cortical > thickness, 
surface area, and volume) based on the n30r83 (aka > Hammersmith) atlas, 
which is in MNI space. The atlas differentiates > between the 
hemispheres by using odd/even numbers in the labels. > > After looking 
through the archives I found a potential solution, which > entails using 
the mri_vol2surf & mri_surf2surf commands. I’ve recon-ed > the MNI brain 
to obtain the proper space; however, I’m unsure of how > exactly to 
implement the commands and which flags are relevant. Any > advice would 
be greatly appreciated. > > Thank you for your time. I look forward to 
hearing from you. > > Best, > > Ryan > > -- > > Ryan Flores > > Clinical 
Research Coordinator > > > > 
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Re: [Freesurfer] [Request of response] Fwd: Error during QDEC

[Douglas Greve]

Those are the qdec tables, not the fsgd file. Look in the qdec output 
folder for a file called y.fsgd. Also please remember to post to the 
list and not to us personally



On 6/15/18 12:40 AM, Seung-Gul Kang (강승걸) wrote:


External Email - Use Caution

Hi Doug,

Thank you for your reply.

I send my FSGD files.
sui3_qdec.table
sui5_qdec.table - This file contains the normalization of SSI score 
(nrSSI).


I want to see the correlation (or regression) between the brain 
surface areas with significant difference between two groups and SSI 
score.

When I enter 'SSI' or 'nrSSI' into covariate in QDEC, then error occurs.

Best regards,
Seung-Gul

*S**eung-Gul Kang, M.D., Ph.D. *
Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center
연구부학장. Dean, Department of Research Affairs; Gachon University 
College of Medicine

인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center
21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea

ᐧ

2018년 6월 15일 (금) 오전 12:26, Douglas N. Greve >님이 작성:


Please send the y.fsgd file


On 06/13/2018 09:30 PM, Seung-Gul Kang (강승걸) wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I send you this e-mail again in anticipation of your help.
>
> I see the error message when I perform QDEC.
> The error message is as below.
>
> Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
>
> cwd /home/sgk
>
> cmdline mri_glmfit --y
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh
> --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods
> --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf
fsaverage lh
> --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C
>
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat

> --C
>
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat

> --C
>

/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat

> --C
>

/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat

> --C
>

/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat

> --C
>

/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat

> --C
>

/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat

> --C
>

/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat
>
> sysnameLinux
>
> hostname localhost.localdomain
>
> machinex86_64
>
> usersgk
>
> FixVertexAreaFlag = 1
>
> UseMaskWithSmoothing1
>
> OneSampleGroupMean 0
>
> y/mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh
>
> logyflag 0
>
> usedti0
>
> FSGD /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd
>
> labelmask/mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label
>
> maskinv 0
>
> glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI
>
> IllCondOK 0
>
> ReScaleX 1
>
> DoFFx 0
>
> Creating output directory /mnt/hgfs/share/suicide/qdec/LH_area_SSI
>
> Loading y from /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh
>
> INFO: gd2mtx_method is dods
>
> Saving design matrix to
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/Xg.dat
>
> Normalized matrix condition is 24522.5
>
> Design matrix --
>
>

1....00015....00024....00021....000149457.5940...000;
>
>

1....00019....00050....00020....000161540.2030...000;
>
>

1....0007....00055....00026....000167295.9060...000;
>
>

0..0001....00010....00031....00027....000175241.7030.000;
>
>

0..0001....00015....00059....00023....000165616.7970.000;
>
>

0..0001....00011....00057....00022....000183255.5940.000;
>
>

1....00026....00037....00023....000159212.2030...000;
>
>

0..0001....00014....00050....00022....000170017.0940.000;
>
>

0..0001....00016....00026....00019....000190217.9060.000;
>
>

0..0001....0001....00039....00019....000156341..000;
>
>

1....00018....00049....00032....000168844.2970